From f8631c472614b5fe2f16301982ed238bf86d00bc Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Sun, 22 Feb 2026 15:49:16 -0500 Subject: [PATCH 1/2] Expand assay value sets and add BioPortal links to enum docs Restructure bio/assays into subdirectory with domain-specific enums: - Move existing NF-OSI assays to bio/assays/nf_osi_assays.yaml - Add dynamic enums for OBI and BAO assay hierarchies (bio_assay.yaml) - Add static enums for enzymology, immunology, protein engineering, toxicology - All ontology CURIEs verified via OLS - Companion enum annotations document microschema coupling Add BioPortal link to all enum documentation pages via enrich_enum_docs.py. Update lab-automation.md view with new assay section. Co-Authored-By: Claude Opus 4.6 --- docs/schema/valuesets.yaml | 1374 +- docs/views/lab-automation.md | 182 + mkdocs.yml | 7 +- project/jsonschema/valuesets.schema.json | 1082 +- scripts/enrich_enum_docs.py | 12 + src/valuesets/datamodel/valuesets.py | 498 + src/valuesets/datamodel/valuesets_pydantic.py | 498 + src/valuesets/enums/__init__.py | 10 +- src/valuesets/enums/bio/assays/__init__.py | 1 + src/valuesets/enums/bio/assays/enzymology.py | 43 + src/valuesets/enums/bio/assays/immunology.py | 43 + .../enums/bio/assays/nf_osi_assays.py | 411 + .../enums/bio/assays/protein_engineering.py | 39 + src/valuesets/enums/bio/assays/toxicology.py | 41 + src/valuesets/merged/merged_hierarchy.yaml | 44558 ++++++++++++---- .../schema/bio/assays/bio_assay.yaml | 62 + .../schema/bio/assays/enzymology.yaml | 81 + .../schema/bio/assays/immunology.yaml | 85 + .../nf_osi_assays.yaml} | 6 +- .../bio/assays/protein_engineering.yaml | 79 + .../schema/bio/assays/toxicology.yaml | 79 + src/valuesets/schema/valuesets.yaml | 6 + 22 files changed, 39550 insertions(+), 9647 deletions(-) create mode 100644 docs/views/lab-automation.md create mode 100644 src/valuesets/enums/bio/assays/__init__.py create mode 100644 src/valuesets/enums/bio/assays/enzymology.py create mode 100644 src/valuesets/enums/bio/assays/immunology.py create mode 100644 src/valuesets/enums/bio/assays/nf_osi_assays.py create mode 100644 src/valuesets/enums/bio/assays/protein_engineering.py create mode 100644 src/valuesets/enums/bio/assays/toxicology.py create mode 100644 src/valuesets/schema/bio/assays/bio_assay.yaml create mode 100644 src/valuesets/schema/bio/assays/enzymology.yaml create mode 100644 src/valuesets/schema/bio/assays/immunology.yaml rename src/valuesets/schema/bio/{assays.yaml => assays/nf_osi_assays.yaml} (99%) create mode 100644 src/valuesets/schema/bio/assays/protein_engineering.yaml create mode 100644 src/valuesets/schema/bio/assays/toxicology.yaml diff --git a/docs/schema/valuesets.yaml b/docs/schema/valuesets.yaml index 4f0379b6..7f8884ed 100644 --- a/docs/schema/valuesets.yaml +++ b/docs/schema/valuesets.yaml @@ -97,6 +97,12 @@ imports: - bio/lipid_categories - bio/proteomics_standards - bio/psi_mi +- bio/assays/nf_osi_assays +- bio/assays/bio_assay +- bio/assays/enzymology +- bio/assays/immunology +- bio/assays/protein_engineering +- bio/assays/toxicology - ecological_interactions - mining_processing - chemistry/chemical_entities @@ -41282,6 +41288,1291 @@ enums: ENDOGENOUS_LEVEL: text: ENDOGENOUS_LEVEL description: Physiological expression + SequencingAssayEnum: + name: SequencingAssayEnum + definition_uri: https://w3id.org/valuesets/SequencingAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Sequencing-based assays including RNA-seq, DNA-seq, and related methods + title: Sequencing Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + RNA_SEQ: + text: RNA_SEQ + description: RNA sequencing to profile transcriptome + meaning: OBI:0001271 + aliases: + - RNA-seq + SINGLE_CELL_RNA_SEQ: + text: SINGLE_CELL_RNA_SEQ + description: Single-cell RNA sequencing + meaning: OBI:0002631 + aliases: + - scRNA-seq + SINGLE_NUCLEUS_RNA_SEQ: + text: SINGLE_NUCLEUS_RNA_SEQ + description: Single-nucleus RNA sequencing + aliases: + - snRNA-seq + SPATIAL_TRANSCRIPTOMICS: + text: SPATIAL_TRANSCRIPTOMICS + description: Spatially resolved transcriptomics + meaning: EFO:0008992 + LNCRNA_SEQ: + text: LNCRNA_SEQ + description: Long non-coding RNA sequencing + aliases: + - lncRNA-seq + MIRNA_SEQ: + text: MIRNA_SEQ + description: MicroRNA sequencing + meaning: OBI:0002112 + aliases: + - miRNA-seq + RIBO_SEQ: + text: RIBO_SEQ + description: Ribosome profiling sequencing + aliases: + - Ribo-seq + WHOLE_GENOME_SEQUENCING: + text: WHOLE_GENOME_SEQUENCING + description: Whole genome sequencing + meaning: OBI:0002117 + aliases: + - WGS + WHOLE_EXOME_SEQUENCING: + text: WHOLE_EXOME_SEQUENCING + description: Whole exome sequencing + meaning: OBI:0002118 + aliases: + - WES + TARGETED_EXOME_SEQUENCING: + text: TARGETED_EXOME_SEQUENCING + description: Targeted exome sequencing panel + NEXT_GENERATION_TARGETED_SEQUENCING: + text: NEXT_GENERATION_TARGETED_SEQUENCING + description: Next generation targeted sequencing panel + SANGER_SEQUENCING: + text: SANGER_SEQUENCING + description: Sanger chain termination sequencing + meaning: OBI:0000695 + ATAC_SEQ: + text: ATAC_SEQ + description: Assay for Transposase-Accessible Chromatin sequencing + meaning: OBI:0002039 + aliases: + - ATAC-seq + SINGLE_CELL_ATAC_SEQ: + text: SINGLE_CELL_ATAC_SEQ + description: Single-cell ATAC-seq + aliases: + - scATAC-seq + CHIP_SEQ: + text: CHIP_SEQ + description: Chromatin immunoprecipitation sequencing + meaning: OBI:0000716 + aliases: + - ChIP-seq + CUT_AND_RUN: + text: CUT_AND_RUN + description: Cleavage Under Targets and Release Using Nuclease + aliases: + - CUT&RUN + BISULFITE_SEQUENCING: + text: BISULFITE_SEQUENCING + description: Bisulfite sequencing for DNA methylation + meaning: OBI:0000748 + aliases: + - BS-seq + ERR_BISULFITE_SEQUENCING: + text: ERR_BISULFITE_SEQUENCING + description: Enzymatic methyl-seq (EM-seq) or similar error-reduced bisulfite + sequencing + OXBS_SEQ: + text: OXBS_SEQ + description: Oxidative bisulfite sequencing + aliases: + - oxBS-seq + HI_C: + text: HI_C + description: High-throughput chromosome conformation capture + meaning: OBI:0002042 + aliases: + - Hi-C + ISO_SEQ: + text: ISO_SEQ + description: Isoform sequencing (PacBio long-read) + aliases: + - Iso-Seq + NOME_SEQ: + text: NOME_SEQ + description: Nucleosome Occupancy and Methylome Sequencing + aliases: + - NOMe-seq + CAPP_SEQ: + text: CAPP_SEQ + description: CAncer Personalized Profiling by deep Sequencing + aliases: + - CAPP-Seq + SAFER_SEQS: + text: SAFER_SEQS + description: Safe-Sequencing System + TCR_REPERTOIRE_SEQUENCING: + text: TCR_REPERTOIRE_SEQUENCING + description: T cell receptor repertoire sequencing + aliases: + - TCR-seq + SCCGI_SEQ: + text: SCCGI_SEQ + description: Single-cell CGI sequencing + aliases: + - scCGI-seq + JUMPING_LIBRARY: + text: JUMPING_LIBRARY + description: Jumping library sequencing for structural variants + SNP_ARRAY: + text: SNP_ARRAY + description: SNP genotyping array + meaning: OBI:0001204 + RNA_ARRAY: + text: RNA_ARRAY + description: RNA expression array + meaning: OBI:0001463 + MIRNA_ARRAY: + text: MIRNA_ARRAY + description: MicroRNA array + METHYLATION_ARRAY: + text: METHYLATION_ARRAY + description: DNA methylation array + meaning: OBI:0001332 + ImagingAssayEnum: + name: ImagingAssayEnum + definition_uri: https://w3id.org/valuesets/ImagingAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Imaging-based assays including microscopy, MRI, and related methods + title: Imaging Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + BRIGHTFIELD_MICROSCOPY: + text: BRIGHTFIELD_MICROSCOPY + description: Brightfield microscopy imaging + meaning: CHMO:0000104 + CONFOCAL_MICROSCOPY: + text: CONFOCAL_MICROSCOPY + description: Confocal laser scanning microscopy + meaning: CHMO:0000545 + THREE_D_CONFOCAL_IMAGING: + text: THREE_D_CONFOCAL_IMAGING + description: Three-dimensional confocal imaging + aliases: + - 3D confocal imaging + FLUORESCENCE_MICROSCOPY: + text: FLUORESCENCE_MICROSCOPY + description: Fluorescence microscopy assay + meaning: CHMO:0000087 + PHASE_CONTRAST_MICROSCOPY: + text: PHASE_CONTRAST_MICROSCOPY + description: Phase-contrast microscopy + meaning: CHMO:0000056 + ATOMIC_FORCE_MICROSCOPY: + text: ATOMIC_FORCE_MICROSCOPY + description: Atomic force microscopy + meaning: CHMO:0000113 + aliases: + - AFM + THREE_D_ELECTRON_MICROSCOPY: + text: THREE_D_ELECTRON_MICROSCOPY + description: Three-dimensional electron microscopy + aliases: + - 3D EM + IMMUNOFLUORESCENCE: + text: IMMUNOFLUORESCENCE + description: Immunofluorescence staining and imaging + meaning: OBI:0003357 + IMMUNOHISTOCHEMISTRY: + text: IMMUNOHISTOCHEMISTRY + description: Immunohistochemistry staining + meaning: OBI:0001986 + aliases: + - IHC + IMMUNOCYTOCHEMISTRY: + text: IMMUNOCYTOCHEMISTRY + description: Immunocytochemistry staining + aliases: + - ICC + HISTOLOGY: + text: HISTOLOGY + description: Histological examination + meaning: OBI:0600020 + FISH: + text: FISH + description: Fluorescence In Situ Hybridization + meaning: OBI:0003094 + aliases: + - Fluorescence In Situ Hybridization + CODEX: + text: CODEX + description: CO-Detection by indEXing imaging + LIVE_IMAGING: + text: LIVE_IMAGING + description: Live cell or tissue imaging + AUTORADIOGRAPHY: + text: AUTORADIOGRAPHY + description: Autoradiography imaging + meaning: CHMO:0000812 + CONVENTIONAL_MRI: + text: CONVENTIONAL_MRI + description: Conventional magnetic resonance imaging + meaning: OBI:0002985 + FUNCTIONAL_MRI: + text: FUNCTIONAL_MRI + description: Functional magnetic resonance imaging + meaning: OBI:0001501 + aliases: + - fMRI + DIFFUSION_MRI: + text: DIFFUSION_MRI + description: Diffusion-weighted MRI + aliases: + - DWI + MPRAGE_MRI: + text: MPRAGE_MRI + description: Magnetization-Prepared Rapid Gradient Echo MRI + aliases: + - MPRAGE + MAGNETIC_RESONANCE_SPECTROSCOPY: + text: MAGNETIC_RESONANCE_SPECTROSCOPY + description: Magnetic resonance spectroscopy + meaning: CHMO:0000566 + aliases: + - MRS + MAGNETIC_RESONANCE_ANGIOGRAPHY: + text: MAGNETIC_RESONANCE_ANGIOGRAPHY + description: Magnetic resonance angiography + meaning: OBI:0002986 + aliases: + - MRA + POSITRON_EMISSION_TOMOGRAPHY: + text: POSITRON_EMISSION_TOMOGRAPHY + description: Positron emission tomography + meaning: OBI:0001912 + aliases: + - PET + OPTICAL_COHERENCE_TOMOGRAPHY: + text: OPTICAL_COHERENCE_TOMOGRAPHY + description: Optical coherence tomography + meaning: CHMO:0000896 + aliases: + - OCT + OPTICAL_TOMOGRAPHY: + text: OPTICAL_TOMOGRAPHY + description: Optical tomography + HIGH_FREQUENCY_ULTRASOUND: + text: HIGH_FREQUENCY_ULTRASOUND + description: High frequency ultrasound imaging + TRANSCRANIAL_DOPPLER: + text: TRANSCRANIAL_DOPPLER + description: Transcranial doppler ultrasonography + IN_VIVO_BIOLUMINESCENCE: + text: IN_VIVO_BIOLUMINESCENCE + description: In vivo bioluminescence imaging + meaning: OBI:0001503 + LASER_SPECKLE_IMAGING: + text: LASER_SPECKLE_IMAGING + description: Laser speckle contrast imaging + SPATIAL_FREQUENCY_DOMAIN_IMAGING: + text: SPATIAL_FREQUENCY_DOMAIN_IMAGING + description: Spatial frequency domain imaging + TRACTION_FORCE_MICROSCOPY: + text: TRACTION_FORCE_MICROSCOPY + description: Traction force microscopy + PHOTOGRAPH: + text: PHOTOGRAPH + description: Photographic documentation + MassSpectrometryAssayEnum: + name: MassSpectrometryAssayEnum + definition_uri: https://w3id.org/valuesets/MassSpectrometryAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Mass spectrometry-based assays for proteomics and metabolomics + title: Mass Spectrometry Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + MASS_SPECTROMETRY: + text: MASS_SPECTROMETRY + description: General mass spectrometry + meaning: CHMO:0000470 + aliases: + - MS + LC_MS: + text: LC_MS + description: Liquid chromatography-mass spectrometry + meaning: CHMO:0000524 + aliases: + - liquid chromatography/mass spectrometry + LC_MS_MS: + text: LC_MS_MS + description: Liquid chromatography-tandem mass spectrometry + meaning: CHMO:0000701 + aliases: + - LC-MS/MS + - liquid chromatography/tandem mass spectrometry + HPLC_MS_MS: + text: HPLC_MS_MS + description: High-performance liquid chromatography/tandem mass spectrometry + aliases: + - high-performance liquid chromatography/tandem mass spectrometry + UHPLC_MS_MS: + text: UHPLC_MS_MS + description: Ultra high-performance liquid chromatography/tandem mass spectrometry + aliases: + - ultra high-performance liquid chromatography/tandem mass spectrometry + FIA_MSMS: + text: FIA_MSMS + description: Flow injection analysis tandem mass spectrometry + aliases: + - FIA-MSMS + LABEL_FREE_MS: + text: LABEL_FREE_MS + description: Label-free mass spectrometry quantification + aliases: + - label free mass spectrometry + TMT_QUANTITATION: + text: TMT_QUANTITATION + description: Tandem mass tag quantitation + aliases: + - TMT quantitation + MUDPIT: + text: MUDPIT + description: Multidimensional Protein Identification Technology + aliases: + - MudPIT + MIB_MS: + text: MIB_MS + description: Multiplexed Inhibitor Beads mass spectrometry + aliases: + - MIB/MS + LC_ECD: + text: LC_ECD + description: Liquid chromatography-electrochemical detection + aliases: + - liquid chromatography-electrochemical detection + FTIR_SPECTROSCOPY: + text: FTIR_SPECTROSCOPY + description: Fourier-transform infrared spectroscopy + meaning: CHMO:0000817 + aliases: + - FTIR spectroscopy + RPPA: + text: RPPA + description: Reverse Phase Protein Array + meaning: OBI:0001975 + aliases: + - RPPA + PROXIMITY_EXTENSION_ASSAY: + text: PROXIMITY_EXTENSION_ASSAY + description: Proximity extension assay + aliases: + - PEA + CellBasedAssayEnum: + name: CellBasedAssayEnum + definition_uri: https://w3id.org/valuesets/CellBasedAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Cell-based assays including viability, proliferation, and functional + assays + title: Cell-Based Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + CELL_VIABILITY_ASSAY: + text: CELL_VIABILITY_ASSAY + description: Cell viability measurement assay + meaning: BAO:0003009 + CELL_PROLIFERATION_ASSAY: + text: CELL_PROLIFERATION_ASSAY + description: Cell proliferation measurement + meaning: BAO:0002100 + CELL_COUNT: + text: CELL_COUNT + description: Cell counting assay + meaning: BAO:0002097 + ALAMAR_BLUE_ABSORBANCE: + text: ALAMAR_BLUE_ABSORBANCE + description: AlamarBlue absorbance assay (2D) + aliases: + - 2D AlamarBlue absorbance + ALAMAR_BLUE_FLUORESCENCE: + text: ALAMAR_BLUE_FLUORESCENCE + description: AlamarBlue fluorescence assay (2D) + aliases: + - 2D AlamarBlue fluorescence + THREE_D_MICROTISSUE_VIABILITY: + text: THREE_D_MICROTISSUE_VIABILITY + description: 3D microtissue viability assay + aliases: + - 3D microtissue viability + BRDU_PROLIFERATION: + text: BRDU_PROLIFERATION + description: BrdU incorporation proliferation assay + meaning: OBI:0001330 + aliases: + - BrdU proliferation assay + EDU_PROLIFERATION: + text: EDU_PROLIFERATION + description: EdU incorporation proliferation assay + aliases: + - EdU proliferation assay + ATPASE_ACTIVITY_ASSAY: + text: ATPASE_ACTIVITY_ASSAY + description: ATPase activity measurement + CAMP_GLO_ASSAY: + text: CAMP_GLO_ASSAY + description: cAMP-Glo Max Assay + aliases: + - cAMP-Glo Max Assay + FLOW_CYTOMETRY: + text: FLOW_CYTOMETRY + description: Flow cytometry analysis + meaning: OBI:0000916 + ELISA: + text: ELISA + description: Enzyme-linked immunosorbent assay + meaning: OBI:0000661 + SANDWICH_ELISA: + text: SANDWICH_ELISA + description: Sandwich ELISA + WESTERN_BLOT: + text: WESTERN_BLOT + description: Western blot analysis + meaning: OBI:0000714 + IMMUNOASSAY: + text: IMMUNOASSAY + description: General immunoassay + meaning: OBI:0000717 + PCR: + text: PCR + description: Polymerase chain reaction + meaning: OBI:0000415 + aliases: + - polymerase chain reaction + QPCR: + text: QPCR + description: Quantitative PCR + meaning: OBI:0000893 + aliases: + - quantitative PCR + NANOSTRING_NCOUNTER: + text: NANOSTRING_NCOUNTER + description: NanoString nCounter Analysis System + MULTI_ELECTRODE_ARRAY: + text: MULTI_ELECTRODE_ARRAY + description: Multi-electrode array recording + meaning: OBI:0002187 + CURRENT_CLAMP_ASSAY: + text: CURRENT_CLAMP_ASSAY + description: Current clamp electrophysiology + WHOLE_CELL_PATCH_CLAMP: + text: WHOLE_CELL_PATCH_CLAMP + description: Whole-cell patch clamp recording + meaning: OBI:0002179 + LOCAL_FIELD_POTENTIAL: + text: LOCAL_FIELD_POTENTIAL + description: Local field potential recording + LONG_TERM_POTENTIATION: + text: LONG_TERM_POTENTIATION + description: Long-term potentiation assay + MIGRATION_ASSAY: + text: MIGRATION_ASSAY + description: Cell migration assay + meaning: BAO:0002110 + IN_VITRO_TUMORIGENESIS: + text: IN_VITRO_TUMORIGENESIS + description: In vitro tumorigenesis assay + IN_VIVO_TUMOR_GROWTH: + text: IN_VIVO_TUMOR_GROWTH + description: In vivo tumor growth assay + IN_VIVO_PDX_VIABILITY: + text: IN_VIVO_PDX_VIABILITY + description: In vivo patient-derived xenograft viability + MATRIGEL_TUMORIGENESIS: + text: MATRIGEL_TUMORIGENESIS + description: Matrigel-based tumorigenesis assay + aliases: + - Matrigel-based tumorigenesis assay + HIGH_CONTENT_SCREEN: + text: HIGH_CONTENT_SCREEN + description: High content screening assay + meaning: BAO:0000514 + CELL_PAINTING: + text: CELL_PAINTING + description: Cell painting morphological profiling + meaning: BAO:0020000 + COMPOUND_SCREEN: + text: COMPOUND_SCREEN + description: Compound library screening + COMBINATION_SCREEN: + text: COMBINATION_SCREEN + description: Drug combination screening + SMALL_MOLECULE_LIBRARY_SCREEN: + text: SMALL_MOLECULE_LIBRARY_SCREEN + description: Small molecule library screen + REPORTER_GENE_ASSAY: + text: REPORTER_GENE_ASSAY + description: Reporter gene assay + meaning: BAO:0000098 + MASSIVELY_PARALLEL_REPORTER_ASSAY: + text: MASSIVELY_PARALLEL_REPORTER_ASSAY + description: Massively parallel reporter assay + aliases: + - MPRA + SPLIT_GFP_ASSAY: + text: SPLIT_GFP_ASSAY + description: Split-GFP protein interaction assay + aliases: + - split-GFP assay + FOCUS_FORMING_ASSAY: + text: FOCUS_FORMING_ASSAY + description: Focus forming assay + OXYGEN_CONSUMPTION_ASSAY: + text: OXYGEN_CONSUMPTION_ASSAY + description: Oxygen consumption rate measurement + meaning: BAO:0003028 + ROS_ASSAY: + text: ROS_ASSAY + description: Reactive oxygen species assay + aliases: + - reactive oxygen species assay + CALCIUM_RETENTION_ASSAY: + text: CALCIUM_RETENTION_ASSAY + description: Calcium retention capacity assay + TRANS_ENDOTHELIAL_RESISTANCE: + text: TRANS_ENDOTHELIAL_RESISTANCE + description: Trans-endothelial electrical resistance measurement + aliases: + - trans-endothelial electrical resistance + CELL_PERMEABILITY_ASSAY: + text: CELL_PERMEABILITY_ASSAY + description: Cell permeability assay + PHARMACOKINETIC_ADME: + text: PHARMACOKINETIC_ADME + description: Pharmacokinetic ADME assay + aliases: + - pharmocokinetic ADME assay + ARRAY: + text: ARRAY + description: General array-based assay + HPLC: + text: HPLC + description: High-performance liquid chromatography + meaning: CHMO:0001009 + ELECTROCHEMILUMINESCENCE: + text: ELECTROCHEMILUMINESCENCE + description: Electrochemiluminescence detection + STR_PROFILE: + text: STR_PROFILE + description: Short tandem repeat profiling + TIDE: + text: TIDE + description: Tracking of Indels by Decomposition + SURVIVAL_ASSAY: + text: SURVIVAL_ASSAY + description: Cell or organism survival assay + ClinicalBehavioralAssayEnum: + name: ClinicalBehavioralAssayEnum + definition_uri: https://w3id.org/valuesets/ClinicalBehavioralAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Clinical assessments and behavioral assays used in research + title: Clinical and Behavioral Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + CLINICAL_DATA: + text: CLINICAL_DATA + description: Clinical data collection + QUESTIONNAIRE: + text: QUESTIONNAIRE + description: Questionnaire-based assessment + meaning: OBI:0001504 + INTERVIEW: + text: INTERVIEW + description: Clinical or research interview + FOCUS_GROUP: + text: FOCUS_GROUP + description: Focus group discussion + SCALE: + text: SCALE + description: Clinical rating scale + NEUROPSYCHOLOGICAL_ASSESSMENT: + text: NEUROPSYCHOLOGICAL_ASSESSMENT + description: Neuropsychological testing + meaning: OBI:0002508 + COGNITIVE_ASSESSMENT: + text: COGNITIVE_ASSESSMENT + description: Cognitive function assessment + NIH_TOOLBOX: + text: NIH_TOOLBOX + description: NIH Toolbox assessment battery + PROMIS_COGNITIVE_FUNCTION: + text: PROMIS_COGNITIVE_FUNCTION + description: PROMIS Cognitive Function measures + N_BACK_TASK: + text: N_BACK_TASK + description: N-back working memory task + aliases: + - n-back task + CORSI_BLOCKS: + text: CORSI_BLOCKS + description: Corsi block-tapping task + CBCL_1_5_5: + text: CBCL_1_5_5 + description: Child Behavior Checklist for Ages 1.5-5 + aliases: + - Child Behavior Checklist for Ages 1.5-5 + CBCL_6_18: + text: CBCL_6_18 + description: Child Behavior Checklist for Ages 6-18 + aliases: + - Child Behavior Checklist for Ages 6-18 + SRS: + text: SRS + description: Social Responsiveness Scale + aliases: + - Social Responsiveness Scale + SRS_2: + text: SRS_2 + description: Social Responsiveness Scale Second Edition + aliases: + - Social Responsiveness Scale Second Edition + BLOOD_CHEMISTRY: + text: BLOOD_CHEMISTRY + description: Blood chemistry measurement + aliases: + - blood chemistry measurement + METABOLIC_SCREENING: + text: METABOLIC_SCREENING + description: Metabolic screening panel + GENOTYPING: + text: GENOTYPING + description: Genotyping assay + meaning: OBI:0000435 + BODY_SIZE_MEASUREMENT: + text: BODY_SIZE_MEASUREMENT + description: Body size trait measurement + meaning: MMO:0000013 + aliases: + - body size trait measurement + GAIT_MEASUREMENT: + text: GAIT_MEASUREMENT + description: Gait analysis measurement + aliases: + - gait measurement + GRIP_STRENGTH: + text: GRIP_STRENGTH + description: Grip strength measurement + HAND_HELD_DYNAMOMETRY: + text: HAND_HELD_DYNAMOMETRY + description: Hand-held dynamometry + SIX_MINUTE_WALK_TEST: + text: SIX_MINUTE_WALK_TEST + description: Six-minute walk test + aliases: + - six-minute walk test + ACTIGRAPHY: + text: ACTIGRAPHY + description: Actigraphy monitoring + POLYSOMNOGRAPHY: + text: POLYSOMNOGRAPHY + description: Polysomnography sleep study + QUANTITATIVE_SENSORY_TESTING: + text: QUANTITATIVE_SENSORY_TESTING + description: Quantitative sensory testing + VON_FREY_TEST: + text: VON_FREY_TEST + description: Von Frey filament test + aliases: + - Von Frey test + ALGOMETRX_NOCIOMETER: + text: ALGOMETRX_NOCIOMETER + description: AlgometRx Nociometer assessment + AUDITORY_BRAINSTEM_RESPONSE: + text: AUDITORY_BRAINSTEM_RESPONSE + description: Auditory brainstem response testing + aliases: + - ABR + PURE_TONE_AVERAGE: + text: PURE_TONE_AVERAGE + description: Pure tone average audiometry + WORD_RECOGNITION_SCORE: + text: WORD_RECOGNITION_SCORE + description: Word recognition score + DPOE: + text: DPOE + description: Distortion product otoacoustic emissions + aliases: + - distortion product otoacoustic emissions + PATTERN_ERG: + text: PATTERN_ERG + description: Pattern electroretinogram + aliases: + - pattern electroretinogram + OPTOKINETIC_REFLEX: + text: OPTOKINETIC_REFLEX + description: Optokinetic reflex assay + aliases: + - optokinetic reflex assay + RICCARDI_ABLON_SCALES: + text: RICCARDI_ABLON_SCALES + description: Riccardi and Ablon clinical severity scales + SKINDEX_16: + text: SKINDEX_16 + description: Skindex-16 dermatology questionnaire + CNF_SKINDEX: + text: CNF_SKINDEX + description: Cutaneous neurofibroma Skindex + aliases: + - cNF-Skindex + CDLQI: + text: CDLQI + description: Children's Dermatology Life Quality Index Questionnaire + aliases: + - Children's Dermatology Life Quality Index Questionnaire + FACEQ_DISTRESS: + text: FACEQ_DISTRESS + description: FACE-Q Appearance-related Distress + aliases: + - FACE-Q Appearance-related Distress + OPEN_FIELD_TEST: + text: OPEN_FIELD_TEST + description: Open field locomotor test + meaning: MMO:0000093 + ELEVATED_PLUS_MAZE: + text: ELEVATED_PLUS_MAZE + description: Elevated plus maze anxiety test + meaning: MMO:0000292 + aliases: + - elevated plus maze test + ROTAROD_TEST: + text: ROTAROD_TEST + description: Rotarod motor coordination test + meaning: MMO:0000091 + aliases: + - rotarod performance test + ACTIVE_AVOIDANCE: + text: ACTIVE_AVOIDANCE + description: Active avoidance learning behavior assay + aliases: + - active avoidance learning behavior assay + CONTEXTUAL_CONDITIONING: + text: CONTEXTUAL_CONDITIONING + description: Contextual conditioning behavior assay + aliases: + - contextual conditioning behavior assay + NOVELTY_RESPONSE: + text: NOVELTY_RESPONSE + description: Novelty response behavior assay + aliases: + - novelty response behavior assay + FEEDING_ASSAY: + text: FEEDING_ASSAY + description: Feeding behavior assay + OBIAssayEnum: + name: OBIAssayEnum + definition_uri: https://w3id.org/valuesets/OBIAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Dynamic enum covering all assays defined in the Ontology for Biomedical + Investigations (OBI), rooted at OBI:0000070 (assay). + title: OBI Assay + from_schema: https://w3id.org/valuesets/bio/assays/bio_assay + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + reachable_from: + source_ontology: obo:obi + source_nodes: + - OBI:0000070 + relationship_types: + - rdfs:subClassOf + include_self: true + BAOBioassayEnum: + name: BAOBioassayEnum + definition_uri: https://w3id.org/valuesets/BAOBioassayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Dynamic enum covering all bioassays defined in the BioAssay Ontology + (BAO), rooted at BAO:0000015 (bioassay). + title: BAO Bioassay + from_schema: https://w3id.org/valuesets/bio/assays/bio_assay + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + reachable_from: + source_ontology: obo:bao + source_nodes: + - BAO:0000015 + relationship_types: + - rdfs:subClassOf + include_self: true + EnzymologyAssayEnum: + name: EnzymologyAssayEnum + definition_uri: https://w3id.org/valuesets/EnzymologyAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Assays for characterizing enzyme function including activity, kinetics, + inhibition, and substrate specificity. + title: Enzymology Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/enzymology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + ENZYME_ACTIVITY_ASSAY: + text: ENZYME_ACTIVITY_ASSAY + description: Measures the effect of a perturbagen on enzyme activity + meaning: BAO:0002994 + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + MICHAELIS_MENTEN_KINETICS: + text: MICHAELIS_MENTEN_KINETICS + description: Enzyme kinetics assay measuring Km and Vmax parameters + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + INHIBITION_ASSAY: + text: INHIBITION_ASSAY + description: Assay to measure enzyme inhibition (IC50, Ki) + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + SUBSTRATE_SPECIFICITY: + text: SUBSTRATE_SPECIFICITY + description: Assay to determine enzyme substrate preference and specificity + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + FLUOROMETRIC_ENZYME_ASSAY: + text: FLUOROMETRIC_ENZYME_ASSAY + description: Enzyme assay using fluorescent substrates or products for detection + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + COLORIMETRIC_ENZYME_ASSAY: + text: COLORIMETRIC_ENZYME_ASSAY + description: Enzyme assay using chromogenic substrates for absorbance-based + detection + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + COUPLED_ENZYME_ASSAY: + text: COUPLED_ENZYME_ASSAY + description: Enzyme assay using a secondary enzyme reaction for signal generation + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + CONTINUOUS_ENZYME_ASSAY: + text: CONTINUOUS_ENZYME_ASSAY + description: Real-time monitoring of enzyme reaction progress + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + ENDPOINT_ENZYME_ASSAY: + text: ENDPOINT_ENZYME_ASSAY + description: Single time-point measurement of enzyme reaction product + annotations: + companion_enum_substrate: + tag: companion_enum_substrate + value: ChemicalEntity + companion_enum_enzyme: + tag: companion_enum_enzyme + value: Protein + ImmunologyAssayEnum: + name: ImmunologyAssayEnum + definition_uri: https://w3id.org/valuesets/ImmunologyAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Assays for detecting and quantifying immune-related molecules including + antibody-based detection, cell sorting, and blotting methods. + title: Immunology Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/immunology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + ELISA: + text: ELISA + description: Enzyme-linked immunosorbent assay for detecting antigens or antibodies + meaning: BAO:0000134 + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + SANDWICH_ELISA: + text: SANDWICH_ELISA + description: Sandwich ELISA using capture and detection antibodies + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + IMMUNOPRECIPITATION: + text: IMMUNOPRECIPITATION + description: Precipitation of a protein antigen from solution using a specific + antibody + meaning: BAO:0002508 + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + FLOW_CYTOMETRY: + text: FLOW_CYTOMETRY + description: Analysis of cell populations using fluorescent antibodies and + light scattering + meaning: BAO:0000005 + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + WESTERN_BLOT: + text: WESTERN_BLOT + description: Protein detection by gel electrophoresis, membrane transfer, + and antibody staining + meaning: OBI:0000854 + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + aliases: + - western blot assay + CYTOKINE_SECRETION_ASSAY: + text: CYTOKINE_SECRETION_ASSAY + description: Measurement of cytokine types and amounts released from cells + meaning: BAO:0003003 + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + IMMUNOBLOT: + text: IMMUNOBLOT + description: Detection of proteins using antibodies on a membrane + meaning: BAO:0002422 + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + COMPLEMENT_FIXATION: + text: COMPLEMENT_FIXATION + description: Serological assay detecting antibodies by complement consumption + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + MULTIPLEX_BEAD_ASSAY: + text: MULTIPLEX_BEAD_ASSAY + description: Simultaneous detection of multiple analytes using antibody-conjugated + beads + annotations: + companion_enum_antibody_target: + tag: companion_enum_antibody_target + value: Protein + companion_enum_detection_method: + tag: companion_enum_detection_method + value: DetectionModeEnum + ProteinEngineeringAssayEnum: + name: ProteinEngineeringAssayEnum + definition_uri: https://w3id.org/valuesets/ProteinEngineeringAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Assays for protein engineering including binding kinetics, biophysical + characterization, and display-based selection methods. + title: Protein Engineering Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/protein_engineering + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + SURFACE_PLASMON_RESONANCE: + text: SURFACE_PLASMON_RESONANCE + description: Real-time label-free measurement of biomolecular binding kinetics + meaning: BAO:0000054 + annotations: + companion_enum_target_protein: + tag: companion_enum_target_protein + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + aliases: + - SPR + BIOLAYER_INTERFEROMETRY: + text: BIOLAYER_INTERFEROMETRY + description: Label-free measurement of biomolecular interactions via interference + patterns + meaning: BAO:0000066 + annotations: + companion_enum_target_protein: + tag: companion_enum_target_protein + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + aliases: + - BLI + - bio layer interferometry + THERMAL_SHIFT_ASSAY: + text: THERMAL_SHIFT_ASSAY + description: Measurement of protein thermal stability via fluorescent dye + binding + meaning: BAO:0010261 + annotations: + companion_enum_target_protein: + tag: companion_enum_target_protein + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + aliases: + - differential scanning fluorimetry + - DSF + CIRCULAR_DICHROISM: + text: CIRCULAR_DICHROISM + description: Assessment of protein secondary and tertiary structure using + polarized light + meaning: BAO:0000161 + annotations: + companion_enum_target_protein: + tag: companion_enum_target_protein + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + aliases: + - CD + PHAGE_DISPLAY: + text: PHAGE_DISPLAY + description: Selection of peptides or proteins displayed on bacteriophage + surface + annotations: + companion_enum_target_protein: + tag: companion_enum_target_protein + value: Protein + YEAST_DISPLAY: + text: YEAST_DISPLAY + description: Selection of proteins displayed on yeast cell surface + annotations: + companion_enum_target_protein: + tag: companion_enum_target_protein + value: Protein + DIRECTED_EVOLUTION_SCREEN: + text: DIRECTED_EVOLUTION_SCREEN + description: High-throughput screening of mutant protein libraries for improved + function + annotations: + companion_enum_target_protein: + tag: companion_enum_target_protein + value: Protein + companion_enum_readout: + tag: companion_enum_readout + value: DetectionModeEnum + ToxicologyAssayEnum: + name: ToxicologyAssayEnum + definition_uri: https://w3id.org/valuesets/ToxicologyAssayEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Assays for evaluating toxicity, genotoxicity, and safety of compounds + including cytotoxicity, mutagenicity, and ADME measurements. + title: Toxicology Assay Types + from_schema: https://w3id.org/valuesets/bio/assays/toxicology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + TOXICITY_ASSAY: + text: TOXICITY_ASSAY + description: General assay measuring degree of substance toxicity to living + cells + meaning: BAO:0002189 + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity + companion_enum_cell_line: + tag: companion_enum_cell_line + value: CellType + MTT_ASSAY: + text: MTT_ASSAY + description: Colorimetric assay measuring cell metabolic activity via MTT + reduction + meaning: BAO:0002457 + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity + companion_enum_cell_line: + tag: companion_enum_cell_line + value: CellType + aliases: + - MTT reduction assay + LDH_RELEASE_ASSAY: + text: LDH_RELEASE_ASSAY + description: Cytotoxicity assay measuring lactate dehydrogenase release from + damaged cells + meaning: BAO:0013056 + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity + companion_enum_cell_line: + tag: companion_enum_cell_line + value: CellType + AMES_TEST: + text: AMES_TEST + description: Mutagenicity assay using bacterial reverse mutation in Salmonella + strains + meaning: BAO:0013054 + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity + COMET_ASSAY: + text: COMET_ASSAY + description: Single cell gel electrophoresis assay measuring DNA strand breaks + meaning: OBI:0302736 + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity + companion_enum_cell_line: + tag: companion_enum_cell_line + value: CellType + MICRONUCLEUS_ASSAY: + text: MICRONUCLEUS_ASSAY + description: Genotoxicity assay detecting chromosomal damage via micronucleus + formation + meaning: BAO:0013055 + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity + companion_enum_cell_line: + tag: companion_enum_cell_line + value: CellType + DOSE_RESPONSE: + text: DOSE_RESPONSE + description: Measurement of biological response as a function of compound + concentration + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity + companion_enum_cell_line: + tag: companion_enum_cell_line + value: CellType + ADME_ASSAY: + text: ADME_ASSAY + description: Absorption, distribution, metabolism, and excretion profiling + annotations: + companion_enum_compound: + tag: companion_enum_compound + value: ChemicalEntity BioticInteractionType: name: BioticInteractionType definition_uri: https://w3id.org/valuesets/BioticInteractionType @@ -71075,6 +72366,83 @@ slots: from_schema: https://w3id.org/common-value-sets/bio/psi_mi slot_uri: valuesets:experimental_preparation range: ExperimentalPreparation + sequencing_assay: + name: sequencing_assay + definition_uri: https://w3id.org/valuesets/sequencing_assay + description: Sequencing-based assay type + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + slot_uri: valuesets:sequencing_assay + range: SequencingAssayEnum + imaging_assay: + name: imaging_assay + definition_uri: https://w3id.org/valuesets/imaging_assay + description: Imaging-based assay type + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + slot_uri: valuesets:imaging_assay + range: ImagingAssayEnum + mass_spectrometry_assay: + name: mass_spectrometry_assay + definition_uri: https://w3id.org/valuesets/mass_spectrometry_assay + description: Mass spectrometry-based assay type + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + slot_uri: valuesets:mass_spectrometry_assay + range: MassSpectrometryAssayEnum + cell_based_assay: + name: cell_based_assay + definition_uri: https://w3id.org/valuesets/cell_based_assay + description: Cell-based assay type + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + slot_uri: valuesets:cell_based_assay + range: CellBasedAssayEnum + clinical_behavioral_assay: + name: clinical_behavioral_assay + definition_uri: https://w3id.org/valuesets/clinical_behavioral_assay + description: Clinical or behavioral assay type + from_schema: https://w3id.org/valuesets/bio/assays/nf_osi_assays + slot_uri: valuesets:clinical_behavioral_assay + range: ClinicalBehavioralAssayEnum + obi_assay: + name: obi_assay + definition_uri: https://w3id.org/valuesets/obi_assay + description: Any assay from the Ontology for Biomedical Investigations (OBI) + from_schema: https://w3id.org/valuesets/bio/assays/bio_assay + slot_uri: valuesets:obi_assay + range: OBIAssayEnum + bao_bioassay: + name: bao_bioassay + definition_uri: https://w3id.org/valuesets/bao_bioassay + description: Any bioassay from the BioAssay Ontology (BAO) + from_schema: https://w3id.org/valuesets/bio/assays/bio_assay + slot_uri: valuesets:bao_bioassay + range: BAOBioassayEnum + enzymology_assay: + name: enzymology_assay + definition_uri: https://w3id.org/valuesets/enzymology_assay + description: Enzymology assay type + from_schema: https://w3id.org/valuesets/bio/assays/enzymology + slot_uri: valuesets:enzymology_assay + range: EnzymologyAssayEnum + immunology_assay: + name: immunology_assay + definition_uri: https://w3id.org/valuesets/immunology_assay + description: Immunology assay type + from_schema: https://w3id.org/valuesets/bio/assays/immunology + slot_uri: valuesets:immunology_assay + range: ImmunologyAssayEnum + protein_engineering_assay: + name: protein_engineering_assay + definition_uri: https://w3id.org/valuesets/protein_engineering_assay + description: Protein engineering assay type + from_schema: https://w3id.org/valuesets/bio/assays/protein_engineering + slot_uri: valuesets:protein_engineering_assay + range: ProteinEngineeringAssayEnum + toxicology_assay: + name: toxicology_assay + definition_uri: https://w3id.org/valuesets/toxicology_assay + description: Toxicology assay type + from_schema: https://w3id.org/valuesets/bio/assays/toxicology + slot_uri: valuesets:toxicology_assay + range: ToxicologyAssayEnum biotic_interaction: name: biotic_interaction definition_uri: https://w3id.org/valuesets/biotic_interaction @@ -72544,7 +73912,7 @@ classes: class_uri: valuesets:Fake metamodel_version: 1.7.0 source_file: valuesets.yaml -source_file_date: '2026-02-15T00:57:11' -source_file_size: 4020 -generation_date: '2026-02-20T20:07:16' +source_file_date: '2026-02-22T15:00:08' +source_file_size: 4175 +generation_date: '2026-02-22T15:32:05' diff --git a/docs/views/lab-automation.md b/docs/views/lab-automation.md new file mode 100644 index 00000000..d4879e08 --- /dev/null +++ b/docs/views/lab-automation.md @@ -0,0 +1,182 @@ +# Lab Automation Value Sets + +Modern laboratories increasingly rely on robotic systems, automated workflows, +and self-driving experimentation. This view collects value sets from across +the lab automation, bioprocessing, assay, specimen processing, and computing +domains that are needed to describe automated laboratory operations end-to-end. + +## Coverage Summary + +| Domain | Schema Sources | Enums | Ontologies | +|--------|---------------|------:|------------| +| [Robotic Systems and Devices](#robotic-systems-and-devices) | lab_automation/autonomous_labs, lab_automation/devices | 5 | OBI | +| [Labware and Consumables](#labware-and-consumables) | lab_automation/labware | 4 | | +| [Liquid Handling and Operations](#liquid-handling-and-operations) | lab_automation/operations | 2 | | +| [Protocols and Orchestration](#protocols-and-orchestration) | lab_automation/protocols | 6 | | +| [Standards and Integration](#standards-and-integration) | lab_automation/standards | 4 | | +| [Thermal Cycling and PCR](#thermal-cycling-and-pcr) | lab_automation/thermal_cycling | 5 | | +| [Sequencing Platforms](#sequencing-platforms) | bio/sequencing_platforms | 4 | OBI, GENEPIO | +| [Specimen Processing](#specimen-processing) | bio/specimen_processing | 5 | OBI, NCIT | +| [Bioprocessing and Scale-Up](#bioprocessing-and-scale-up) | bioprocessing/biomanufacturing, bioprocessing/scale_up | 6 | OBI, CHEBI | +| [Assays](#assays) | bio/assays/* | 12+ | OBI, BAO | + +--- + +## Assays + +Laboratory assays are the core measurements that automated systems perform. +This section covers both broad ontology-backed dynamic enums and curated +domain-specific static enums with companion annotations for microschema coupling. + +### Dynamic Enums (Ontology-backed) + +- [OBIAssayEnum](../elements/OBIAssayEnum.md) -- all OBI assay subclasses (OBI:0000070) +- [BAOBioassayEnum](../elements/BAOBioassayEnum.md) -- all BAO bioassay subclasses (BAO:0000015) + +### Domain-Specific Static Enums + +- [EnzymologyAssayEnum](../elements/EnzymologyAssayEnum.md) -- enzyme activity, kinetics, inhibition, substrate specificity +- [ImmunologyAssayEnum](../elements/ImmunologyAssayEnum.md) -- ELISA, flow cytometry, western blot, immunoprecipitation +- [ProteinEngineeringAssayEnum](../elements/ProteinEngineeringAssayEnum.md) -- SPR, BLI, thermal shift, display technologies +- [ToxicologyAssayEnum](../elements/ToxicologyAssayEnum.md) -- cytotoxicity, genotoxicity, ADME, dose-response + +### NF-OSI Assay Enums + +- [SequencingAssayEnum](../elements/SequencingAssayEnum.md) -- RNA-seq, ATAC-seq, ChIP-seq, whole genome sequencing +- [ImagingAssayEnum](../elements/ImagingAssayEnum.md) -- confocal, electron microscopy, MRI, live-cell imaging +- [MassSpectrometryAssayEnum](../elements/MassSpectrometryAssayEnum.md) -- LC-MS, MALDI, proteomics, metabolomics +- [CellBasedAssayEnum](../elements/CellBasedAssayEnum.md) -- viability, proliferation, migration, reporter assays +- [ClinicalBehavioralAssayEnum](../elements/ClinicalBehavioralAssayEnum.md) -- behavioral testing, clinical assessments + +--- + +## Robotic Systems and Devices + +Autonomous labs combine robotic hardware, AI experiment planners, and +high-throughput screening platforms. These enums describe the components +of an automated laboratory and the experimental design methods that drive them. + +### Enums + +- [AutonomousLabComponentType](../elements/AutonomousLabComponentType.md) -- robotic handlers, automated synthesizers, HTS platforms, AI planners +- [LabAutomationWorkflowType](../elements/LabAutomationWorkflowType.md) -- closed-loop optimization, self-driving experimentation +- [ExperimentalDesignMethodType](../elements/ExperimentalDesignMethodType.md) -- Bayesian optimization, active learning, DOE +- [LaboratoryDeviceTypeEnum](../elements/LaboratoryDeviceTypeEnum.md) -- liquid handlers, centrifuges, plate readers, thermal cyclers +- [RoboticArmTypeEnum](../elements/RoboticArmTypeEnum.md) -- flexible channel, multi-channel, gripper arms + +--- + +## Labware and Consumables + +Standardized labware is essential for robotic interoperability. These enums +cover microplate formats, container types, and surface treatments. + +### Enums + +- [MicroplateFormatEnum](../elements/MicroplateFormatEnum.md) -- 6 through 1536-well plate formats +- [ContainerTypeEnum](../elements/ContainerTypeEnum.md) -- microplates, deep well plates, tube racks, reservoirs +- [PlateMaterialEnum](../elements/PlateMaterialEnum.md) -- polystyrene, polypropylene, glass +- [PlateCoatingEnum](../elements/PlateCoatingEnum.md) -- tissue culture treated, protein binding surfaces + +--- + +## Liquid Handling and Operations + +Liquid handling is the backbone of lab automation. These enums describe +pipetting operations and sample processing steps performed by robotic systems. + +### Enums + +- [LiquidHandlingOperationEnum](../elements/LiquidHandlingOperationEnum.md) -- aspirate, dispense, transfer, serial dilution, plate stamping +- [SampleProcessingOperationEnum](../elements/SampleProcessingOperationEnum.md) -- centrifugation, incubation, thermal cycling, washing, detection + +--- + +## Protocols and Orchestration + +Automated workflows require protocol management, scheduling, and error handling. +These enums describe how protocols are executed and orchestrated across instruments. + +### Enums + +- [WorkflowOrchestrationTypeEnum](../elements/WorkflowOrchestrationTypeEnum.md) -- static, dynamic, event-driven, parallel processing +- [SchedulerTypeEnum](../elements/SchedulerTypeEnum.md) -- priority-based, FIFO, resource-aware, deadline-driven +- [ProtocolStateEnum](../elements/ProtocolStateEnum.md) -- pending, running, paused, completed, failed +- [ExecutionModeEnum](../elements/ExecutionModeEnum.md) -- automated, manual, semi-automated, simulation, dry run +- [WorkflowErrorHandlingEnum](../elements/WorkflowErrorHandlingEnum.md) -- retry, abort, skip and continue, rollback +- [IntegrationSystemEnum](../elements/IntegrationSystemEnum.md) -- LIMS, ELN, MES, SCADA + +--- + +## Standards and Integration + +Lab automation standards ensure interoperability between instruments from +different vendors. These enums cover communication protocols, labware standards, +and integration features. + +### Enums + +- [AutomationStandardEnum](../elements/AutomationStandardEnum.md) -- SiLA 2, LabOP, Autoprotocol, CLSI standards +- [CommunicationProtocolEnum](../elements/CommunicationProtocolEnum.md) -- gRPC, REST API, OPC UA, Modbus +- [LabwareStandardEnum](../elements/LabwareStandardEnum.md) -- ANSI/SLAS microplate standards, SBS footprint +- [IntegrationFeatureEnum](../elements/IntegrationFeatureEnum.md) -- barcode tracking, audit trail, electronic signatures + +--- + +## Thermal Cycling and PCR + +PCR and qPCR are among the most automated laboratory procedures. These enums +describe cycler types, reaction configurations, and detection methods. + +### Enums + +- [ThermalCyclerTypeEnum](../elements/ThermalCyclerTypeEnum.md) -- standard, real-time qPCR, digital PCR, gradient +- [PCROperationTypeEnum](../elements/PCROperationTypeEnum.md) -- standard PCR, RT-qPCR, multiplex, touchdown, digital PCR +- [DetectionModeEnum](../elements/DetectionModeEnum.md) -- SYBR Green, TaqMan, molecular beacon, FRET +- [PCRPlateTypeEnum](../elements/PCRPlateTypeEnum.md) -- 96-well, 384-well, tube strips +- [ThermalCyclingStepEnum](../elements/ThermalCyclingStepEnum.md) -- denaturation, annealing, extension, melt curve + +--- + +## Sequencing Platforms + +Next-generation sequencing is a core automated workflow. These enums describe +instrument platforms, chemistries, library preparations, and data formats. + +### Enums + +- [SequencingPlatform](../elements/SequencingPlatform.md) -- Illumina, PacBio, Oxford Nanopore, Element, MGI +- [SequencingChemistry](../elements/SequencingChemistry.md) -- sequencing by synthesis, SMRT, nanopore +- [LibraryPreparation](../elements/LibraryPreparation.md) -- genomic DNA, RNA-seq, single-cell, metagenomics +- [SequenceFileFormat](../elements/SequenceFileFormat.md) -- FASTQ, BAM, CRAM, VCF, GFF3 + +--- + +## Specimen Processing + +Sample preparation is the critical first step in any automated pipeline. These +enums describe how specimens are collected, preserved, and processed. + +### Enums + +- [SpecimenCollectionMethodEnum](../elements/SpecimenCollectionMethodEnum.md) -- biopsy, venipuncture, swab, lavage +- [SpecimenPreparationMethodEnum](../elements/SpecimenPreparationMethodEnum.md) -- FFPE, cryopreservation, flash freezing, RNAlater +- [SpecimenTypeEnum](../elements/SpecimenTypeEnum.md) -- tissue, blood, plasma, serum, urine, CSF +- [AnalyteTypeEnum](../elements/AnalyteTypeEnum.md) -- DNA, RNA, protein, cfDNA +- [SourceMaterialTypeEnum](../elements/SourceMaterialTypeEnum.md) -- primary tumor, blood-derived, cell lines, xenografts + +--- + +## Bioprocessing and Scale-Up + +Automated biomanufacturing scales from microfluidic devices to commercial +fermenters. These enums cover reactor types, operating modes, and purification. + +### Enums + +- [BiomanufacturingScaleType](../elements/BiomanufacturingScaleType.md) -- micro through commercial scale +- [BioreactorTypeEnum](../elements/BioreactorTypeEnum.md) -- stirred tank, airlift, wave bag, photobioreactor +- [FermentationModeEnum](../elements/FermentationModeEnum.md) -- batch, fed-batch, continuous, perfusion +- [DownstreamProcessEnum](../elements/DownstreamProcessEnum.md) -- centrifugation, filtration, chromatography, extraction +- [SterilizationMethodEnum](../elements/SterilizationMethodEnum.md) -- steam in place, autoclave, filter sterilization +- [BioprocessOptimizationType](../elements/BioprocessOptimizationType.md) -- media optimization, PAT, digital twin modeling diff --git a/mkdocs.yml b/mkdocs.yml index 5157128f..148cdb81 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -33,8 +33,11 @@ nav: - how-to-guides/dynamic-valuesets-validation.md - how-to-guides/sync-uniprot-species.md - Slot Generation: slot-generation.md - - Subsets: - - DOE Genesis Mission: subsets/genesis-mission.md + - Views: + - DOE Genesis Mission: views/genesis-mission.md + - Microbial Ecology: views/microbial-ecology.md + - Rare Disease: views/rare-disease.md + - Lab Automation: views/lab-automation.md - Slides: slides/index.md - About: about.md diff --git a/project/jsonschema/valuesets.schema.json b/project/jsonschema/valuesets.schema.json index b0e6e1d8..818eb8a1 100644 --- a/project/jsonschema/valuesets.schema.json +++ b/project/jsonschema/valuesets.schema.json @@ -405,6 +405,21 @@ "title": "AnomalyDetectionEnum", "type": "string" }, + "AquiferType": { + "description": "Classification of aquifer types based on confinement, geology, and hydraulic characteristics.", + "enum": [ + "UNCONFINED", + "CONFINED", + "SEMI_CONFINED", + "PERCHED", + "ARTESIAN", + "FRACTURED_ROCK", + "KARST", + "ALLUVIAL" + ], + "title": "AquiferType", + "type": "string" + }, "ArchiveFormatEnum": { "description": "Archive and compression formats", "enum": [ @@ -647,6 +662,21 @@ "title": "AutomobilePaintColorEnum", "type": "string" }, + "AutonomousLabComponentType": { + "description": "Types of hardware and software components that comprise an AI-driven autonomous laboratory system", + "enum": [ + "ROBOTIC_SAMPLE_HANDLER", + "AUTOMATED_SYNTHESIZER", + "HIGH_THROUGHPUT_SCREENING_PLATFORM", + "AUTOMATED_CHARACTERIZATION_INSTRUMENT", + "AI_EXPERIMENT_PLANNER", + "DATA_MANAGEMENT_SYSTEM", + "SAFETY_MONITORING_SYSTEM", + "SAMPLE_STORAGE_SYSTEM" + ], + "title": "AutonomousLabComponentType", + "type": "string" + }, "AutonomyLevel": { "description": "Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for Topic 1 initiatives).", "enum": [ @@ -674,6 +704,11 @@ "title": "AviationLightColorEnum", "type": "string" }, + "BAOBioassayEnum": { + "description": "Dynamic enum covering all bioassays defined in the BioAssay Ontology (BAO), rooted at BAO:0000015 (bioassay).", + "title": "BAOBioassayEnum", + "type": "string" + }, "BMIClassificationEnum": { "description": "", "enum": [ @@ -797,6 +832,21 @@ "title": "BioconversionProcess", "type": "string" }, + "BioextractionMethodType": { + "description": "Biological methods for extracting metals and minerals from unconventional resources using microorganisms or plants", + "enum": [ + "HEAP_BIOLEACHING", + "STIRRED_TANK_BIOLEACHING", + "IN_SITU_BIOLEACHING", + "PHYTOMINING", + "BIOSORPTION", + "BIOACCUMULATION", + "BIOPRECIPITATION", + "BIOFLOTATION" + ], + "title": "BioextractionMethodType", + "type": "string" + }, "BiofuelGeneration": { "description": "Classification of biofuels by feedstock source and technology generation.", "enum": [ @@ -896,6 +946,18 @@ "title": "BiologicalSexEnum", "type": "string" }, + "BiomanufacturingScaleType": { + "description": "Scale classifications for biomanufacturing operations, from micro-scale screening through commercial production", + "enum": [ + "BENCH_SCALE", + "PILOT_SCALE", + "DEMONSTRATION_SCALE", + "COMMERCIAL_SCALE", + "MICRO_SCALE" + ], + "title": "BiomanufacturingScaleType", + "type": "string" + }, "BiomassFeedstockType": { "description": "Types of biomass materials used as feedstocks for bioenergy production. Includes dedicated energy crops, agricultural residues, forest residues, and waste streams.", "enum": [ @@ -922,6 +984,38 @@ "title": "BiomassFeedstockType", "type": "string" }, + "BioprocessOptimizationType": { + "description": "Strategies and approaches for optimizing biomanufacturing processes to improve yield, productivity, and product quality", + "enum": [ + "MEDIA_OPTIMIZATION", + "STRAIN_ENGINEERING", + "PROCESS_INTENSIFICATION", + "CONTINUOUS_PROCESSING", + "FED_BATCH_OPTIMIZATION", + "DOWNSTREAM_PURIFICATION", + "IN_LINE_ANALYTICS", + "DIGITAL_TWIN_MODELING" + ], + "title": "BioprocessOptimizationType", + "type": "string" + }, + "BioproductCategoryType": { + "description": "Categories of products derived from biological manufacturing processes", + "enum": [ + "BIOFUEL", + "BIOCHEMICAL", + "BIOPLASTIC", + "BIOSURFACTANT", + "BIOACTIVE_COMPOUND", + "INDUSTRIAL_ENZYME", + "BIOFERTILIZER", + "BIOPESTICIDE", + "BIOPHARMACEUTICAL", + "FOOD_INGREDIENT" + ], + "title": "BioproductCategoryType", + "type": "string" + }, "BioreactorTypeEnum": { "description": "Types of bioreactors used in fermentation and cell culture", "enum": [ @@ -1069,6 +1163,22 @@ "title": "BronstedAcidBaseRoleEnum", "type": "string" }, + "BuildingEnergyPerformanceLevel": { + "description": "Energy performance certification levels and standards for buildings", + "enum": [ + "NET_ZERO_ENERGY", + "NET_POSITIVE_ENERGY", + "PASSIVE_HOUSE", + "LEED_CERTIFIED", + "LEED_SILVER", + "LEED_GOLD", + "LEED_PLATINUM", + "ENERGY_STAR_CERTIFIED", + "CODE_MINIMUM" + ], + "title": "BuildingEnergyPerformanceLevel", + "type": "string" + }, "BuildingEnergyStandard": { "description": "Building energy efficiency standards and certifications", "enum": [ @@ -1089,6 +1199,22 @@ "title": "BuildingEnergyStandard", "type": "string" }, + "BuildingSystemType": { + "description": "Types of building systems for mechanical, electrical, and structural infrastructure", + "enum": [ + "HVAC", + "ELECTRICAL", + "PLUMBING", + "STRUCTURAL", + "BUILDING_ENVELOPE", + "FIRE_PROTECTION", + "LIGHTING", + "BUILDING_AUTOMATION", + "RENEWABLE_ENERGY_INTEGRATION" + ], + "title": "BuildingSystemType", + "type": "string" + }, "BusinessActivityTypeEnum": { "description": "Types of primary business activities", "enum": [ @@ -1282,6 +1408,62 @@ "title": "CdsPhaseType", "type": "string" }, + "CellBasedAssayEnum": { + "description": "Cell-based assays including viability, proliferation, and functional assays", + "enum": [ + "CELL_VIABILITY_ASSAY", + "CELL_PROLIFERATION_ASSAY", + "CELL_COUNT", + "ALAMAR_BLUE_ABSORBANCE", + "ALAMAR_BLUE_FLUORESCENCE", + "THREE_D_MICROTISSUE_VIABILITY", + "BRDU_PROLIFERATION", + "EDU_PROLIFERATION", + "ATPASE_ACTIVITY_ASSAY", + "CAMP_GLO_ASSAY", + "FLOW_CYTOMETRY", + "ELISA", + "SANDWICH_ELISA", + "WESTERN_BLOT", + "IMMUNOASSAY", + "PCR", + "QPCR", + "NANOSTRING_NCOUNTER", + "MULTI_ELECTRODE_ARRAY", + "CURRENT_CLAMP_ASSAY", + "WHOLE_CELL_PATCH_CLAMP", + "LOCAL_FIELD_POTENTIAL", + "LONG_TERM_POTENTIATION", + "MIGRATION_ASSAY", + "IN_VITRO_TUMORIGENESIS", + "IN_VIVO_TUMOR_GROWTH", + "IN_VIVO_PDX_VIABILITY", + "MATRIGEL_TUMORIGENESIS", + "HIGH_CONTENT_SCREEN", + "CELL_PAINTING", + "COMPOUND_SCREEN", + "COMBINATION_SCREEN", + "SMALL_MOLECULE_LIBRARY_SCREEN", + "REPORTER_GENE_ASSAY", + "MASSIVELY_PARALLEL_REPORTER_ASSAY", + "SPLIT_GFP_ASSAY", + "FOCUS_FORMING_ASSAY", + "OXYGEN_CONSUMPTION_ASSAY", + "ROS_ASSAY", + "CALCIUM_RETENTION_ASSAY", + "TRANS_ENDOTHELIAL_RESISTANCE", + "CELL_PERMEABILITY_ASSAY", + "PHARMACOKINETIC_ADME", + "ARRAY", + "HPLC", + "ELECTROCHEMILUMINESCENCE", + "STR_PROFILE", + "TIDE", + "SURVIVAL_ASSAY" + ], + "title": "CellBasedAssayEnum", + "type": "string" + }, "CellCycleCheckpoint": { "description": "Cell cycle checkpoints that regulate progression", "enum": [ @@ -1364,6 +1546,22 @@ "title": "ChemicalEntity", "type": "string" }, + "ChipFabricationNodeType": { + "description": "Semiconductor fabrication process node sizes defining transistor feature dimensions", + "enum": [ + "NODE_3NM", + "NODE_5NM", + "NODE_7NM", + "NODE_10NM", + "NODE_14NM", + "NODE_22NM", + "NODE_28NM", + "NODE_45NM", + "MATURE_NODE" + ], + "title": "ChipFabricationNodeType", + "type": "string" + }, "ChiralityEnum": { "description": "Chirality/stereochemistry descriptors", "enum": [ @@ -1419,6 +1617,59 @@ "title": "CitationStyle", "type": "string" }, + "ClinicalBehavioralAssayEnum": { + "description": "Clinical assessments and behavioral assays used in research", + "enum": [ + "CLINICAL_DATA", + "QUESTIONNAIRE", + "INTERVIEW", + "FOCUS_GROUP", + "SCALE", + "NEUROPSYCHOLOGICAL_ASSESSMENT", + "COGNITIVE_ASSESSMENT", + "NIH_TOOLBOX", + "PROMIS_COGNITIVE_FUNCTION", + "N_BACK_TASK", + "CORSI_BLOCKS", + "CBCL_1_5_5", + "CBCL_6_18", + "SRS", + "SRS_2", + "BLOOD_CHEMISTRY", + "METABOLIC_SCREENING", + "GENOTYPING", + "BODY_SIZE_MEASUREMENT", + "GAIT_MEASUREMENT", + "GRIP_STRENGTH", + "HAND_HELD_DYNAMOMETRY", + "SIX_MINUTE_WALK_TEST", + "ACTIGRAPHY", + "POLYSOMNOGRAPHY", + "QUANTITATIVE_SENSORY_TESTING", + "VON_FREY_TEST", + "ALGOMETRX_NOCIOMETER", + "AUDITORY_BRAINSTEM_RESPONSE", + "PURE_TONE_AVERAGE", + "WORD_RECOGNITION_SCORE", + "DPOE", + "PATTERN_ERG", + "OPTOKINETIC_REFLEX", + "RICCARDI_ABLON_SCALES", + "SKINDEX_16", + "CNF_SKINDEX", + "CDLQI", + "FACEQ_DISTRESS", + "OPEN_FIELD_TEST", + "ELEVATED_PLUS_MAZE", + "ROTAROD_TEST", + "ACTIVE_AVOIDANCE", + "CONTEXTUAL_CONDITIONING", + "NOVELTY_RESPONSE", + "FEEDING_ASSAY" + ], + "title": "ClinicalBehavioralAssayEnum", + "type": "string" + }, "ClinicalFinding": { "description": "Clinical findings and observations", "title": "ClinicalFinding", @@ -2249,6 +2500,32 @@ "title": "DataAbsentEnum", "type": "string" }, + "DataCenterCoolingType": { + "description": "Types of cooling systems used in data center facilities", + "enum": [ + "AIR_COOLING", + "LIQUID_COOLING", + "IMMERSION_COOLING", + "REAR_DOOR_HEAT_EXCHANGER", + "EVAPORATIVE_COOLING", + "GEOTHERMAL_COOLING", + "FREE_AIR_COOLING", + "DIRECT_TO_CHIP_LIQUID_COOLING" + ], + "title": "DataCenterCoolingType", + "type": "string" + }, + "DataCenterTierLevel": { + "description": "Uptime Institute data center tier classification levels defining infrastructure reliability", + "enum": [ + "TIER_I", + "TIER_II", + "TIER_III", + "TIER_IV" + ], + "title": "DataCenterTierLevel", + "type": "string" + }, "DataCiteContributorType": { "description": "Types of contributors to research resources from DataCite 4.6.\nThese describe organizational and functional roles rather than\nspecific contribution activities (see CRediT/ResearchRole for those).", "enum": [ @@ -2557,6 +2834,20 @@ "title": "DecisionMakingStyleEnum", "type": "string" }, + "DecommissioningPhaseType": { + "description": "Phases in the decommissioning lifecycle of nuclear facilities", + "enum": [ + "CHARACTERIZATION", + "DECONTAMINATION", + "DISMANTLEMENT", + "WASTE_MANAGEMENT", + "SITE_RESTORATION", + "LONG_TERM_MONITORING", + "LICENSE_TERMINATION" + ], + "title": "DecommissioningPhaseType", + "type": "string" + }, "DefectClassificationEnum": { "description": "Manufacturing defect classification", "enum": [ @@ -2619,6 +2910,21 @@ "title": "Detector", "type": "string" }, + "DetectorType": { + "description": "Types of detectors used in particle physics experiments", + "enum": [ + "CALORIMETER", + "TRACKING_DETECTOR", + "TIME_PROJECTION_CHAMBER", + "CHERENKOV_DETECTOR", + "SCINTILLATOR", + "SILICON_STRIP_DETECTOR", + "DRIFT_CHAMBER", + "MUON_SPECTROMETER" + ], + "title": "DetectorType", + "type": "string" + }, "DiagnosticTestTypeEnum": { "description": "", "enum": [ @@ -3074,6 +3380,22 @@ "title": "EnzymeClassEnum", "type": "string" }, + "EnzymologyAssayEnum": { + "description": "Assays for characterizing enzyme function including activity, kinetics, inhibition, and substrate specificity.", + "enum": [ + "ENZYME_ACTIVITY_ASSAY", + "MICHAELIS_MENTEN_KINETICS", + "INHIBITION_ASSAY", + "SUBSTRATE_SPECIFICITY", + "FLUOROMETRIC_ENZYME_ASSAY", + "COLORIMETRIC_ENZYME_ASSAY", + "COUPLED_ENZYME_ASSAY", + "CONTINUOUS_ENZYME_ASSAY", + "ENDPOINT_ENZYME_ASSAY" + ], + "title": "EnzymologyAssayEnum", + "type": "string" + }, "EthnicityOMB1997Enum": { "description": "Ethnicity categories following OMB 1997 standards used by NIH and federal agencies", "enum": [ @@ -3097,6 +3419,22 @@ "title": "ExecutionModeEnum", "type": "string" }, + "ExperimentalDesignMethodType": { + "description": "Computational and statistical methods used for experimental design in autonomous laboratory workflows", + "enum": [ + "BAYESIAN_OPTIMIZATION", + "ACTIVE_LEARNING", + "REINFORCEMENT_LEARNING", + "EVOLUTIONARY_ALGORITHM", + "RANDOM_SEARCH", + "GRID_SEARCH", + "LATIN_HYPERCUBE_SAMPLING", + "DESIGN_OF_EXPERIMENTS", + "MULTI_OBJECTIVE_OPTIMIZATION" + ], + "title": "ExperimentalDesignMethodType", + "type": "string" + }, "ExperimentalPreparation": { "description": "Sample preparation methods", "enum": [ @@ -3240,23 +3578,23 @@ "type": "string" }, "ExtractableTargetElement": { - "description": "Target elements for extraction, particularly rare earth elements (REE) and critical minerals.", - "enum": [ - "REE_LA", - "REE_CE", - "REE_PR", - "REE_ND", - "REE_PM", - "REE_SM", - "REE_EU", - "REE_GD", - "REE_TB", - "REE_DY", - "REE_HO", - "REE_ER", - "REE_TM", - "REE_YB", - "REE_LU", + "description": "Target elements for extraction in mining operations, including rare earth elements (REE), critical minerals, and battery metals. These elements are strategically important for clean energy technologies, electronics, and defense applications.", + "enum": [ + "LA", + "CE", + "PR", + "ND", + "PM", + "SM", + "EU", + "GD", + "TB", + "DY", + "HO", + "ER", + "TM", + "YB", + "LU", "SC", "CO", "NI", @@ -3671,6 +4009,30 @@ "title": "FuelFormEnum", "type": "string" }, + "FundamentalParticleType": { + "description": "Standard Model fundamental particles classified by type", + "enum": [ + "ELECTRON", + "MUON", + "TAU", + "ELECTRON_NEUTRINO", + "MUON_NEUTRINO", + "TAU_NEUTRINO", + "UP_QUARK", + "DOWN_QUARK", + "CHARM_QUARK", + "STRANGE_QUARK", + "TOP_QUARK", + "BOTTOM_QUARK", + "PHOTON", + "GLUON", + "W_BOSON", + "Z_BOSON", + "HIGGS_BOSON" + ], + "title": "FundamentalParticleType", + "type": "string" + }, "FundingType": { "description": "Types of research funding", "enum": [ @@ -3688,6 +4050,47 @@ "title": "FundingType", "type": "string" }, + "FusionConfinementType": { + "description": "Methods for confining plasma in fusion energy experiments and reactors", + "enum": [ + "MAGNETIC_CONFINEMENT_TOKAMAK", + "MAGNETIC_CONFINEMENT_STELLARATOR", + "INERTIAL_CONFINEMENT", + "MAGNETO_INERTIAL", + "LASER_DRIVEN", + "Z_PINCH", + "FIELD_REVERSED_CONFIGURATION", + "SPHEROMAK" + ], + "title": "FusionConfinementType", + "type": "string" + }, + "FusionFuelType": { + "description": "Types of nuclear fuel mixtures used in fusion reactions", + "enum": [ + "DEUTERIUM_TRITIUM", + "DEUTERIUM_DEUTERIUM", + "DEUTERIUM_HELIUM3", + "PROTON_BORON11" + ], + "title": "FusionFuelType", + "type": "string" + }, + "FusionPlasmaParameterType": { + "description": "Key physical parameters measured and optimized in fusion plasma experiments", + "enum": [ + "PLASMA_TEMPERATURE", + "PLASMA_DENSITY", + "CONFINEMENT_TIME", + "BETA_VALUE", + "ENERGY_GAIN_FACTOR_Q", + "LAWSON_CRITERION", + "PLASMA_CURRENT", + "MAGNETIC_FIELD_STRENGTH" + ], + "title": "FusionPlasmaParameterType", + "type": "string" + }, "GOElectronicMethods": { "description": "Electronic annotation methods used in Gene Ontology, identified by GO_REF codes", "enum": [ @@ -3908,6 +4311,24 @@ "title": "GeologicalEra", "type": "string" }, + "GeophysicalMethodType": { + "description": "Types of geophysical investigation methods used for subsurface characterization, resource exploration, and environmental monitoring.", + "enum": [ + "SEISMIC_REFLECTION", + "SEISMIC_REFRACTION", + "GROUND_PENETRATING_RADAR", + "ELECTRICAL_RESISTIVITY_TOMOGRAPHY", + "MAGNETOTELLURICS", + "GRAVITY_SURVEY", + "MAGNETIC_SURVEY", + "WELL_LOGGING", + "DISTRIBUTED_ACOUSTIC_SENSING", + "DISTRIBUTED_TEMPERATURE_SENSING", + "CROSSWELL_TOMOGRAPHY" + ], + "title": "GeophysicalMethodType", + "type": "string" + }, "GeothermalApplication": { "description": "Applications and uses of geothermal energy.", "enum": [ @@ -4001,6 +4422,56 @@ "title": "GravitySdohDomainEnum", "type": "string" }, + "GridComponentType": { + "description": "Types of physical components in electrical transmission and distribution grids", + "enum": [ + "TRANSMISSION_LINE", + "DISTRIBUTION_LINE", + "TRANSFORMER", + "SUBSTATION", + "CIRCUIT_BREAKER", + "CAPACITOR_BANK", + "FACTS_DEVICE", + "SMART_METER", + "INVERTER", + "RELAY" + ], + "title": "GridComponentType", + "type": "string" + }, + "GridEnergyStorageType": { + "description": "Types of energy storage technologies used for grid-scale and distributed applications", + "enum": [ + "LITHIUM_ION_BATTERY", + "FLOW_BATTERY", + "PUMPED_HYDROELECTRIC", + "COMPRESSED_AIR", + "FLYWHEEL", + "SUPERCAPACITOR", + "THERMAL_STORAGE", + "HYDROGEN_STORAGE", + "GRAVITY_STORAGE", + "SODIUM_ION_BATTERY" + ], + "title": "GridEnergyStorageType", + "type": "string" + }, + "GridManagementStrategyType": { + "description": "Strategies for managing and optimizing the operation of electrical grids", + "enum": [ + "DEMAND_RESPONSE", + "LOAD_BALANCING", + "FREQUENCY_REGULATION", + "VOLTAGE_CONTROL", + "PEAK_SHAVING", + "DISTRIBUTED_GENERATION", + "MICROGRID_OPERATION", + "VIRTUAL_POWER_PLANT", + "GRID_SCALE_STORAGE_DISPATCH" + ], + "title": "GridManagementStrategyType", + "type": "string" + }, "GridType": { "description": "Types of electrical grid systems", "enum": [ @@ -4014,6 +4485,23 @@ "title": "GridType", "type": "string" }, + "GroundwaterProcessType": { + "description": "Types of physical, chemical, and biological processes occurring in groundwater systems.", + "enum": [ + "RECHARGE", + "DISCHARGE", + "BASEFLOW", + "LATERAL_FLOW", + "VERTICAL_LEAKAGE", + "SALTWATER_INTRUSION", + "CONTAMINANT_TRANSPORT", + "BIODEGRADATION", + "SORPTION", + "PRECIPITATION_DISSOLUTION" + ], + "title": "GroundwaterProcessType", + "type": "string" + }, "HHEARExposureAssessedEnum": { "description": "Categories of environmental exposures assessed in Human Health Exposure Analysis Resource (HHEAR) studies. Based on the HHEAR value set HHEARVS:00008 (Study Environmental Exposures Assessed).", "enum": [ @@ -4289,6 +4777,21 @@ "title": "HydrogenType", "type": "string" }, + "HydrogeologyWellType": { + "description": "Classification of wells used for groundwater access, monitoring, and management.", + "enum": [ + "MONITORING_WELL", + "PRODUCTION_WELL", + "INJECTION_WELL", + "OBSERVATION_WELL", + "PIEZOMETER", + "EXTRACTION_WELL", + "RECHARGE_WELL", + "GEOTHERMAL_WELL" + ], + "title": "HydrogeologyWellType", + "type": "string" + }, "IAEAWasteClassificationEnum": { "description": "IAEA General Safety Requirements radioactive waste classification scheme", "enum": [ @@ -4516,11 +5019,65 @@ "title": "ImageFileFormatEnum", "type": "string" }, + "ImagingAssayEnum": { + "description": "Imaging-based assays including microscopy, MRI, and related methods", + "enum": [ + "BRIGHTFIELD_MICROSCOPY", + "CONFOCAL_MICROSCOPY", + "THREE_D_CONFOCAL_IMAGING", + "FLUORESCENCE_MICROSCOPY", + "PHASE_CONTRAST_MICROSCOPY", + "ATOMIC_FORCE_MICROSCOPY", + "THREE_D_ELECTRON_MICROSCOPY", + "IMMUNOFLUORESCENCE", + "IMMUNOHISTOCHEMISTRY", + "IMMUNOCYTOCHEMISTRY", + "HISTOLOGY", + "FISH", + "CODEX", + "LIVE_IMAGING", + "AUTORADIOGRAPHY", + "CONVENTIONAL_MRI", + "FUNCTIONAL_MRI", + "DIFFUSION_MRI", + "MPRAGE_MRI", + "MAGNETIC_RESONANCE_SPECTROSCOPY", + "MAGNETIC_RESONANCE_ANGIOGRAPHY", + "POSITRON_EMISSION_TOMOGRAPHY", + "OPTICAL_COHERENCE_TOMOGRAPHY", + "OPTICAL_TOMOGRAPHY", + "HIGH_FREQUENCY_ULTRASOUND", + "TRANSCRANIAL_DOPPLER", + "IN_VIVO_BIOLUMINESCENCE", + "LASER_SPECKLE_IMAGING", + "SPATIAL_FREQUENCY_DOMAIN_IMAGING", + "TRACTION_FORCE_MICROSCOPY", + "PHOTOGRAPH" + ], + "title": "ImagingAssayEnum", + "type": "string" + }, "ImmuneCell": { "description": "Immune system cell types (leukocytes and their subtypes)", "title": "ImmuneCell", "type": "string" }, + "ImmunologyAssayEnum": { + "description": "Assays for detecting and quantifying immune-related molecules including antibody-based detection, cell sorting, and blotting methods.", + "enum": [ + "ELISA", + "SANDWICH_ELISA", + "IMMUNOPRECIPITATION", + "FLOW_CYTOMETRY", + "WESTERN_BLOT", + "CYTOKINE_SECRETION_ASSAY", + "IMMUNOBLOT", + "COMPLEMENT_FIXATION", + "MULTIPLEX_BEAD_ASSAY" + ], + "title": "ImmunologyAssayEnum", + "type": "string" + }, "InSituChemistryRegime": { "description": "Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, temperature, and ionic strength.", "enum": [ @@ -5064,6 +5621,19 @@ "title": "KaryotypicSexEnum", "type": "string" }, + "LabAutomationWorkflowType": { + "description": "Types of automated workflows implemented in autonomous laboratory systems", + "enum": [ + "CLOSED_LOOP_OPTIMIZATION", + "HIGH_THROUGHPUT_SCREENING", + "AUTOMATED_SYNTHESIS", + "AUTONOMOUS_CHARACTERIZATION", + "SELF_DRIVING_EXPERIMENTATION", + "ROBOTIC_SAMPLE_PREPARATION" + ], + "title": "LabAutomationWorkflowType", + "type": "string" + }, "LaboratoryDeviceTypeEnum": { "description": "Types of automated laboratory devices and equipment", "enum": [ @@ -5523,6 +6093,26 @@ "title": "ManagementMethodologyEnum", "type": "string" }, + "ManufacturingProcessType": { + "description": "Types of manufacturing processes including additive, subtractive, and formative methods", + "enum": [ + "ADDITIVE_MANUFACTURING", + "SUBTRACTIVE_MANUFACTURING", + "FORMATIVE_MANUFACTURING", + "CASTING", + "FORGING", + "WELDING", + "MACHINING", + "INJECTION_MOLDING", + "EXTRUSION", + "POWDER_METALLURGY", + "CHEMICAL_VAPOR_DEPOSITION", + "PHYSICAL_VAPOR_DEPOSITION", + "ELECTROFORMING" + ], + "title": "ManufacturingProcessType", + "type": "string" + }, "ManuscriptSection": { "description": "Sections of a scientific manuscript or publication", "enum": [ @@ -5657,6 +6247,27 @@ "title": "MassSpectrometerVendor", "type": "string" }, + "MassSpectrometryAssayEnum": { + "description": "Mass spectrometry-based assays for proteomics and metabolomics", + "enum": [ + "MASS_SPECTROMETRY", + "LC_MS", + "LC_MS_MS", + "HPLC_MS_MS", + "UHPLC_MS_MS", + "FIA_MSMS", + "LABEL_FREE_MS", + "TMT_QUANTITATION", + "MUDPIT", + "MIB_MS", + "LC_ECD", + "FTIR_SPECTROSCOPY", + "RPPA", + "PROXIMITY_EXTENSION_ASSAY" + ], + "title": "MassSpectrometryAssayEnum", + "type": "string" + }, "MassUnitEnum": { "description": "Units of mass measurement", "enum": [ @@ -5688,6 +6299,40 @@ "title": "MaterialClassEnum", "type": "string" }, + "MaterialPropertyPredictionType": { + "description": "Material properties that are commonly targeted for computational prediction in materials discovery and design", + "enum": [ + "BAND_GAP", + "ELASTIC_MODULUS", + "THERMAL_CONDUCTIVITY", + "DIELECTRIC_CONSTANT", + "MAGNETIC_MOMENT", + "FORMATION_ENERGY", + "SURFACE_ENERGY", + "DEFECT_ENERGY", + "PHASE_STABILITY", + "MECHANICAL_STRENGTH" + ], + "title": "MaterialPropertyPredictionType", + "type": "string" + }, + "MaterialsSimulationType": { + "description": "Computational simulation methods used in materials science for predicting structure, properties, and behavior of materials", + "enum": [ + "DENSITY_FUNCTIONAL_THEORY", + "MOLECULAR_DYNAMICS", + "MONTE_CARLO", + "PHASE_FIELD_MODELING", + "FINITE_ELEMENT_ANALYSIS", + "CONTINUUM_MECHANICS", + "TIGHT_BINDING", + "AB_INITIO_MOLECULAR_DYNAMICS", + "MACHINE_LEARNING_POTENTIAL", + "COARSE_GRAINED_SIMULATION" + ], + "title": "MaterialsSimulationType", + "type": "string" + }, "MechanicalBehaviorEnum": { "description": "Mechanical behavior of materials under stress", "enum": [ @@ -6272,6 +6917,22 @@ "title": "NuclearFacilityTypeEnum", "type": "string" }, + "NuclearForensicsMethodType": { + "description": "Analytical methods used in nuclear forensics for material characterization and attribution", + "enum": [ + "ISOTOPE_RATIO_ANALYSIS", + "MASS_SPECTROMETRY", + "GAMMA_SPECTROSCOPY", + "ALPHA_SPECTROSCOPY", + "NEUTRON_ACTIVATION_ANALYSIS", + "RADIOCHEMICAL_SEPARATION", + "ELECTRON_MICROSCOPY", + "X_RAY_FLUORESCENCE", + "AGE_DATING" + ], + "title": "NuclearForensicsMethodType", + "type": "string" + }, "NuclearFuelTypeEnum": { "description": "Types of nuclear fuel materials and compositions", "enum": [ @@ -6293,6 +6954,23 @@ "title": "NuclearFuelTypeEnum", "type": "string" }, + "NuclearRemediationType": { + "description": "Methods for remediating radioactive contamination at nuclear sites", + "enum": [ + "SOIL_EXCAVATION", + "GROUNDWATER_PUMP_AND_TREAT", + "IN_SITU_BIOREMEDIATION", + "VITRIFICATION", + "STABILIZATION", + "CAPPING", + "PHYTOREMEDIATION", + "ELECTROKINETIC_REMEDIATION", + "CHEMICAL_OXIDATION", + "MONITORED_NATURAL_ATTENUATION" + ], + "title": "NuclearRemediationType", + "type": "string" + }, "NuclearSecurityCategoryEnum": { "description": "IAEA nuclear material security categories (INFCIRC/225)", "enum": [ @@ -6317,6 +6995,19 @@ "title": "NuclearShipTypeEnum", "type": "string" }, + "NuclearThreatCategoryType": { + "description": "Categories of nuclear and radiological threat scenarios for security assessment", + "enum": [ + "IMPROVISED_NUCLEAR_DEVICE", + "RADIOLOGICAL_DISPERSAL_DEVICE", + "NUCLEAR_FACILITY_SABOTAGE", + "NUCLEAR_MATERIAL_THEFT", + "NUCLEAR_SMUGGLING", + "ENVIRONMENTAL_RELEASE" + ], + "title": "NuclearThreatCategoryType", + "type": "string" + }, "NucleotideModificationEnum": { "description": "Common nucleotide modifications", "enum": [ @@ -6332,6 +7023,11 @@ "title": "NucleotideModificationEnum", "type": "string" }, + "OBIAssayEnum": { + "description": "Dynamic enum covering all assays defined in the Ontology for Biomedical Investigations (OBI), rooted at OBI:0000070 (assay).", + "title": "OBIAssayEnum", + "type": "string" + }, "OWLProfileEnum": { "description": "OWL 2 profiles that provide different tradeoffs between expressiveness and computational complexity", "enum": [ @@ -6918,6 +7614,21 @@ "title": "ParticipantVitalStatusEnum", "type": "string" }, + "ParticleAcceleratorType": { + "description": "Types of particle accelerator facilities used in high-energy physics research", + "enum": [ + "LINEAR_ACCELERATOR", + "SYNCHROTRON", + "CYCLOTRON", + "STORAGE_RING", + "FREE_ELECTRON_LASER", + "COLLIDER", + "SPALLATION_SOURCE", + "BETATRON" + ], + "title": "ParticleAcceleratorType", + "type": "string" + }, "PeakAnnotationSeriesLabel": { "description": "Types of peak annotations in mass spectrometry data", "enum": [ @@ -7521,6 +8232,20 @@ "title": "Protein", "type": "string" }, + "ProteinEngineeringAssayEnum": { + "description": "Assays for protein engineering including binding kinetics, biophysical characterization, and display-based selection methods.", + "enum": [ + "SURFACE_PLASMON_RESONANCE", + "BIOLAYER_INTERFEROMETRY", + "THERMAL_SHIFT_ASSAY", + "CIRCULAR_DICHROISM", + "PHAGE_DISPLAY", + "YEAST_DISPLAY", + "DIRECTED_EVOLUTION_SCREEN" + ], + "title": "ProteinEngineeringAssayEnum", + "type": "string" + }, "ProteinEvidenceForExistence": { "description": "The evidence for the existence of a biological entity. See https://www.uniprot.org/help/protein_existence and https://www.ncbi.nlm.nih.gov/genbank/evidence/.", "enum": [ @@ -7759,6 +8484,21 @@ "title": "QuantityKindEnum", "type": "string" }, + "QuantumAlgorithmCategoryType": { + "description": "Categories of quantum algorithms by their primary application domain", + "enum": [ + "OPTIMIZATION", + "SIMULATION", + "MACHINE_LEARNING", + "CRYPTOGRAPHY", + "LINEAR_ALGEBRA", + "SEARCH", + "ERROR_CORRECTION", + "VARIATIONAL" + ], + "title": "QuantumAlgorithmCategoryType", + "type": "string" + }, "Quarter": { "description": "Calendar quarters", "enum": [ @@ -7770,6 +8510,21 @@ "title": "Quarter", "type": "string" }, + "QubitType": { + "description": "Types of physical qubit implementations used in quantum computing hardware", + "enum": [ + "SUPERCONDUCTING", + "TRAPPED_ION", + "PHOTONIC", + "TOPOLOGICAL", + "NEUTRAL_ATOM", + "QUANTUM_DOT", + "NITROGEN_VACANCY_CENTER", + "SPIN_QUBIT" + ], + "title": "QubitType", + "type": "string" + }, "RNABaseEnum": { "description": "Standard RNA nucleotide bases (canonical)", "enum": [ @@ -7831,6 +8586,23 @@ "title": "RadiationProtectionZoneEnum", "type": "string" }, + "RadioactiveContaminantType": { + "description": "Common radioactive contaminants found at nuclear cleanup sites", + "enum": [ + "CESIUM_137", + "STRONTIUM_90", + "TECHNETIUM_99", + "TRITIUM", + "URANIUM", + "PLUTONIUM", + "AMERICIUM_241", + "IODINE_129", + "COBALT_60", + "RADIUM_226" + ], + "title": "RadioactiveContaminantType", + "type": "string" + }, "ReactionConditionEnum": { "description": "Reaction conditions", "enum": [ @@ -8168,6 +8940,34 @@ "title": "RelativeTimeEnum", "type": "string" }, + "RemoteSensingDataType": { + "description": "Classification of data types acquired by remote sensing instruments, covering electromagnetic and potential field measurements.", + "enum": [ + "MULTISPECTRAL", + "HYPERSPECTRAL", + "SYNTHETIC_APERTURE_RADAR", + "LIDAR", + "THERMAL_INFRARED", + "MICROWAVE_RADIOMETRY", + "GRAVIMETRY", + "MAGNETOMETRY", + "PHOTOGRAMMETRY" + ], + "title": "RemoteSensingDataType", + "type": "string" + }, + "RemoteSensingPlatformType": { + "description": "Classification of platforms used to carry remote sensing instruments for earth observation and environmental monitoring.", + "enum": [ + "SATELLITE", + "AIRBORNE", + "UAV_DRONE", + "GROUND_BASED", + "SHIPBORNE" + ], + "title": "RemoteSensingPlatformType", + "type": "string" + }, "ResearchField": { "description": "Major research fields and disciplines", "enum": [ @@ -8261,6 +9061,21 @@ "title": "ResearchRole", "type": "string" }, + "ReservoirCharacterizationMethodType": { + "description": "Methods and techniques used to characterize subsurface reservoirs for energy extraction and storage applications", + "enum": [ + "WELL_TEST_ANALYSIS", + "SEISMIC_INTERPRETATION", + "CORE_ANALYSIS", + "WIRELINE_LOGGING", + "TRACER_TEST", + "PRESSURE_TRANSIENT_ANALYSIS", + "PRODUCTION_HISTORY_MATCHING", + "GEOSTATISTICAL_MODELING" + ], + "title": "ReservoirCharacterizationMethodType", + "type": "string" + }, "RightsBasis": { "description": "The basis for the right or permission granted for an object.\nBased on PREMIS rights basis vocabulary.", "enum": [ @@ -8386,6 +9201,21 @@ "title": "SectionLocationEnum", "type": "string" }, + "SemiconductorMaterialType": { + "description": "Types of semiconductor materials used in microelectronics fabrication", + "enum": [ + "SILICON", + "GALLIUM_ARSENIDE", + "SILICON_CARBIDE", + "GALLIUM_NITRIDE", + "INDIUM_PHOSPHIDE", + "GERMANIUM", + "SILICON_GERMANIUM", + "DIAMOND" + ], + "title": "SemiconductorMaterialType", + "type": "string" + }, "SensorWhileDrillingFeature": { "description": "Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering applications.", "enum": [ @@ -8550,6 +9380,44 @@ "title": "SequencingApplication", "type": "string" }, + "SequencingAssayEnum": { + "description": "Sequencing-based assays including RNA-seq, DNA-seq, and related methods", + "enum": [ + "RNA_SEQ", + "SINGLE_CELL_RNA_SEQ", + "SINGLE_NUCLEUS_RNA_SEQ", + "SPATIAL_TRANSCRIPTOMICS", + "LNCRNA_SEQ", + "MIRNA_SEQ", + "RIBO_SEQ", + "WHOLE_GENOME_SEQUENCING", + "WHOLE_EXOME_SEQUENCING", + "TARGETED_EXOME_SEQUENCING", + "NEXT_GENERATION_TARGETED_SEQUENCING", + "SANGER_SEQUENCING", + "ATAC_SEQ", + "SINGLE_CELL_ATAC_SEQ", + "CHIP_SEQ", + "CUT_AND_RUN", + "BISULFITE_SEQUENCING", + "ERR_BISULFITE_SEQUENCING", + "OXBS_SEQ", + "HI_C", + "ISO_SEQ", + "NOME_SEQ", + "CAPP_SEQ", + "SAFER_SEQS", + "TCR_REPERTOIRE_SEQUENCING", + "SCCGI_SEQ", + "JUMPING_LIBRARY", + "SNP_ARRAY", + "RNA_ARRAY", + "MIRNA_ARRAY", + "METHYLATION_ARRAY" + ], + "title": "SequencingAssayEnum", + "type": "string" + }, "SequencingChemistry": { "description": "Fundamental chemical methods used for DNA/RNA sequencing", "enum": [ @@ -8644,6 +9512,21 @@ "title": "SkinToneEnum", "type": "string" }, + "SmartManufacturingTechnologyType": { + "description": "Types of digital and intelligent technologies used in modern manufacturing environments", + "enum": [ + "DIGITAL_TWIN", + "INDUSTRIAL_IOT", + "PREDICTIVE_MAINTENANCE", + "COMPUTER_VISION_INSPECTION", + "ROBOTIC_ASSEMBLY", + "AUTOMATED_QUALITY_CONTROL", + "SUPPLY_CHAIN_OPTIMIZATION", + "PROCESS_SIMULATION" + ], + "title": "SmartManufacturingTechnologyType", + "type": "string" + }, "SmokingStatusEnum": { "description": "Tobacco and nicotine consumption status", "enum": [ @@ -9106,6 +9989,72 @@ "title": "SubatomicParticleEnum", "type": "string" }, + "SubsurfaceEnergyResourceType": { + "description": "Types of subsurface energy resources including geothermal, hydrocarbon, and other geological energy assets", + "enum": [ + "GEOTHERMAL_RESERVOIR", + "ENHANCED_GEOTHERMAL_SYSTEM", + "OIL_RESERVOIR", + "NATURAL_GAS_RESERVOIR", + "COALBED_METHANE", + "GAS_HYDRATE", + "HOT_DRY_ROCK", + "SEDIMENTARY_BASIN", + "VOLCANIC_SYSTEM" + ], + "title": "SubsurfaceEnergyResourceType", + "type": "string" + }, + "SubsurfaceFormationType": { + "description": "Classification of subsurface geological formations relevant to energy exploration, carbon storage, geothermal systems, and groundwater resources.", + "enum": [ + "AQUIFER", + "AQUITARD", + "RESERVOIR_ROCK", + "CAPROCK", + "FAULT_ZONE", + "KARST", + "PERMAFROST", + "UNCONSOLIDATED_SEDIMENT", + "FRACTURED_BEDROCK", + "COAL_SEAM", + "SALT_DOME", + "SHALE" + ], + "title": "SubsurfaceFormationType", + "type": "string" + }, + "SubsurfacePropertyType": { + "description": "Physical and hydraulic properties of subsurface formations relevant to resource characterization and reservoir modeling.", + "enum": [ + "POROSITY", + "PERMEABILITY", + "THERMAL_CONDUCTIVITY", + "SPECIFIC_HEAT_CAPACITY", + "BULK_DENSITY", + "FLUID_SATURATION", + "PORE_PRESSURE", + "GEOTHERMAL_GRADIENT", + "HYDRAULIC_CONDUCTIVITY", + "ELASTIC_MODULUS", + "SEISMIC_VELOCITY" + ], + "title": "SubsurfacePropertyType", + "type": "string" + }, + "SubsurfaceStorageType": { + "description": "Types of subsurface energy and material storage technologies utilizing geological formations", + "enum": [ + "CARBON_CAPTURE_AND_STORAGE", + "HYDROGEN_STORAGE", + "COMPRESSED_AIR_ENERGY_STORAGE", + "NATURAL_GAS_STORAGE", + "THERMAL_ENERGY_STORAGE", + "NUCLEAR_WASTE_REPOSITORY" + ], + "title": "SubsurfaceStorageType", + "type": "string" + }, "SupplierRelationshipTypeEnum": { "description": "Types of supplier relationship management", "enum": [ @@ -9174,6 +10123,20 @@ "title": "SynthesisMethodEnum", "type": "string" }, + "TailingCharacterizationType": { + "description": "Types of measurements and analyses used to characterize mine tailings and other mineral processing residues for resource recovery potential", + "enum": [ + "PARTICLE_SIZE_DISTRIBUTION", + "MINERALOGICAL_COMPOSITION", + "ACID_GENERATING_POTENTIAL", + "METAL_CONTENT", + "MOISTURE_CONTENT", + "GEOTECHNICAL_STABILITY", + "ENVIRONMENTAL_RISK_CLASSIFICATION" + ], + "title": "TailingCharacterizationType", + "type": "string" + }, "TaxonomicRank": { "description": "Standard taxonomic ranks used in biological classification", "enum": [ @@ -9414,6 +10377,21 @@ "title": "ToxicityClassificationEnum", "type": "string" }, + "ToxicologyAssayEnum": { + "description": "Assays for evaluating toxicity, genotoxicity, and safety of compounds including cytotoxicity, mutagenicity, and ADME measurements.", + "enum": [ + "TOXICITY_ASSAY", + "MTT_ASSAY", + "LDH_RELEASE_ASSAY", + "AMES_TEST", + "COMET_ASSAY", + "MICRONUCLEUS_ASSAY", + "DOSE_RESPONSE", + "ADME_ASSAY" + ], + "title": "ToxicologyAssayEnum", + "type": "string" + }, "TraditionalPigmentEnum": { "description": "Traditional artist pigments and their colors", "enum": [ @@ -9673,6 +10651,25 @@ "title": "USStateCodeEnum", "type": "string" }, + "UnconventionalMineralResourceType": { + "description": "Types of unconventional mineral resources including industrial waste streams, mining residues, and brines that contain recoverable critical minerals and metals", + "enum": [ + "MINE_TAILINGS", + "WASTE_ROCK", + "ACID_MINE_DRAINAGE", + "COAL_COMBUSTION_RESIDUALS", + "RED_MUD", + "PHOSPHOGYPSUM", + "SLAG", + "FLY_ASH", + "ELECTRONIC_WASTE", + "SPENT_CATALYSTS", + "GEOTHERMAL_BRINE", + "OIL_FIELD_BRINE" + ], + "title": "UnconventionalMineralResourceType", + "type": "string" + }, "UniProtSpeciesCode": { "description": "UniProt species mnemonic codes for reference proteomes with associated metadata", "enum": [ @@ -10286,6 +11283,57 @@ "title": "WaterContaminantEnum", "type": "string" }, + "WaterQualityParameterType": { + "description": "Physical, chemical, and biological parameters used to assess water quality for various applications.", + "enum": [ + "PH", + "DISSOLVED_OXYGEN", + "TOTAL_DISSOLVED_SOLIDS", + "TURBIDITY", + "CONDUCTIVITY", + "BIOLOGICAL_OXYGEN_DEMAND", + "CHEMICAL_OXYGEN_DEMAND", + "NITRATE", + "PHOSPHATE", + "HEAVY_METALS", + "COLIFORM_BACTERIA", + "TEMPERATURE" + ], + "title": "WaterQualityParameterType", + "type": "string" + }, + "WaterResourceType": { + "description": "Classification of water resources by source, quality, and origin.", + "enum": [ + "SURFACE_WATER", + "GROUNDWATER", + "PRODUCED_WATER", + "BRACKISH_WATER", + "SEAWATER", + "STORMWATER", + "WASTEWATER", + "RECLAIMED_WATER", + "GLACIAL_MELTWATER" + ], + "title": "WaterResourceType", + "type": "string" + }, + "WaterUseCategoryType": { + "description": "Classification of water use categories relevant to the water-energy nexus and national water resource planning.", + "enum": [ + "AGRICULTURAL_IRRIGATION", + "INDUSTRIAL_COOLING", + "MUNICIPAL_SUPPLY", + "THERMOELECTRIC_POWER", + "HYDROELECTRIC", + "MINING", + "LIVESTOCK", + "AQUACULTURE", + "ENVIRONMENTAL_FLOW" + ], + "title": "WaterUseCategoryType", + "type": "string" + }, "WebColorEnum": { "description": "Standard HTML/CSS named colors (147 colors)", "enum": [ diff --git a/scripts/enrich_enum_docs.py b/scripts/enrich_enum_docs.py index b98d33e6..5a0f308a 100644 --- a/scripts/enrich_enum_docs.py +++ b/scripts/enrich_enum_docs.py @@ -11,6 +11,7 @@ import sys import yaml from pathlib import Path +from urllib.parse import quote from valuesets.utils.query_describer import describe_enum_query, fetch_label_from_ols @@ -186,6 +187,17 @@ def enrich_enum_doc(doc_path: Path, enum_name: str, enum_info: dict, label_cache content = re.sub(pattern, r"\1" + enrichment, content) modified = True + # Add BioPortal link after the URI line + already_has_bioportal = "" in content + if not already_has_bioportal: + uri_pattern = r"(URI: \[valuesets:" + re.escape(enum_name) + r"\]\(https://w3id\.org/valuesets/" + re.escape(enum_name) + r"\)\n)" + if re.search(uri_pattern, content): + concept_uri = f"https://w3id.org/valuesets/{enum_name}" + bp_url = f"https://bioportal.bioontology.org/ontologies/VALUESETS?p=classes&conceptid={quote(concept_uri, safe='')}" + bp_link = f"\n\n[View in BioPortal]({bp_url})\n" + content = re.sub(uri_pattern, r"\1" + bp_link, content) + modified = True + # Enrich static enums with annotation table (if they have annotations) if not already_has_annotations: annotation_table = build_annotation_table(defn, prefix_map) diff --git a/src/valuesets/datamodel/valuesets.py b/src/valuesets/datamodel/valuesets.py index d11d73bc..c40c7404 100644 --- a/src/valuesets/datamodel/valuesets.py +++ b/src/valuesets/datamodel/valuesets.py @@ -12793,6 +12793,504 @@ class ExperimentalPreparation(RichEnum): "ENDOGENOUS_LEVEL": {'description': 'Physiological expression'}, } +class SequencingAssayEnum(RichEnum): + """ + Sequencing-based assays including RNA-seq, DNA-seq, and related methods + """ + # Enum members + RNA_SEQ = "RNA_SEQ" + SINGLE_CELL_RNA_SEQ = "SINGLE_CELL_RNA_SEQ" + SINGLE_NUCLEUS_RNA_SEQ = "SINGLE_NUCLEUS_RNA_SEQ" + SPATIAL_TRANSCRIPTOMICS = "SPATIAL_TRANSCRIPTOMICS" + LNCRNA_SEQ = "LNCRNA_SEQ" + MIRNA_SEQ = "MIRNA_SEQ" + RIBO_SEQ = "RIBO_SEQ" + WHOLE_GENOME_SEQUENCING = "WHOLE_GENOME_SEQUENCING" + WHOLE_EXOME_SEQUENCING = "WHOLE_EXOME_SEQUENCING" + TARGETED_EXOME_SEQUENCING = "TARGETED_EXOME_SEQUENCING" + NEXT_GENERATION_TARGETED_SEQUENCING = "NEXT_GENERATION_TARGETED_SEQUENCING" + SANGER_SEQUENCING = "SANGER_SEQUENCING" + ATAC_SEQ = "ATAC_SEQ" + SINGLE_CELL_ATAC_SEQ = "SINGLE_CELL_ATAC_SEQ" + CHIP_SEQ = "CHIP_SEQ" + CUT_AND_RUN = "CUT_AND_RUN" + BISULFITE_SEQUENCING = "BISULFITE_SEQUENCING" + ERR_BISULFITE_SEQUENCING = "ERR_BISULFITE_SEQUENCING" + OXBS_SEQ = "OXBS_SEQ" + HI_C = "HI_C" + ISO_SEQ = "ISO_SEQ" + NOME_SEQ = "NOME_SEQ" + CAPP_SEQ = "CAPP_SEQ" + SAFER_SEQS = "SAFER_SEQS" + TCR_REPERTOIRE_SEQUENCING = "TCR_REPERTOIRE_SEQUENCING" + SCCGI_SEQ = "SCCGI_SEQ" + JUMPING_LIBRARY = "JUMPING_LIBRARY" + SNP_ARRAY = "SNP_ARRAY" + RNA_ARRAY = "RNA_ARRAY" + MIRNA_ARRAY = "MIRNA_ARRAY" + METHYLATION_ARRAY = "METHYLATION_ARRAY" + +# Set metadata after class creation to avoid it becoming an enum member +SequencingAssayEnum._metadata = { + "RNA_SEQ": {'description': 'RNA sequencing to profile transcriptome', 'meaning': 'OBI:0001271', 'aliases': ['RNA-seq']}, + "SINGLE_CELL_RNA_SEQ": {'description': 'Single-cell RNA sequencing', 'meaning': 'OBI:0002631', 'aliases': ['scRNA-seq']}, + "SINGLE_NUCLEUS_RNA_SEQ": {'description': 'Single-nucleus RNA sequencing', 'aliases': ['snRNA-seq']}, + "SPATIAL_TRANSCRIPTOMICS": {'description': 'Spatially resolved transcriptomics', 'meaning': 'EFO:0008992'}, + "LNCRNA_SEQ": {'description': 'Long non-coding RNA sequencing', 'aliases': ['lncRNA-seq']}, + "MIRNA_SEQ": {'description': 'MicroRNA sequencing', 'meaning': 'OBI:0002112', 'aliases': ['miRNA-seq']}, + "RIBO_SEQ": {'description': 'Ribosome profiling sequencing', 'aliases': ['Ribo-seq']}, + "WHOLE_GENOME_SEQUENCING": {'description': 'Whole genome sequencing', 'meaning': 'OBI:0002117', 'aliases': ['WGS']}, + "WHOLE_EXOME_SEQUENCING": {'description': 'Whole exome sequencing', 'meaning': 'OBI:0002118', 'aliases': ['WES']}, + "TARGETED_EXOME_SEQUENCING": {'description': 'Targeted exome sequencing panel'}, + "NEXT_GENERATION_TARGETED_SEQUENCING": {'description': 'Next generation targeted sequencing panel'}, + "SANGER_SEQUENCING": {'description': 'Sanger chain termination sequencing', 'meaning': 'OBI:0000695'}, + "ATAC_SEQ": {'description': 'Assay for Transposase-Accessible Chromatin sequencing', 'meaning': 'OBI:0002039', 'aliases': ['ATAC-seq']}, + "SINGLE_CELL_ATAC_SEQ": {'description': 'Single-cell ATAC-seq', 'aliases': ['scATAC-seq']}, + "CHIP_SEQ": {'description': 'Chromatin immunoprecipitation sequencing', 'meaning': 'OBI:0000716', 'aliases': ['ChIP-seq']}, + "CUT_AND_RUN": {'description': 'Cleavage Under Targets and Release Using Nuclease', 'aliases': ['CUT&RUN']}, + "BISULFITE_SEQUENCING": {'description': 'Bisulfite sequencing for DNA methylation', 'meaning': 'OBI:0000748', 'aliases': ['BS-seq']}, + "ERR_BISULFITE_SEQUENCING": {'description': 'Enzymatic methyl-seq (EM-seq) or similar error-reduced bisulfite sequencing'}, + "OXBS_SEQ": {'description': 'Oxidative bisulfite sequencing', 'aliases': ['oxBS-seq']}, + "HI_C": {'description': 'High-throughput chromosome conformation capture', 'meaning': 'OBI:0002042', 'aliases': ['Hi-C']}, + "ISO_SEQ": {'description': 'Isoform sequencing (PacBio long-read)', 'aliases': ['Iso-Seq']}, + "NOME_SEQ": {'description': 'Nucleosome Occupancy and Methylome Sequencing', 'aliases': ['NOMe-seq']}, + "CAPP_SEQ": {'description': 'CAncer Personalized Profiling by deep Sequencing', 'aliases': ['CAPP-Seq']}, + "SAFER_SEQS": {'description': 'Safe-Sequencing System'}, + "TCR_REPERTOIRE_SEQUENCING": {'description': 'T cell receptor repertoire sequencing', 'aliases': ['TCR-seq']}, + "SCCGI_SEQ": {'description': 'Single-cell CGI sequencing', 'aliases': ['scCGI-seq']}, + "JUMPING_LIBRARY": {'description': 'Jumping library sequencing for structural variants'}, + "SNP_ARRAY": {'description': 'SNP genotyping array', 'meaning': 'OBI:0001204'}, + "RNA_ARRAY": {'description': 'RNA expression array', 'meaning': 'OBI:0001463'}, + "MIRNA_ARRAY": {'description': 'MicroRNA array'}, + "METHYLATION_ARRAY": {'description': 'DNA methylation array', 'meaning': 'OBI:0001332'}, +} + +class ImagingAssayEnum(RichEnum): + """ + Imaging-based assays including microscopy, MRI, and related methods + """ + # Enum members + BRIGHTFIELD_MICROSCOPY = "BRIGHTFIELD_MICROSCOPY" + CONFOCAL_MICROSCOPY = "CONFOCAL_MICROSCOPY" + THREE_D_CONFOCAL_IMAGING = "THREE_D_CONFOCAL_IMAGING" + FLUORESCENCE_MICROSCOPY = "FLUORESCENCE_MICROSCOPY" + PHASE_CONTRAST_MICROSCOPY = "PHASE_CONTRAST_MICROSCOPY" + ATOMIC_FORCE_MICROSCOPY = "ATOMIC_FORCE_MICROSCOPY" + THREE_D_ELECTRON_MICROSCOPY = "THREE_D_ELECTRON_MICROSCOPY" + IMMUNOFLUORESCENCE = "IMMUNOFLUORESCENCE" + IMMUNOHISTOCHEMISTRY = "IMMUNOHISTOCHEMISTRY" + IMMUNOCYTOCHEMISTRY = "IMMUNOCYTOCHEMISTRY" + HISTOLOGY = "HISTOLOGY" + FISH = "FISH" + CODEX = "CODEX" + LIVE_IMAGING = "LIVE_IMAGING" + AUTORADIOGRAPHY = "AUTORADIOGRAPHY" + CONVENTIONAL_MRI = "CONVENTIONAL_MRI" + FUNCTIONAL_MRI = "FUNCTIONAL_MRI" + DIFFUSION_MRI = "DIFFUSION_MRI" + MPRAGE_MRI = "MPRAGE_MRI" + MAGNETIC_RESONANCE_SPECTROSCOPY = "MAGNETIC_RESONANCE_SPECTROSCOPY" + MAGNETIC_RESONANCE_ANGIOGRAPHY = "MAGNETIC_RESONANCE_ANGIOGRAPHY" + POSITRON_EMISSION_TOMOGRAPHY = "POSITRON_EMISSION_TOMOGRAPHY" + OPTICAL_COHERENCE_TOMOGRAPHY = "OPTICAL_COHERENCE_TOMOGRAPHY" + OPTICAL_TOMOGRAPHY = "OPTICAL_TOMOGRAPHY" + HIGH_FREQUENCY_ULTRASOUND = "HIGH_FREQUENCY_ULTRASOUND" + TRANSCRANIAL_DOPPLER = "TRANSCRANIAL_DOPPLER" + IN_VIVO_BIOLUMINESCENCE = "IN_VIVO_BIOLUMINESCENCE" + LASER_SPECKLE_IMAGING = "LASER_SPECKLE_IMAGING" + SPATIAL_FREQUENCY_DOMAIN_IMAGING = "SPATIAL_FREQUENCY_DOMAIN_IMAGING" + TRACTION_FORCE_MICROSCOPY = "TRACTION_FORCE_MICROSCOPY" + PHOTOGRAPH = "PHOTOGRAPH" + +# Set metadata after class creation to avoid it becoming an enum member +ImagingAssayEnum._metadata = { + "BRIGHTFIELD_MICROSCOPY": {'description': 'Brightfield microscopy imaging', 'meaning': 'CHMO:0000104'}, + "CONFOCAL_MICROSCOPY": {'description': 'Confocal laser scanning microscopy', 'meaning': 'CHMO:0000545'}, + "THREE_D_CONFOCAL_IMAGING": {'description': 'Three-dimensional confocal imaging', 'aliases': ['3D confocal imaging']}, + "FLUORESCENCE_MICROSCOPY": {'description': 'Fluorescence microscopy assay', 'meaning': 'CHMO:0000087'}, + "PHASE_CONTRAST_MICROSCOPY": {'description': 'Phase-contrast microscopy', 'meaning': 'CHMO:0000056'}, + "ATOMIC_FORCE_MICROSCOPY": {'description': 'Atomic force microscopy', 'meaning': 'CHMO:0000113', 'aliases': ['AFM']}, + "THREE_D_ELECTRON_MICROSCOPY": {'description': 'Three-dimensional electron microscopy', 'aliases': ['3D EM']}, + "IMMUNOFLUORESCENCE": {'description': 'Immunofluorescence staining and imaging', 'meaning': 'OBI:0003357'}, + "IMMUNOHISTOCHEMISTRY": {'description': 'Immunohistochemistry staining', 'meaning': 'OBI:0001986', 'aliases': ['IHC']}, + "IMMUNOCYTOCHEMISTRY": {'description': 'Immunocytochemistry staining', 'aliases': ['ICC']}, + "HISTOLOGY": {'description': 'Histological examination', 'meaning': 'OBI:0600020'}, + "FISH": {'description': 'Fluorescence In Situ Hybridization', 'meaning': 'OBI:0003094', 'aliases': ['Fluorescence In Situ Hybridization']}, + "CODEX": {'description': 'CO-Detection by indEXing imaging'}, + "LIVE_IMAGING": {'description': 'Live cell or tissue imaging'}, + "AUTORADIOGRAPHY": {'description': 'Autoradiography imaging', 'meaning': 'CHMO:0000812'}, + "CONVENTIONAL_MRI": {'description': 'Conventional magnetic resonance imaging', 'meaning': 'OBI:0002985'}, + "FUNCTIONAL_MRI": {'description': 'Functional magnetic resonance imaging', 'meaning': 'OBI:0001501', 'aliases': ['fMRI']}, + "DIFFUSION_MRI": {'description': 'Diffusion-weighted MRI', 'aliases': ['DWI']}, + "MPRAGE_MRI": {'description': 'Magnetization-Prepared Rapid Gradient Echo MRI', 'aliases': ['MPRAGE']}, + "MAGNETIC_RESONANCE_SPECTROSCOPY": {'description': 'Magnetic resonance spectroscopy', 'meaning': 'CHMO:0000566', 'aliases': ['MRS']}, + "MAGNETIC_RESONANCE_ANGIOGRAPHY": {'description': 'Magnetic resonance angiography', 'meaning': 'OBI:0002986', 'aliases': ['MRA']}, + "POSITRON_EMISSION_TOMOGRAPHY": {'description': 'Positron emission tomography', 'meaning': 'OBI:0001912', 'aliases': ['PET']}, + "OPTICAL_COHERENCE_TOMOGRAPHY": {'description': 'Optical coherence tomography', 'meaning': 'CHMO:0000896', 'aliases': ['OCT']}, + "OPTICAL_TOMOGRAPHY": {'description': 'Optical tomography'}, + "HIGH_FREQUENCY_ULTRASOUND": {'description': 'High frequency ultrasound imaging'}, + "TRANSCRANIAL_DOPPLER": {'description': 'Transcranial doppler ultrasonography'}, + "IN_VIVO_BIOLUMINESCENCE": {'description': 'In vivo bioluminescence imaging', 'meaning': 'OBI:0001503'}, + "LASER_SPECKLE_IMAGING": {'description': 'Laser speckle contrast imaging'}, + "SPATIAL_FREQUENCY_DOMAIN_IMAGING": {'description': 'Spatial frequency domain imaging'}, + "TRACTION_FORCE_MICROSCOPY": {'description': 'Traction force microscopy'}, + "PHOTOGRAPH": {'description': 'Photographic documentation'}, +} + +class MassSpectrometryAssayEnum(RichEnum): + """ + Mass spectrometry-based assays for proteomics and metabolomics + """ + # Enum members + MASS_SPECTROMETRY = "MASS_SPECTROMETRY" + LC_MS = "LC_MS" + LC_MS_MS = "LC_MS_MS" + HPLC_MS_MS = "HPLC_MS_MS" + UHPLC_MS_MS = "UHPLC_MS_MS" + FIA_MSMS = "FIA_MSMS" + LABEL_FREE_MS = "LABEL_FREE_MS" + TMT_QUANTITATION = "TMT_QUANTITATION" + MUDPIT = "MUDPIT" + MIB_MS = "MIB_MS" + LC_ECD = "LC_ECD" + FTIR_SPECTROSCOPY = "FTIR_SPECTROSCOPY" + RPPA = "RPPA" + PROXIMITY_EXTENSION_ASSAY = "PROXIMITY_EXTENSION_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +MassSpectrometryAssayEnum._metadata = { + "MASS_SPECTROMETRY": {'description': 'General mass spectrometry', 'meaning': 'CHMO:0000470', 'aliases': ['MS']}, + "LC_MS": {'description': 'Liquid chromatography-mass spectrometry', 'meaning': 'CHMO:0000524', 'aliases': ['liquid chromatography/mass spectrometry']}, + "LC_MS_MS": {'description': 'Liquid chromatography-tandem mass spectrometry', 'meaning': 'CHMO:0000701', 'aliases': ['LC-MS/MS', 'liquid chromatography/tandem mass spectrometry']}, + "HPLC_MS_MS": {'description': 'High-performance liquid chromatography/tandem mass spectrometry', 'aliases': ['high-performance liquid chromatography/tandem mass spectrometry']}, + "UHPLC_MS_MS": {'description': 'Ultra high-performance liquid chromatography/tandem mass spectrometry', 'aliases': ['ultra high-performance liquid chromatography/tandem mass spectrometry']}, + "FIA_MSMS": {'description': 'Flow injection analysis tandem mass spectrometry', 'aliases': ['FIA-MSMS']}, + "LABEL_FREE_MS": {'description': 'Label-free mass spectrometry quantification', 'aliases': ['label free mass spectrometry']}, + "TMT_QUANTITATION": {'description': 'Tandem mass tag quantitation', 'aliases': ['TMT quantitation']}, + "MUDPIT": {'description': 'Multidimensional Protein Identification Technology', 'aliases': ['MudPIT']}, + "MIB_MS": {'description': 'Multiplexed Inhibitor Beads mass spectrometry', 'aliases': ['MIB/MS']}, + "LC_ECD": {'description': 'Liquid chromatography-electrochemical detection', 'aliases': ['liquid chromatography-electrochemical detection']}, + "FTIR_SPECTROSCOPY": {'description': 'Fourier-transform infrared spectroscopy', 'meaning': 'CHMO:0000817', 'aliases': ['FTIR spectroscopy']}, + "RPPA": {'description': 'Reverse Phase Protein Array', 'meaning': 'OBI:0001975', 'aliases': ['RPPA']}, + "PROXIMITY_EXTENSION_ASSAY": {'description': 'Proximity extension assay', 'aliases': ['PEA']}, +} + +class CellBasedAssayEnum(RichEnum): + """ + Cell-based assays including viability, proliferation, and functional assays + """ + # Enum members + CELL_VIABILITY_ASSAY = "CELL_VIABILITY_ASSAY" + CELL_PROLIFERATION_ASSAY = "CELL_PROLIFERATION_ASSAY" + CELL_COUNT = "CELL_COUNT" + ALAMAR_BLUE_ABSORBANCE = "ALAMAR_BLUE_ABSORBANCE" + ALAMAR_BLUE_FLUORESCENCE = "ALAMAR_BLUE_FLUORESCENCE" + THREE_D_MICROTISSUE_VIABILITY = "THREE_D_MICROTISSUE_VIABILITY" + BRDU_PROLIFERATION = "BRDU_PROLIFERATION" + EDU_PROLIFERATION = "EDU_PROLIFERATION" + ATPASE_ACTIVITY_ASSAY = "ATPASE_ACTIVITY_ASSAY" + CAMP_GLO_ASSAY = "CAMP_GLO_ASSAY" + FLOW_CYTOMETRY = "FLOW_CYTOMETRY" + ELISA = "ELISA" + SANDWICH_ELISA = "SANDWICH_ELISA" + WESTERN_BLOT = "WESTERN_BLOT" + IMMUNOASSAY = "IMMUNOASSAY" + PCR = "PCR" + QPCR = "QPCR" + NANOSTRING_NCOUNTER = "NANOSTRING_NCOUNTER" + MULTI_ELECTRODE_ARRAY = "MULTI_ELECTRODE_ARRAY" + CURRENT_CLAMP_ASSAY = "CURRENT_CLAMP_ASSAY" + WHOLE_CELL_PATCH_CLAMP = "WHOLE_CELL_PATCH_CLAMP" + LOCAL_FIELD_POTENTIAL = "LOCAL_FIELD_POTENTIAL" + LONG_TERM_POTENTIATION = "LONG_TERM_POTENTIATION" + MIGRATION_ASSAY = "MIGRATION_ASSAY" + IN_VITRO_TUMORIGENESIS = "IN_VITRO_TUMORIGENESIS" + IN_VIVO_TUMOR_GROWTH = "IN_VIVO_TUMOR_GROWTH" + IN_VIVO_PDX_VIABILITY = "IN_VIVO_PDX_VIABILITY" + MATRIGEL_TUMORIGENESIS = "MATRIGEL_TUMORIGENESIS" + HIGH_CONTENT_SCREEN = "HIGH_CONTENT_SCREEN" + CELL_PAINTING = "CELL_PAINTING" + COMPOUND_SCREEN = "COMPOUND_SCREEN" + COMBINATION_SCREEN = "COMBINATION_SCREEN" + SMALL_MOLECULE_LIBRARY_SCREEN = "SMALL_MOLECULE_LIBRARY_SCREEN" + REPORTER_GENE_ASSAY = "REPORTER_GENE_ASSAY" + MASSIVELY_PARALLEL_REPORTER_ASSAY = "MASSIVELY_PARALLEL_REPORTER_ASSAY" + SPLIT_GFP_ASSAY = "SPLIT_GFP_ASSAY" + FOCUS_FORMING_ASSAY = "FOCUS_FORMING_ASSAY" + OXYGEN_CONSUMPTION_ASSAY = "OXYGEN_CONSUMPTION_ASSAY" + ROS_ASSAY = "ROS_ASSAY" + CALCIUM_RETENTION_ASSAY = "CALCIUM_RETENTION_ASSAY" + TRANS_ENDOTHELIAL_RESISTANCE = "TRANS_ENDOTHELIAL_RESISTANCE" + CELL_PERMEABILITY_ASSAY = "CELL_PERMEABILITY_ASSAY" + PHARMACOKINETIC_ADME = "PHARMACOKINETIC_ADME" + ARRAY = "ARRAY" + HPLC = "HPLC" + ELECTROCHEMILUMINESCENCE = "ELECTROCHEMILUMINESCENCE" + STR_PROFILE = "STR_PROFILE" + TIDE = "TIDE" + SURVIVAL_ASSAY = "SURVIVAL_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +CellBasedAssayEnum._metadata = { + "CELL_VIABILITY_ASSAY": {'description': 'Cell viability measurement assay', 'meaning': 'BAO:0003009'}, + "CELL_PROLIFERATION_ASSAY": {'description': 'Cell proliferation measurement', 'meaning': 'BAO:0002100'}, + "CELL_COUNT": {'description': 'Cell counting assay', 'meaning': 'BAO:0002097'}, + "ALAMAR_BLUE_ABSORBANCE": {'description': 'AlamarBlue absorbance assay (2D)', 'aliases': ['2D AlamarBlue absorbance']}, + "ALAMAR_BLUE_FLUORESCENCE": {'description': 'AlamarBlue fluorescence assay (2D)', 'aliases': ['2D AlamarBlue fluorescence']}, + "THREE_D_MICROTISSUE_VIABILITY": {'description': '3D microtissue viability assay', 'aliases': ['3D microtissue viability']}, + "BRDU_PROLIFERATION": {'description': 'BrdU incorporation proliferation assay', 'meaning': 'OBI:0001330', 'aliases': ['BrdU proliferation assay']}, + "EDU_PROLIFERATION": {'description': 'EdU incorporation proliferation assay', 'aliases': ['EdU proliferation assay']}, + "ATPASE_ACTIVITY_ASSAY": {'description': 'ATPase activity measurement'}, + "CAMP_GLO_ASSAY": {'description': 'cAMP-Glo Max Assay', 'aliases': ['cAMP-Glo Max Assay']}, + "FLOW_CYTOMETRY": {'description': 'Flow cytometry analysis', 'meaning': 'OBI:0000916'}, + "ELISA": {'description': 'Enzyme-linked immunosorbent assay', 'meaning': 'OBI:0000661'}, + "SANDWICH_ELISA": {'description': 'Sandwich ELISA'}, + "WESTERN_BLOT": {'description': 'Western blot analysis', 'meaning': 'OBI:0000714'}, + "IMMUNOASSAY": {'description': 'General immunoassay', 'meaning': 'OBI:0000717'}, + "PCR": {'description': 'Polymerase chain reaction', 'meaning': 'OBI:0000415', 'aliases': ['polymerase chain reaction']}, + "QPCR": {'description': 'Quantitative PCR', 'meaning': 'OBI:0000893', 'aliases': ['quantitative PCR']}, + "NANOSTRING_NCOUNTER": {'description': 'NanoString nCounter Analysis System'}, + "MULTI_ELECTRODE_ARRAY": {'description': 'Multi-electrode array recording', 'meaning': 'OBI:0002187'}, + "CURRENT_CLAMP_ASSAY": {'description': 'Current clamp electrophysiology'}, + "WHOLE_CELL_PATCH_CLAMP": {'description': 'Whole-cell patch clamp recording', 'meaning': 'OBI:0002179'}, + "LOCAL_FIELD_POTENTIAL": {'description': 'Local field potential recording'}, + "LONG_TERM_POTENTIATION": {'description': 'Long-term potentiation assay'}, + "MIGRATION_ASSAY": {'description': 'Cell migration assay', 'meaning': 'BAO:0002110'}, + "IN_VITRO_TUMORIGENESIS": {'description': 'In vitro tumorigenesis assay'}, + "IN_VIVO_TUMOR_GROWTH": {'description': 'In vivo tumor growth assay'}, + "IN_VIVO_PDX_VIABILITY": {'description': 'In vivo patient-derived xenograft viability'}, + "MATRIGEL_TUMORIGENESIS": {'description': 'Matrigel-based tumorigenesis assay', 'aliases': ['Matrigel-based tumorigenesis assay']}, + "HIGH_CONTENT_SCREEN": {'description': 'High content screening assay', 'meaning': 'BAO:0000514'}, + "CELL_PAINTING": {'description': 'Cell painting morphological profiling', 'meaning': 'BAO:0020000'}, + "COMPOUND_SCREEN": {'description': 'Compound library screening'}, + "COMBINATION_SCREEN": {'description': 'Drug combination screening'}, + "SMALL_MOLECULE_LIBRARY_SCREEN": {'description': 'Small molecule library screen'}, + "REPORTER_GENE_ASSAY": {'description': 'Reporter gene assay', 'meaning': 'BAO:0000098'}, + "MASSIVELY_PARALLEL_REPORTER_ASSAY": {'description': 'Massively parallel reporter assay', 'aliases': ['MPRA']}, + "SPLIT_GFP_ASSAY": {'description': 'Split-GFP protein interaction assay', 'aliases': ['split-GFP assay']}, + "FOCUS_FORMING_ASSAY": {'description': 'Focus forming assay'}, + "OXYGEN_CONSUMPTION_ASSAY": {'description': 'Oxygen consumption rate measurement', 'meaning': 'BAO:0003028'}, + "ROS_ASSAY": {'description': 'Reactive oxygen species assay', 'aliases': ['reactive oxygen species assay']}, + "CALCIUM_RETENTION_ASSAY": {'description': 'Calcium retention capacity assay'}, + "TRANS_ENDOTHELIAL_RESISTANCE": {'description': 'Trans-endothelial electrical resistance measurement', 'aliases': ['trans-endothelial electrical resistance']}, + "CELL_PERMEABILITY_ASSAY": {'description': 'Cell permeability assay'}, + "PHARMACOKINETIC_ADME": {'description': 'Pharmacokinetic ADME assay', 'aliases': ['pharmocokinetic ADME assay']}, + "ARRAY": {'description': 'General array-based assay'}, + "HPLC": {'description': 'High-performance liquid chromatography', 'meaning': 'CHMO:0001009'}, + "ELECTROCHEMILUMINESCENCE": {'description': 'Electrochemiluminescence detection'}, + "STR_PROFILE": {'description': 'Short tandem repeat profiling'}, + "TIDE": {'description': 'Tracking of Indels by Decomposition'}, + "SURVIVAL_ASSAY": {'description': 'Cell or organism survival assay'}, +} + +class ClinicalBehavioralAssayEnum(RichEnum): + """ + Clinical assessments and behavioral assays used in research + """ + # Enum members + CLINICAL_DATA = "CLINICAL_DATA" + QUESTIONNAIRE = "QUESTIONNAIRE" + INTERVIEW = "INTERVIEW" + FOCUS_GROUP = "FOCUS_GROUP" + SCALE = "SCALE" + NEUROPSYCHOLOGICAL_ASSESSMENT = "NEUROPSYCHOLOGICAL_ASSESSMENT" + COGNITIVE_ASSESSMENT = "COGNITIVE_ASSESSMENT" + NIH_TOOLBOX = "NIH_TOOLBOX" + PROMIS_COGNITIVE_FUNCTION = "PROMIS_COGNITIVE_FUNCTION" + N_BACK_TASK = "N_BACK_TASK" + CORSI_BLOCKS = "CORSI_BLOCKS" + CBCL_1_5_5 = "CBCL_1_5_5" + CBCL_6_18 = "CBCL_6_18" + SRS = "SRS" + SRS_2 = "SRS_2" + BLOOD_CHEMISTRY = "BLOOD_CHEMISTRY" + METABOLIC_SCREENING = "METABOLIC_SCREENING" + GENOTYPING = "GENOTYPING" + BODY_SIZE_MEASUREMENT = "BODY_SIZE_MEASUREMENT" + GAIT_MEASUREMENT = "GAIT_MEASUREMENT" + GRIP_STRENGTH = "GRIP_STRENGTH" + HAND_HELD_DYNAMOMETRY = "HAND_HELD_DYNAMOMETRY" + SIX_MINUTE_WALK_TEST = "SIX_MINUTE_WALK_TEST" + ACTIGRAPHY = "ACTIGRAPHY" + POLYSOMNOGRAPHY = "POLYSOMNOGRAPHY" + QUANTITATIVE_SENSORY_TESTING = "QUANTITATIVE_SENSORY_TESTING" + VON_FREY_TEST = "VON_FREY_TEST" + ALGOMETRX_NOCIOMETER = "ALGOMETRX_NOCIOMETER" + AUDITORY_BRAINSTEM_RESPONSE = "AUDITORY_BRAINSTEM_RESPONSE" + PURE_TONE_AVERAGE = "PURE_TONE_AVERAGE" + WORD_RECOGNITION_SCORE = "WORD_RECOGNITION_SCORE" + DPOE = "DPOE" + PATTERN_ERG = "PATTERN_ERG" + OPTOKINETIC_REFLEX = "OPTOKINETIC_REFLEX" + RICCARDI_ABLON_SCALES = "RICCARDI_ABLON_SCALES" + SKINDEX_16 = "SKINDEX_16" + CNF_SKINDEX = "CNF_SKINDEX" + CDLQI = "CDLQI" + FACEQ_DISTRESS = "FACEQ_DISTRESS" + OPEN_FIELD_TEST = "OPEN_FIELD_TEST" + ELEVATED_PLUS_MAZE = "ELEVATED_PLUS_MAZE" + ROTAROD_TEST = "ROTAROD_TEST" + ACTIVE_AVOIDANCE = "ACTIVE_AVOIDANCE" + CONTEXTUAL_CONDITIONING = "CONTEXTUAL_CONDITIONING" + NOVELTY_RESPONSE = "NOVELTY_RESPONSE" + FEEDING_ASSAY = "FEEDING_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +ClinicalBehavioralAssayEnum._metadata = { + "CLINICAL_DATA": {'description': 'Clinical data collection'}, + "QUESTIONNAIRE": {'description': 'Questionnaire-based assessment', 'meaning': 'OBI:0001504'}, + "INTERVIEW": {'description': 'Clinical or research interview'}, + "FOCUS_GROUP": {'description': 'Focus group discussion'}, + "SCALE": {'description': 'Clinical rating scale'}, + "NEUROPSYCHOLOGICAL_ASSESSMENT": {'description': 'Neuropsychological testing', 'meaning': 'OBI:0002508'}, + "COGNITIVE_ASSESSMENT": {'description': 'Cognitive function assessment'}, + "NIH_TOOLBOX": {'description': 'NIH Toolbox assessment battery'}, + "PROMIS_COGNITIVE_FUNCTION": {'description': 'PROMIS Cognitive Function measures'}, + "N_BACK_TASK": {'description': 'N-back working memory task', 'aliases': ['n-back task']}, + "CORSI_BLOCKS": {'description': 'Corsi block-tapping task'}, + "CBCL_1_5_5": {'description': 'Child Behavior Checklist for Ages 1.5-5', 'aliases': ['Child Behavior Checklist for Ages 1.5-5']}, + "CBCL_6_18": {'description': 'Child Behavior Checklist for Ages 6-18', 'aliases': ['Child Behavior Checklist for Ages 6-18']}, + "SRS": {'description': 'Social Responsiveness Scale', 'aliases': ['Social Responsiveness Scale']}, + "SRS_2": {'description': 'Social Responsiveness Scale Second Edition', 'aliases': ['Social Responsiveness Scale Second Edition']}, + "BLOOD_CHEMISTRY": {'description': 'Blood chemistry measurement', 'aliases': ['blood chemistry measurement']}, + "METABOLIC_SCREENING": {'description': 'Metabolic screening panel'}, + "GENOTYPING": {'description': 'Genotyping assay', 'meaning': 'OBI:0000435'}, + "BODY_SIZE_MEASUREMENT": {'description': 'Body size trait measurement', 'meaning': 'MMO:0000013', 'aliases': ['body size trait measurement']}, + "GAIT_MEASUREMENT": {'description': 'Gait analysis measurement', 'aliases': ['gait measurement']}, + "GRIP_STRENGTH": {'description': 'Grip strength measurement'}, + "HAND_HELD_DYNAMOMETRY": {'description': 'Hand-held dynamometry'}, + "SIX_MINUTE_WALK_TEST": {'description': 'Six-minute walk test', 'aliases': ['six-minute walk test']}, + "ACTIGRAPHY": {'description': 'Actigraphy monitoring'}, + "POLYSOMNOGRAPHY": {'description': 'Polysomnography sleep study'}, + "QUANTITATIVE_SENSORY_TESTING": {'description': 'Quantitative sensory testing'}, + "VON_FREY_TEST": {'description': 'Von Frey filament test', 'aliases': ['Von Frey test']}, + "ALGOMETRX_NOCIOMETER": {'description': 'AlgometRx Nociometer assessment'}, + "AUDITORY_BRAINSTEM_RESPONSE": {'description': 'Auditory brainstem response testing', 'aliases': ['ABR']}, + "PURE_TONE_AVERAGE": {'description': 'Pure tone average audiometry'}, + "WORD_RECOGNITION_SCORE": {'description': 'Word recognition score'}, + "DPOE": {'description': 'Distortion product otoacoustic emissions', 'aliases': ['distortion product otoacoustic emissions']}, + "PATTERN_ERG": {'description': 'Pattern electroretinogram', 'aliases': ['pattern electroretinogram']}, + "OPTOKINETIC_REFLEX": {'description': 'Optokinetic reflex assay', 'aliases': ['optokinetic reflex assay']}, + "RICCARDI_ABLON_SCALES": {'description': 'Riccardi and Ablon clinical severity scales'}, + "SKINDEX_16": {'description': 'Skindex-16 dermatology questionnaire'}, + "CNF_SKINDEX": {'description': 'Cutaneous neurofibroma Skindex', 'aliases': ['cNF-Skindex']}, + "CDLQI": {'description': "Children's Dermatology Life Quality Index Questionnaire", 'aliases': ["Children's Dermatology Life Quality Index Questionnaire"]}, + "FACEQ_DISTRESS": {'description': 'FACE-Q Appearance-related Distress', 'aliases': ['FACE-Q Appearance-related Distress']}, + "OPEN_FIELD_TEST": {'description': 'Open field locomotor test', 'meaning': 'MMO:0000093'}, + "ELEVATED_PLUS_MAZE": {'description': 'Elevated plus maze anxiety test', 'meaning': 'MMO:0000292', 'aliases': ['elevated plus maze test']}, + "ROTAROD_TEST": {'description': 'Rotarod motor coordination test', 'meaning': 'MMO:0000091', 'aliases': ['rotarod performance test']}, + "ACTIVE_AVOIDANCE": {'description': 'Active avoidance learning behavior assay', 'aliases': ['active avoidance learning behavior assay']}, + "CONTEXTUAL_CONDITIONING": {'description': 'Contextual conditioning behavior assay', 'aliases': ['contextual conditioning behavior assay']}, + "NOVELTY_RESPONSE": {'description': 'Novelty response behavior assay', 'aliases': ['novelty response behavior assay']}, + "FEEDING_ASSAY": {'description': 'Feeding behavior assay'}, +} + +class EnzymologyAssayEnum(RichEnum): + """ + Assays for characterizing enzyme function including activity, kinetics, inhibition, and substrate specificity. + """ + # Enum members + ENZYME_ACTIVITY_ASSAY = "ENZYME_ACTIVITY_ASSAY" + MICHAELIS_MENTEN_KINETICS = "MICHAELIS_MENTEN_KINETICS" + INHIBITION_ASSAY = "INHIBITION_ASSAY" + SUBSTRATE_SPECIFICITY = "SUBSTRATE_SPECIFICITY" + FLUOROMETRIC_ENZYME_ASSAY = "FLUOROMETRIC_ENZYME_ASSAY" + COLORIMETRIC_ENZYME_ASSAY = "COLORIMETRIC_ENZYME_ASSAY" + COUPLED_ENZYME_ASSAY = "COUPLED_ENZYME_ASSAY" + CONTINUOUS_ENZYME_ASSAY = "CONTINUOUS_ENZYME_ASSAY" + ENDPOINT_ENZYME_ASSAY = "ENDPOINT_ENZYME_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +EnzymologyAssayEnum._metadata = { + "ENZYME_ACTIVITY_ASSAY": {'description': 'Measures the effect of a perturbagen on enzyme activity', 'meaning': 'BAO:0002994', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "MICHAELIS_MENTEN_KINETICS": {'description': 'Enzyme kinetics assay measuring Km and Vmax parameters', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "INHIBITION_ASSAY": {'description': 'Assay to measure enzyme inhibition (IC50, Ki)', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "SUBSTRATE_SPECIFICITY": {'description': 'Assay to determine enzyme substrate preference and specificity', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "FLUOROMETRIC_ENZYME_ASSAY": {'description': 'Enzyme assay using fluorescent substrates or products for detection', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "COLORIMETRIC_ENZYME_ASSAY": {'description': 'Enzyme assay using chromogenic substrates for absorbance-based detection', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "COUPLED_ENZYME_ASSAY": {'description': 'Enzyme assay using a secondary enzyme reaction for signal generation', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "CONTINUOUS_ENZYME_ASSAY": {'description': 'Real-time monitoring of enzyme reaction progress', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "ENDPOINT_ENZYME_ASSAY": {'description': 'Single time-point measurement of enzyme reaction product', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, +} + +class ImmunologyAssayEnum(RichEnum): + """ + Assays for detecting and quantifying immune-related molecules including antibody-based detection, cell sorting, and blotting methods. + """ + # Enum members + ELISA = "ELISA" + SANDWICH_ELISA = "SANDWICH_ELISA" + IMMUNOPRECIPITATION = "IMMUNOPRECIPITATION" + FLOW_CYTOMETRY = "FLOW_CYTOMETRY" + WESTERN_BLOT = "WESTERN_BLOT" + CYTOKINE_SECRETION_ASSAY = "CYTOKINE_SECRETION_ASSAY" + IMMUNOBLOT = "IMMUNOBLOT" + COMPLEMENT_FIXATION = "COMPLEMENT_FIXATION" + MULTIPLEX_BEAD_ASSAY = "MULTIPLEX_BEAD_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +ImmunologyAssayEnum._metadata = { + "ELISA": {'description': 'Enzyme-linked immunosorbent assay for detecting antigens or antibodies', 'meaning': 'BAO:0000134', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "SANDWICH_ELISA": {'description': 'Sandwich ELISA using capture and detection antibodies', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "IMMUNOPRECIPITATION": {'description': 'Precipitation of a protein antigen from solution using a specific antibody', 'meaning': 'BAO:0002508', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "FLOW_CYTOMETRY": {'description': 'Analysis of cell populations using fluorescent antibodies and light scattering', 'meaning': 'BAO:0000005', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "WESTERN_BLOT": {'description': 'Protein detection by gel electrophoresis, membrane transfer, and antibody staining', 'meaning': 'OBI:0000854', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}, 'aliases': ['western blot assay']}, + "CYTOKINE_SECRETION_ASSAY": {'description': 'Measurement of cytokine types and amounts released from cells', 'meaning': 'BAO:0003003', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "IMMUNOBLOT": {'description': 'Detection of proteins using antibodies on a membrane', 'meaning': 'BAO:0002422', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "COMPLEMENT_FIXATION": {'description': 'Serological assay detecting antibodies by complement consumption', 'annotations': {'companion_enum_antibody_target': 'Protein'}}, + "MULTIPLEX_BEAD_ASSAY": {'description': 'Simultaneous detection of multiple analytes using antibody-conjugated beads', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, +} + +class ProteinEngineeringAssayEnum(RichEnum): + """ + Assays for protein engineering including binding kinetics, biophysical characterization, and display-based selection methods. + """ + # Enum members + SURFACE_PLASMON_RESONANCE = "SURFACE_PLASMON_RESONANCE" + BIOLAYER_INTERFEROMETRY = "BIOLAYER_INTERFEROMETRY" + THERMAL_SHIFT_ASSAY = "THERMAL_SHIFT_ASSAY" + CIRCULAR_DICHROISM = "CIRCULAR_DICHROISM" + PHAGE_DISPLAY = "PHAGE_DISPLAY" + YEAST_DISPLAY = "YEAST_DISPLAY" + DIRECTED_EVOLUTION_SCREEN = "DIRECTED_EVOLUTION_SCREEN" + +# Set metadata after class creation to avoid it becoming an enum member +ProteinEngineeringAssayEnum._metadata = { + "SURFACE_PLASMON_RESONANCE": {'description': 'Real-time label-free measurement of biomolecular binding kinetics', 'meaning': 'BAO:0000054', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['SPR']}, + "BIOLAYER_INTERFEROMETRY": {'description': 'Label-free measurement of biomolecular interactions via interference patterns', 'meaning': 'BAO:0000066', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['BLI', 'bio layer interferometry']}, + "THERMAL_SHIFT_ASSAY": {'description': 'Measurement of protein thermal stability via fluorescent dye binding', 'meaning': 'BAO:0010261', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['differential scanning fluorimetry', 'DSF']}, + "CIRCULAR_DICHROISM": {'description': 'Assessment of protein secondary and tertiary structure using polarized light', 'meaning': 'BAO:0000161', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['CD']}, + "PHAGE_DISPLAY": {'description': 'Selection of peptides or proteins displayed on bacteriophage surface', 'annotations': {'companion_enum_target_protein': 'Protein'}}, + "YEAST_DISPLAY": {'description': 'Selection of proteins displayed on yeast cell surface', 'annotations': {'companion_enum_target_protein': 'Protein'}}, + "DIRECTED_EVOLUTION_SCREEN": {'description': 'High-throughput screening of mutant protein libraries for improved function', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, +} + +class ToxicologyAssayEnum(RichEnum): + """ + Assays for evaluating toxicity, genotoxicity, and safety of compounds including cytotoxicity, mutagenicity, and ADME measurements. + """ + # Enum members + TOXICITY_ASSAY = "TOXICITY_ASSAY" + MTT_ASSAY = "MTT_ASSAY" + LDH_RELEASE_ASSAY = "LDH_RELEASE_ASSAY" + AMES_TEST = "AMES_TEST" + COMET_ASSAY = "COMET_ASSAY" + MICRONUCLEUS_ASSAY = "MICRONUCLEUS_ASSAY" + DOSE_RESPONSE = "DOSE_RESPONSE" + ADME_ASSAY = "ADME_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +ToxicologyAssayEnum._metadata = { + "TOXICITY_ASSAY": {'description': 'General assay measuring degree of substance toxicity to living cells', 'meaning': 'BAO:0002189', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "MTT_ASSAY": {'description': 'Colorimetric assay measuring cell metabolic activity via MTT reduction', 'meaning': 'BAO:0002457', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}, 'aliases': ['MTT reduction assay']}, + "LDH_RELEASE_ASSAY": {'description': 'Cytotoxicity assay measuring lactate dehydrogenase release from damaged cells', 'meaning': 'BAO:0013056', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "AMES_TEST": {'description': 'Mutagenicity assay using bacterial reverse mutation in Salmonella strains', 'meaning': 'BAO:0013054', 'annotations': {'companion_enum_compound': 'ChemicalEntity'}}, + "COMET_ASSAY": {'description': 'Single cell gel electrophoresis assay measuring DNA strand breaks', 'meaning': 'OBI:0302736', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "MICRONUCLEUS_ASSAY": {'description': 'Genotoxicity assay detecting chromosomal damage via micronucleus formation', 'meaning': 'BAO:0013055', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "DOSE_RESPONSE": {'description': 'Measurement of biological response as a function of compound concentration', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "ADME_ASSAY": {'description': 'Absorption, distribution, metabolism, and excretion profiling', 'annotations': {'companion_enum_compound': 'ChemicalEntity'}}, +} + class BioticInteractionType(RichEnum): """ Types of biotic interactions between organisms, based on RO:0002437 (biotically interacts with). These represent ecological relationships where at least one partner is an organism. diff --git a/src/valuesets/datamodel/valuesets_pydantic.py b/src/valuesets/datamodel/valuesets_pydantic.py index d11d73bc..c40c7404 100644 --- a/src/valuesets/datamodel/valuesets_pydantic.py +++ b/src/valuesets/datamodel/valuesets_pydantic.py @@ -12793,6 +12793,504 @@ class ExperimentalPreparation(RichEnum): "ENDOGENOUS_LEVEL": {'description': 'Physiological expression'}, } +class SequencingAssayEnum(RichEnum): + """ + Sequencing-based assays including RNA-seq, DNA-seq, and related methods + """ + # Enum members + RNA_SEQ = "RNA_SEQ" + SINGLE_CELL_RNA_SEQ = "SINGLE_CELL_RNA_SEQ" + SINGLE_NUCLEUS_RNA_SEQ = "SINGLE_NUCLEUS_RNA_SEQ" + SPATIAL_TRANSCRIPTOMICS = "SPATIAL_TRANSCRIPTOMICS" + LNCRNA_SEQ = "LNCRNA_SEQ" + MIRNA_SEQ = "MIRNA_SEQ" + RIBO_SEQ = "RIBO_SEQ" + WHOLE_GENOME_SEQUENCING = "WHOLE_GENOME_SEQUENCING" + WHOLE_EXOME_SEQUENCING = "WHOLE_EXOME_SEQUENCING" + TARGETED_EXOME_SEQUENCING = "TARGETED_EXOME_SEQUENCING" + NEXT_GENERATION_TARGETED_SEQUENCING = "NEXT_GENERATION_TARGETED_SEQUENCING" + SANGER_SEQUENCING = "SANGER_SEQUENCING" + ATAC_SEQ = "ATAC_SEQ" + SINGLE_CELL_ATAC_SEQ = "SINGLE_CELL_ATAC_SEQ" + CHIP_SEQ = "CHIP_SEQ" + CUT_AND_RUN = "CUT_AND_RUN" + BISULFITE_SEQUENCING = "BISULFITE_SEQUENCING" + ERR_BISULFITE_SEQUENCING = "ERR_BISULFITE_SEQUENCING" + OXBS_SEQ = "OXBS_SEQ" + HI_C = "HI_C" + ISO_SEQ = "ISO_SEQ" + NOME_SEQ = "NOME_SEQ" + CAPP_SEQ = "CAPP_SEQ" + SAFER_SEQS = "SAFER_SEQS" + TCR_REPERTOIRE_SEQUENCING = "TCR_REPERTOIRE_SEQUENCING" + SCCGI_SEQ = "SCCGI_SEQ" + JUMPING_LIBRARY = "JUMPING_LIBRARY" + SNP_ARRAY = "SNP_ARRAY" + RNA_ARRAY = "RNA_ARRAY" + MIRNA_ARRAY = "MIRNA_ARRAY" + METHYLATION_ARRAY = "METHYLATION_ARRAY" + +# Set metadata after class creation to avoid it becoming an enum member +SequencingAssayEnum._metadata = { + "RNA_SEQ": {'description': 'RNA sequencing to profile transcriptome', 'meaning': 'OBI:0001271', 'aliases': ['RNA-seq']}, + "SINGLE_CELL_RNA_SEQ": {'description': 'Single-cell RNA sequencing', 'meaning': 'OBI:0002631', 'aliases': ['scRNA-seq']}, + "SINGLE_NUCLEUS_RNA_SEQ": {'description': 'Single-nucleus RNA sequencing', 'aliases': ['snRNA-seq']}, + "SPATIAL_TRANSCRIPTOMICS": {'description': 'Spatially resolved transcriptomics', 'meaning': 'EFO:0008992'}, + "LNCRNA_SEQ": {'description': 'Long non-coding RNA sequencing', 'aliases': ['lncRNA-seq']}, + "MIRNA_SEQ": {'description': 'MicroRNA sequencing', 'meaning': 'OBI:0002112', 'aliases': ['miRNA-seq']}, + "RIBO_SEQ": {'description': 'Ribosome profiling sequencing', 'aliases': ['Ribo-seq']}, + "WHOLE_GENOME_SEQUENCING": {'description': 'Whole genome sequencing', 'meaning': 'OBI:0002117', 'aliases': ['WGS']}, + "WHOLE_EXOME_SEQUENCING": {'description': 'Whole exome sequencing', 'meaning': 'OBI:0002118', 'aliases': ['WES']}, + "TARGETED_EXOME_SEQUENCING": {'description': 'Targeted exome sequencing panel'}, + "NEXT_GENERATION_TARGETED_SEQUENCING": {'description': 'Next generation targeted sequencing panel'}, + "SANGER_SEQUENCING": {'description': 'Sanger chain termination sequencing', 'meaning': 'OBI:0000695'}, + "ATAC_SEQ": {'description': 'Assay for Transposase-Accessible Chromatin sequencing', 'meaning': 'OBI:0002039', 'aliases': ['ATAC-seq']}, + "SINGLE_CELL_ATAC_SEQ": {'description': 'Single-cell ATAC-seq', 'aliases': ['scATAC-seq']}, + "CHIP_SEQ": {'description': 'Chromatin immunoprecipitation sequencing', 'meaning': 'OBI:0000716', 'aliases': ['ChIP-seq']}, + "CUT_AND_RUN": {'description': 'Cleavage Under Targets and Release Using Nuclease', 'aliases': ['CUT&RUN']}, + "BISULFITE_SEQUENCING": {'description': 'Bisulfite sequencing for DNA methylation', 'meaning': 'OBI:0000748', 'aliases': ['BS-seq']}, + "ERR_BISULFITE_SEQUENCING": {'description': 'Enzymatic methyl-seq (EM-seq) or similar error-reduced bisulfite sequencing'}, + "OXBS_SEQ": {'description': 'Oxidative bisulfite sequencing', 'aliases': ['oxBS-seq']}, + "HI_C": {'description': 'High-throughput chromosome conformation capture', 'meaning': 'OBI:0002042', 'aliases': ['Hi-C']}, + "ISO_SEQ": {'description': 'Isoform sequencing (PacBio long-read)', 'aliases': ['Iso-Seq']}, + "NOME_SEQ": {'description': 'Nucleosome Occupancy and Methylome Sequencing', 'aliases': ['NOMe-seq']}, + "CAPP_SEQ": {'description': 'CAncer Personalized Profiling by deep Sequencing', 'aliases': ['CAPP-Seq']}, + "SAFER_SEQS": {'description': 'Safe-Sequencing System'}, + "TCR_REPERTOIRE_SEQUENCING": {'description': 'T cell receptor repertoire sequencing', 'aliases': ['TCR-seq']}, + "SCCGI_SEQ": {'description': 'Single-cell CGI sequencing', 'aliases': ['scCGI-seq']}, + "JUMPING_LIBRARY": {'description': 'Jumping library sequencing for structural variants'}, + "SNP_ARRAY": {'description': 'SNP genotyping array', 'meaning': 'OBI:0001204'}, + "RNA_ARRAY": {'description': 'RNA expression array', 'meaning': 'OBI:0001463'}, + "MIRNA_ARRAY": {'description': 'MicroRNA array'}, + "METHYLATION_ARRAY": {'description': 'DNA methylation array', 'meaning': 'OBI:0001332'}, +} + +class ImagingAssayEnum(RichEnum): + """ + Imaging-based assays including microscopy, MRI, and related methods + """ + # Enum members + BRIGHTFIELD_MICROSCOPY = "BRIGHTFIELD_MICROSCOPY" + CONFOCAL_MICROSCOPY = "CONFOCAL_MICROSCOPY" + THREE_D_CONFOCAL_IMAGING = "THREE_D_CONFOCAL_IMAGING" + FLUORESCENCE_MICROSCOPY = "FLUORESCENCE_MICROSCOPY" + PHASE_CONTRAST_MICROSCOPY = "PHASE_CONTRAST_MICROSCOPY" + ATOMIC_FORCE_MICROSCOPY = "ATOMIC_FORCE_MICROSCOPY" + THREE_D_ELECTRON_MICROSCOPY = "THREE_D_ELECTRON_MICROSCOPY" + IMMUNOFLUORESCENCE = "IMMUNOFLUORESCENCE" + IMMUNOHISTOCHEMISTRY = "IMMUNOHISTOCHEMISTRY" + IMMUNOCYTOCHEMISTRY = "IMMUNOCYTOCHEMISTRY" + HISTOLOGY = "HISTOLOGY" + FISH = "FISH" + CODEX = "CODEX" + LIVE_IMAGING = "LIVE_IMAGING" + AUTORADIOGRAPHY = "AUTORADIOGRAPHY" + CONVENTIONAL_MRI = "CONVENTIONAL_MRI" + FUNCTIONAL_MRI = "FUNCTIONAL_MRI" + DIFFUSION_MRI = "DIFFUSION_MRI" + MPRAGE_MRI = "MPRAGE_MRI" + MAGNETIC_RESONANCE_SPECTROSCOPY = "MAGNETIC_RESONANCE_SPECTROSCOPY" + MAGNETIC_RESONANCE_ANGIOGRAPHY = "MAGNETIC_RESONANCE_ANGIOGRAPHY" + POSITRON_EMISSION_TOMOGRAPHY = "POSITRON_EMISSION_TOMOGRAPHY" + OPTICAL_COHERENCE_TOMOGRAPHY = "OPTICAL_COHERENCE_TOMOGRAPHY" + OPTICAL_TOMOGRAPHY = "OPTICAL_TOMOGRAPHY" + HIGH_FREQUENCY_ULTRASOUND = "HIGH_FREQUENCY_ULTRASOUND" + TRANSCRANIAL_DOPPLER = "TRANSCRANIAL_DOPPLER" + IN_VIVO_BIOLUMINESCENCE = "IN_VIVO_BIOLUMINESCENCE" + LASER_SPECKLE_IMAGING = "LASER_SPECKLE_IMAGING" + SPATIAL_FREQUENCY_DOMAIN_IMAGING = "SPATIAL_FREQUENCY_DOMAIN_IMAGING" + TRACTION_FORCE_MICROSCOPY = "TRACTION_FORCE_MICROSCOPY" + PHOTOGRAPH = "PHOTOGRAPH" + +# Set metadata after class creation to avoid it becoming an enum member +ImagingAssayEnum._metadata = { + "BRIGHTFIELD_MICROSCOPY": {'description': 'Brightfield microscopy imaging', 'meaning': 'CHMO:0000104'}, + "CONFOCAL_MICROSCOPY": {'description': 'Confocal laser scanning microscopy', 'meaning': 'CHMO:0000545'}, + "THREE_D_CONFOCAL_IMAGING": {'description': 'Three-dimensional confocal imaging', 'aliases': ['3D confocal imaging']}, + "FLUORESCENCE_MICROSCOPY": {'description': 'Fluorescence microscopy assay', 'meaning': 'CHMO:0000087'}, + "PHASE_CONTRAST_MICROSCOPY": {'description': 'Phase-contrast microscopy', 'meaning': 'CHMO:0000056'}, + "ATOMIC_FORCE_MICROSCOPY": {'description': 'Atomic force microscopy', 'meaning': 'CHMO:0000113', 'aliases': ['AFM']}, + "THREE_D_ELECTRON_MICROSCOPY": {'description': 'Three-dimensional electron microscopy', 'aliases': ['3D EM']}, + "IMMUNOFLUORESCENCE": {'description': 'Immunofluorescence staining and imaging', 'meaning': 'OBI:0003357'}, + "IMMUNOHISTOCHEMISTRY": {'description': 'Immunohistochemistry staining', 'meaning': 'OBI:0001986', 'aliases': ['IHC']}, + "IMMUNOCYTOCHEMISTRY": {'description': 'Immunocytochemistry staining', 'aliases': ['ICC']}, + "HISTOLOGY": {'description': 'Histological examination', 'meaning': 'OBI:0600020'}, + "FISH": {'description': 'Fluorescence In Situ Hybridization', 'meaning': 'OBI:0003094', 'aliases': ['Fluorescence In Situ Hybridization']}, + "CODEX": {'description': 'CO-Detection by indEXing imaging'}, + "LIVE_IMAGING": {'description': 'Live cell or tissue imaging'}, + "AUTORADIOGRAPHY": {'description': 'Autoradiography imaging', 'meaning': 'CHMO:0000812'}, + "CONVENTIONAL_MRI": {'description': 'Conventional magnetic resonance imaging', 'meaning': 'OBI:0002985'}, + "FUNCTIONAL_MRI": {'description': 'Functional magnetic resonance imaging', 'meaning': 'OBI:0001501', 'aliases': ['fMRI']}, + "DIFFUSION_MRI": {'description': 'Diffusion-weighted MRI', 'aliases': ['DWI']}, + "MPRAGE_MRI": {'description': 'Magnetization-Prepared Rapid Gradient Echo MRI', 'aliases': ['MPRAGE']}, + "MAGNETIC_RESONANCE_SPECTROSCOPY": {'description': 'Magnetic resonance spectroscopy', 'meaning': 'CHMO:0000566', 'aliases': ['MRS']}, + "MAGNETIC_RESONANCE_ANGIOGRAPHY": {'description': 'Magnetic resonance angiography', 'meaning': 'OBI:0002986', 'aliases': ['MRA']}, + "POSITRON_EMISSION_TOMOGRAPHY": {'description': 'Positron emission tomography', 'meaning': 'OBI:0001912', 'aliases': ['PET']}, + "OPTICAL_COHERENCE_TOMOGRAPHY": {'description': 'Optical coherence tomography', 'meaning': 'CHMO:0000896', 'aliases': ['OCT']}, + "OPTICAL_TOMOGRAPHY": {'description': 'Optical tomography'}, + "HIGH_FREQUENCY_ULTRASOUND": {'description': 'High frequency ultrasound imaging'}, + "TRANSCRANIAL_DOPPLER": {'description': 'Transcranial doppler ultrasonography'}, + "IN_VIVO_BIOLUMINESCENCE": {'description': 'In vivo bioluminescence imaging', 'meaning': 'OBI:0001503'}, + "LASER_SPECKLE_IMAGING": {'description': 'Laser speckle contrast imaging'}, + "SPATIAL_FREQUENCY_DOMAIN_IMAGING": {'description': 'Spatial frequency domain imaging'}, + "TRACTION_FORCE_MICROSCOPY": {'description': 'Traction force microscopy'}, + "PHOTOGRAPH": {'description': 'Photographic documentation'}, +} + +class MassSpectrometryAssayEnum(RichEnum): + """ + Mass spectrometry-based assays for proteomics and metabolomics + """ + # Enum members + MASS_SPECTROMETRY = "MASS_SPECTROMETRY" + LC_MS = "LC_MS" + LC_MS_MS = "LC_MS_MS" + HPLC_MS_MS = "HPLC_MS_MS" + UHPLC_MS_MS = "UHPLC_MS_MS" + FIA_MSMS = "FIA_MSMS" + LABEL_FREE_MS = "LABEL_FREE_MS" + TMT_QUANTITATION = "TMT_QUANTITATION" + MUDPIT = "MUDPIT" + MIB_MS = "MIB_MS" + LC_ECD = "LC_ECD" + FTIR_SPECTROSCOPY = "FTIR_SPECTROSCOPY" + RPPA = "RPPA" + PROXIMITY_EXTENSION_ASSAY = "PROXIMITY_EXTENSION_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +MassSpectrometryAssayEnum._metadata = { + "MASS_SPECTROMETRY": {'description': 'General mass spectrometry', 'meaning': 'CHMO:0000470', 'aliases': ['MS']}, + "LC_MS": {'description': 'Liquid chromatography-mass spectrometry', 'meaning': 'CHMO:0000524', 'aliases': ['liquid chromatography/mass spectrometry']}, + "LC_MS_MS": {'description': 'Liquid chromatography-tandem mass spectrometry', 'meaning': 'CHMO:0000701', 'aliases': ['LC-MS/MS', 'liquid chromatography/tandem mass spectrometry']}, + "HPLC_MS_MS": {'description': 'High-performance liquid chromatography/tandem mass spectrometry', 'aliases': ['high-performance liquid chromatography/tandem mass spectrometry']}, + "UHPLC_MS_MS": {'description': 'Ultra high-performance liquid chromatography/tandem mass spectrometry', 'aliases': ['ultra high-performance liquid chromatography/tandem mass spectrometry']}, + "FIA_MSMS": {'description': 'Flow injection analysis tandem mass spectrometry', 'aliases': ['FIA-MSMS']}, + "LABEL_FREE_MS": {'description': 'Label-free mass spectrometry quantification', 'aliases': ['label free mass spectrometry']}, + "TMT_QUANTITATION": {'description': 'Tandem mass tag quantitation', 'aliases': ['TMT quantitation']}, + "MUDPIT": {'description': 'Multidimensional Protein Identification Technology', 'aliases': ['MudPIT']}, + "MIB_MS": {'description': 'Multiplexed Inhibitor Beads mass spectrometry', 'aliases': ['MIB/MS']}, + "LC_ECD": {'description': 'Liquid chromatography-electrochemical detection', 'aliases': ['liquid chromatography-electrochemical detection']}, + "FTIR_SPECTROSCOPY": {'description': 'Fourier-transform infrared spectroscopy', 'meaning': 'CHMO:0000817', 'aliases': ['FTIR spectroscopy']}, + "RPPA": {'description': 'Reverse Phase Protein Array', 'meaning': 'OBI:0001975', 'aliases': ['RPPA']}, + "PROXIMITY_EXTENSION_ASSAY": {'description': 'Proximity extension assay', 'aliases': ['PEA']}, +} + +class CellBasedAssayEnum(RichEnum): + """ + Cell-based assays including viability, proliferation, and functional assays + """ + # Enum members + CELL_VIABILITY_ASSAY = "CELL_VIABILITY_ASSAY" + CELL_PROLIFERATION_ASSAY = "CELL_PROLIFERATION_ASSAY" + CELL_COUNT = "CELL_COUNT" + ALAMAR_BLUE_ABSORBANCE = "ALAMAR_BLUE_ABSORBANCE" + ALAMAR_BLUE_FLUORESCENCE = "ALAMAR_BLUE_FLUORESCENCE" + THREE_D_MICROTISSUE_VIABILITY = "THREE_D_MICROTISSUE_VIABILITY" + BRDU_PROLIFERATION = "BRDU_PROLIFERATION" + EDU_PROLIFERATION = "EDU_PROLIFERATION" + ATPASE_ACTIVITY_ASSAY = "ATPASE_ACTIVITY_ASSAY" + CAMP_GLO_ASSAY = "CAMP_GLO_ASSAY" + FLOW_CYTOMETRY = "FLOW_CYTOMETRY" + ELISA = "ELISA" + SANDWICH_ELISA = "SANDWICH_ELISA" + WESTERN_BLOT = "WESTERN_BLOT" + IMMUNOASSAY = "IMMUNOASSAY" + PCR = "PCR" + QPCR = "QPCR" + NANOSTRING_NCOUNTER = "NANOSTRING_NCOUNTER" + MULTI_ELECTRODE_ARRAY = "MULTI_ELECTRODE_ARRAY" + CURRENT_CLAMP_ASSAY = "CURRENT_CLAMP_ASSAY" + WHOLE_CELL_PATCH_CLAMP = "WHOLE_CELL_PATCH_CLAMP" + LOCAL_FIELD_POTENTIAL = "LOCAL_FIELD_POTENTIAL" + LONG_TERM_POTENTIATION = "LONG_TERM_POTENTIATION" + MIGRATION_ASSAY = "MIGRATION_ASSAY" + IN_VITRO_TUMORIGENESIS = "IN_VITRO_TUMORIGENESIS" + IN_VIVO_TUMOR_GROWTH = "IN_VIVO_TUMOR_GROWTH" + IN_VIVO_PDX_VIABILITY = "IN_VIVO_PDX_VIABILITY" + MATRIGEL_TUMORIGENESIS = "MATRIGEL_TUMORIGENESIS" + HIGH_CONTENT_SCREEN = "HIGH_CONTENT_SCREEN" + CELL_PAINTING = "CELL_PAINTING" + COMPOUND_SCREEN = "COMPOUND_SCREEN" + COMBINATION_SCREEN = "COMBINATION_SCREEN" + SMALL_MOLECULE_LIBRARY_SCREEN = "SMALL_MOLECULE_LIBRARY_SCREEN" + REPORTER_GENE_ASSAY = "REPORTER_GENE_ASSAY" + MASSIVELY_PARALLEL_REPORTER_ASSAY = "MASSIVELY_PARALLEL_REPORTER_ASSAY" + SPLIT_GFP_ASSAY = "SPLIT_GFP_ASSAY" + FOCUS_FORMING_ASSAY = "FOCUS_FORMING_ASSAY" + OXYGEN_CONSUMPTION_ASSAY = "OXYGEN_CONSUMPTION_ASSAY" + ROS_ASSAY = "ROS_ASSAY" + CALCIUM_RETENTION_ASSAY = "CALCIUM_RETENTION_ASSAY" + TRANS_ENDOTHELIAL_RESISTANCE = "TRANS_ENDOTHELIAL_RESISTANCE" + CELL_PERMEABILITY_ASSAY = "CELL_PERMEABILITY_ASSAY" + PHARMACOKINETIC_ADME = "PHARMACOKINETIC_ADME" + ARRAY = "ARRAY" + HPLC = "HPLC" + ELECTROCHEMILUMINESCENCE = "ELECTROCHEMILUMINESCENCE" + STR_PROFILE = "STR_PROFILE" + TIDE = "TIDE" + SURVIVAL_ASSAY = "SURVIVAL_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +CellBasedAssayEnum._metadata = { + "CELL_VIABILITY_ASSAY": {'description': 'Cell viability measurement assay', 'meaning': 'BAO:0003009'}, + "CELL_PROLIFERATION_ASSAY": {'description': 'Cell proliferation measurement', 'meaning': 'BAO:0002100'}, + "CELL_COUNT": {'description': 'Cell counting assay', 'meaning': 'BAO:0002097'}, + "ALAMAR_BLUE_ABSORBANCE": {'description': 'AlamarBlue absorbance assay (2D)', 'aliases': ['2D AlamarBlue absorbance']}, + "ALAMAR_BLUE_FLUORESCENCE": {'description': 'AlamarBlue fluorescence assay (2D)', 'aliases': ['2D AlamarBlue fluorescence']}, + "THREE_D_MICROTISSUE_VIABILITY": {'description': '3D microtissue viability assay', 'aliases': ['3D microtissue viability']}, + "BRDU_PROLIFERATION": {'description': 'BrdU incorporation proliferation assay', 'meaning': 'OBI:0001330', 'aliases': ['BrdU proliferation assay']}, + "EDU_PROLIFERATION": {'description': 'EdU incorporation proliferation assay', 'aliases': ['EdU proliferation assay']}, + "ATPASE_ACTIVITY_ASSAY": {'description': 'ATPase activity measurement'}, + "CAMP_GLO_ASSAY": {'description': 'cAMP-Glo Max Assay', 'aliases': ['cAMP-Glo Max Assay']}, + "FLOW_CYTOMETRY": {'description': 'Flow cytometry analysis', 'meaning': 'OBI:0000916'}, + "ELISA": {'description': 'Enzyme-linked immunosorbent assay', 'meaning': 'OBI:0000661'}, + "SANDWICH_ELISA": {'description': 'Sandwich ELISA'}, + "WESTERN_BLOT": {'description': 'Western blot analysis', 'meaning': 'OBI:0000714'}, + "IMMUNOASSAY": {'description': 'General immunoassay', 'meaning': 'OBI:0000717'}, + "PCR": {'description': 'Polymerase chain reaction', 'meaning': 'OBI:0000415', 'aliases': ['polymerase chain reaction']}, + "QPCR": {'description': 'Quantitative PCR', 'meaning': 'OBI:0000893', 'aliases': ['quantitative PCR']}, + "NANOSTRING_NCOUNTER": {'description': 'NanoString nCounter Analysis System'}, + "MULTI_ELECTRODE_ARRAY": {'description': 'Multi-electrode array recording', 'meaning': 'OBI:0002187'}, + "CURRENT_CLAMP_ASSAY": {'description': 'Current clamp electrophysiology'}, + "WHOLE_CELL_PATCH_CLAMP": {'description': 'Whole-cell patch clamp recording', 'meaning': 'OBI:0002179'}, + "LOCAL_FIELD_POTENTIAL": {'description': 'Local field potential recording'}, + "LONG_TERM_POTENTIATION": {'description': 'Long-term potentiation assay'}, + "MIGRATION_ASSAY": {'description': 'Cell migration assay', 'meaning': 'BAO:0002110'}, + "IN_VITRO_TUMORIGENESIS": {'description': 'In vitro tumorigenesis assay'}, + "IN_VIVO_TUMOR_GROWTH": {'description': 'In vivo tumor growth assay'}, + "IN_VIVO_PDX_VIABILITY": {'description': 'In vivo patient-derived xenograft viability'}, + "MATRIGEL_TUMORIGENESIS": {'description': 'Matrigel-based tumorigenesis assay', 'aliases': ['Matrigel-based tumorigenesis assay']}, + "HIGH_CONTENT_SCREEN": {'description': 'High content screening assay', 'meaning': 'BAO:0000514'}, + "CELL_PAINTING": {'description': 'Cell painting morphological profiling', 'meaning': 'BAO:0020000'}, + "COMPOUND_SCREEN": {'description': 'Compound library screening'}, + "COMBINATION_SCREEN": {'description': 'Drug combination screening'}, + "SMALL_MOLECULE_LIBRARY_SCREEN": {'description': 'Small molecule library screen'}, + "REPORTER_GENE_ASSAY": {'description': 'Reporter gene assay', 'meaning': 'BAO:0000098'}, + "MASSIVELY_PARALLEL_REPORTER_ASSAY": {'description': 'Massively parallel reporter assay', 'aliases': ['MPRA']}, + "SPLIT_GFP_ASSAY": {'description': 'Split-GFP protein interaction assay', 'aliases': ['split-GFP assay']}, + "FOCUS_FORMING_ASSAY": {'description': 'Focus forming assay'}, + "OXYGEN_CONSUMPTION_ASSAY": {'description': 'Oxygen consumption rate measurement', 'meaning': 'BAO:0003028'}, + "ROS_ASSAY": {'description': 'Reactive oxygen species assay', 'aliases': ['reactive oxygen species assay']}, + "CALCIUM_RETENTION_ASSAY": {'description': 'Calcium retention capacity assay'}, + "TRANS_ENDOTHELIAL_RESISTANCE": {'description': 'Trans-endothelial electrical resistance measurement', 'aliases': ['trans-endothelial electrical resistance']}, + "CELL_PERMEABILITY_ASSAY": {'description': 'Cell permeability assay'}, + "PHARMACOKINETIC_ADME": {'description': 'Pharmacokinetic ADME assay', 'aliases': ['pharmocokinetic ADME assay']}, + "ARRAY": {'description': 'General array-based assay'}, + "HPLC": {'description': 'High-performance liquid chromatography', 'meaning': 'CHMO:0001009'}, + "ELECTROCHEMILUMINESCENCE": {'description': 'Electrochemiluminescence detection'}, + "STR_PROFILE": {'description': 'Short tandem repeat profiling'}, + "TIDE": {'description': 'Tracking of Indels by Decomposition'}, + "SURVIVAL_ASSAY": {'description': 'Cell or organism survival assay'}, +} + +class ClinicalBehavioralAssayEnum(RichEnum): + """ + Clinical assessments and behavioral assays used in research + """ + # Enum members + CLINICAL_DATA = "CLINICAL_DATA" + QUESTIONNAIRE = "QUESTIONNAIRE" + INTERVIEW = "INTERVIEW" + FOCUS_GROUP = "FOCUS_GROUP" + SCALE = "SCALE" + NEUROPSYCHOLOGICAL_ASSESSMENT = "NEUROPSYCHOLOGICAL_ASSESSMENT" + COGNITIVE_ASSESSMENT = "COGNITIVE_ASSESSMENT" + NIH_TOOLBOX = "NIH_TOOLBOX" + PROMIS_COGNITIVE_FUNCTION = "PROMIS_COGNITIVE_FUNCTION" + N_BACK_TASK = "N_BACK_TASK" + CORSI_BLOCKS = "CORSI_BLOCKS" + CBCL_1_5_5 = "CBCL_1_5_5" + CBCL_6_18 = "CBCL_6_18" + SRS = "SRS" + SRS_2 = "SRS_2" + BLOOD_CHEMISTRY = "BLOOD_CHEMISTRY" + METABOLIC_SCREENING = "METABOLIC_SCREENING" + GENOTYPING = "GENOTYPING" + BODY_SIZE_MEASUREMENT = "BODY_SIZE_MEASUREMENT" + GAIT_MEASUREMENT = "GAIT_MEASUREMENT" + GRIP_STRENGTH = "GRIP_STRENGTH" + HAND_HELD_DYNAMOMETRY = "HAND_HELD_DYNAMOMETRY" + SIX_MINUTE_WALK_TEST = "SIX_MINUTE_WALK_TEST" + ACTIGRAPHY = "ACTIGRAPHY" + POLYSOMNOGRAPHY = "POLYSOMNOGRAPHY" + QUANTITATIVE_SENSORY_TESTING = "QUANTITATIVE_SENSORY_TESTING" + VON_FREY_TEST = "VON_FREY_TEST" + ALGOMETRX_NOCIOMETER = "ALGOMETRX_NOCIOMETER" + AUDITORY_BRAINSTEM_RESPONSE = "AUDITORY_BRAINSTEM_RESPONSE" + PURE_TONE_AVERAGE = "PURE_TONE_AVERAGE" + WORD_RECOGNITION_SCORE = "WORD_RECOGNITION_SCORE" + DPOE = "DPOE" + PATTERN_ERG = "PATTERN_ERG" + OPTOKINETIC_REFLEX = "OPTOKINETIC_REFLEX" + RICCARDI_ABLON_SCALES = "RICCARDI_ABLON_SCALES" + SKINDEX_16 = "SKINDEX_16" + CNF_SKINDEX = "CNF_SKINDEX" + CDLQI = "CDLQI" + FACEQ_DISTRESS = "FACEQ_DISTRESS" + OPEN_FIELD_TEST = "OPEN_FIELD_TEST" + ELEVATED_PLUS_MAZE = "ELEVATED_PLUS_MAZE" + ROTAROD_TEST = "ROTAROD_TEST" + ACTIVE_AVOIDANCE = "ACTIVE_AVOIDANCE" + CONTEXTUAL_CONDITIONING = "CONTEXTUAL_CONDITIONING" + NOVELTY_RESPONSE = "NOVELTY_RESPONSE" + FEEDING_ASSAY = "FEEDING_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +ClinicalBehavioralAssayEnum._metadata = { + "CLINICAL_DATA": {'description': 'Clinical data collection'}, + "QUESTIONNAIRE": {'description': 'Questionnaire-based assessment', 'meaning': 'OBI:0001504'}, + "INTERVIEW": {'description': 'Clinical or research interview'}, + "FOCUS_GROUP": {'description': 'Focus group discussion'}, + "SCALE": {'description': 'Clinical rating scale'}, + "NEUROPSYCHOLOGICAL_ASSESSMENT": {'description': 'Neuropsychological testing', 'meaning': 'OBI:0002508'}, + "COGNITIVE_ASSESSMENT": {'description': 'Cognitive function assessment'}, + "NIH_TOOLBOX": {'description': 'NIH Toolbox assessment battery'}, + "PROMIS_COGNITIVE_FUNCTION": {'description': 'PROMIS Cognitive Function measures'}, + "N_BACK_TASK": {'description': 'N-back working memory task', 'aliases': ['n-back task']}, + "CORSI_BLOCKS": {'description': 'Corsi block-tapping task'}, + "CBCL_1_5_5": {'description': 'Child Behavior Checklist for Ages 1.5-5', 'aliases': ['Child Behavior Checklist for Ages 1.5-5']}, + "CBCL_6_18": {'description': 'Child Behavior Checklist for Ages 6-18', 'aliases': ['Child Behavior Checklist for Ages 6-18']}, + "SRS": {'description': 'Social Responsiveness Scale', 'aliases': ['Social Responsiveness Scale']}, + "SRS_2": {'description': 'Social Responsiveness Scale Second Edition', 'aliases': ['Social Responsiveness Scale Second Edition']}, + "BLOOD_CHEMISTRY": {'description': 'Blood chemistry measurement', 'aliases': ['blood chemistry measurement']}, + "METABOLIC_SCREENING": {'description': 'Metabolic screening panel'}, + "GENOTYPING": {'description': 'Genotyping assay', 'meaning': 'OBI:0000435'}, + "BODY_SIZE_MEASUREMENT": {'description': 'Body size trait measurement', 'meaning': 'MMO:0000013', 'aliases': ['body size trait measurement']}, + "GAIT_MEASUREMENT": {'description': 'Gait analysis measurement', 'aliases': ['gait measurement']}, + "GRIP_STRENGTH": {'description': 'Grip strength measurement'}, + "HAND_HELD_DYNAMOMETRY": {'description': 'Hand-held dynamometry'}, + "SIX_MINUTE_WALK_TEST": {'description': 'Six-minute walk test', 'aliases': ['six-minute walk test']}, + "ACTIGRAPHY": {'description': 'Actigraphy monitoring'}, + "POLYSOMNOGRAPHY": {'description': 'Polysomnography sleep study'}, + "QUANTITATIVE_SENSORY_TESTING": {'description': 'Quantitative sensory testing'}, + "VON_FREY_TEST": {'description': 'Von Frey filament test', 'aliases': ['Von Frey test']}, + "ALGOMETRX_NOCIOMETER": {'description': 'AlgometRx Nociometer assessment'}, + "AUDITORY_BRAINSTEM_RESPONSE": {'description': 'Auditory brainstem response testing', 'aliases': ['ABR']}, + "PURE_TONE_AVERAGE": {'description': 'Pure tone average audiometry'}, + "WORD_RECOGNITION_SCORE": {'description': 'Word recognition score'}, + "DPOE": {'description': 'Distortion product otoacoustic emissions', 'aliases': ['distortion product otoacoustic emissions']}, + "PATTERN_ERG": {'description': 'Pattern electroretinogram', 'aliases': ['pattern electroretinogram']}, + "OPTOKINETIC_REFLEX": {'description': 'Optokinetic reflex assay', 'aliases': ['optokinetic reflex assay']}, + "RICCARDI_ABLON_SCALES": {'description': 'Riccardi and Ablon clinical severity scales'}, + "SKINDEX_16": {'description': 'Skindex-16 dermatology questionnaire'}, + "CNF_SKINDEX": {'description': 'Cutaneous neurofibroma Skindex', 'aliases': ['cNF-Skindex']}, + "CDLQI": {'description': "Children's Dermatology Life Quality Index Questionnaire", 'aliases': ["Children's Dermatology Life Quality Index Questionnaire"]}, + "FACEQ_DISTRESS": {'description': 'FACE-Q Appearance-related Distress', 'aliases': ['FACE-Q Appearance-related Distress']}, + "OPEN_FIELD_TEST": {'description': 'Open field locomotor test', 'meaning': 'MMO:0000093'}, + "ELEVATED_PLUS_MAZE": {'description': 'Elevated plus maze anxiety test', 'meaning': 'MMO:0000292', 'aliases': ['elevated plus maze test']}, + "ROTAROD_TEST": {'description': 'Rotarod motor coordination test', 'meaning': 'MMO:0000091', 'aliases': ['rotarod performance test']}, + "ACTIVE_AVOIDANCE": {'description': 'Active avoidance learning behavior assay', 'aliases': ['active avoidance learning behavior assay']}, + "CONTEXTUAL_CONDITIONING": {'description': 'Contextual conditioning behavior assay', 'aliases': ['contextual conditioning behavior assay']}, + "NOVELTY_RESPONSE": {'description': 'Novelty response behavior assay', 'aliases': ['novelty response behavior assay']}, + "FEEDING_ASSAY": {'description': 'Feeding behavior assay'}, +} + +class EnzymologyAssayEnum(RichEnum): + """ + Assays for characterizing enzyme function including activity, kinetics, inhibition, and substrate specificity. + """ + # Enum members + ENZYME_ACTIVITY_ASSAY = "ENZYME_ACTIVITY_ASSAY" + MICHAELIS_MENTEN_KINETICS = "MICHAELIS_MENTEN_KINETICS" + INHIBITION_ASSAY = "INHIBITION_ASSAY" + SUBSTRATE_SPECIFICITY = "SUBSTRATE_SPECIFICITY" + FLUOROMETRIC_ENZYME_ASSAY = "FLUOROMETRIC_ENZYME_ASSAY" + COLORIMETRIC_ENZYME_ASSAY = "COLORIMETRIC_ENZYME_ASSAY" + COUPLED_ENZYME_ASSAY = "COUPLED_ENZYME_ASSAY" + CONTINUOUS_ENZYME_ASSAY = "CONTINUOUS_ENZYME_ASSAY" + ENDPOINT_ENZYME_ASSAY = "ENDPOINT_ENZYME_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +EnzymologyAssayEnum._metadata = { + "ENZYME_ACTIVITY_ASSAY": {'description': 'Measures the effect of a perturbagen on enzyme activity', 'meaning': 'BAO:0002994', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "MICHAELIS_MENTEN_KINETICS": {'description': 'Enzyme kinetics assay measuring Km and Vmax parameters', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "INHIBITION_ASSAY": {'description': 'Assay to measure enzyme inhibition (IC50, Ki)', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "SUBSTRATE_SPECIFICITY": {'description': 'Assay to determine enzyme substrate preference and specificity', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "FLUOROMETRIC_ENZYME_ASSAY": {'description': 'Enzyme assay using fluorescent substrates or products for detection', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "COLORIMETRIC_ENZYME_ASSAY": {'description': 'Enzyme assay using chromogenic substrates for absorbance-based detection', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "COUPLED_ENZYME_ASSAY": {'description': 'Enzyme assay using a secondary enzyme reaction for signal generation', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "CONTINUOUS_ENZYME_ASSAY": {'description': 'Real-time monitoring of enzyme reaction progress', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "ENDPOINT_ENZYME_ASSAY": {'description': 'Single time-point measurement of enzyme reaction product', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, +} + +class ImmunologyAssayEnum(RichEnum): + """ + Assays for detecting and quantifying immune-related molecules including antibody-based detection, cell sorting, and blotting methods. + """ + # Enum members + ELISA = "ELISA" + SANDWICH_ELISA = "SANDWICH_ELISA" + IMMUNOPRECIPITATION = "IMMUNOPRECIPITATION" + FLOW_CYTOMETRY = "FLOW_CYTOMETRY" + WESTERN_BLOT = "WESTERN_BLOT" + CYTOKINE_SECRETION_ASSAY = "CYTOKINE_SECRETION_ASSAY" + IMMUNOBLOT = "IMMUNOBLOT" + COMPLEMENT_FIXATION = "COMPLEMENT_FIXATION" + MULTIPLEX_BEAD_ASSAY = "MULTIPLEX_BEAD_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +ImmunologyAssayEnum._metadata = { + "ELISA": {'description': 'Enzyme-linked immunosorbent assay for detecting antigens or antibodies', 'meaning': 'BAO:0000134', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "SANDWICH_ELISA": {'description': 'Sandwich ELISA using capture and detection antibodies', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "IMMUNOPRECIPITATION": {'description': 'Precipitation of a protein antigen from solution using a specific antibody', 'meaning': 'BAO:0002508', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "FLOW_CYTOMETRY": {'description': 'Analysis of cell populations using fluorescent antibodies and light scattering', 'meaning': 'BAO:0000005', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "WESTERN_BLOT": {'description': 'Protein detection by gel electrophoresis, membrane transfer, and antibody staining', 'meaning': 'OBI:0000854', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}, 'aliases': ['western blot assay']}, + "CYTOKINE_SECRETION_ASSAY": {'description': 'Measurement of cytokine types and amounts released from cells', 'meaning': 'BAO:0003003', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "IMMUNOBLOT": {'description': 'Detection of proteins using antibodies on a membrane', 'meaning': 'BAO:0002422', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "COMPLEMENT_FIXATION": {'description': 'Serological assay detecting antibodies by complement consumption', 'annotations': {'companion_enum_antibody_target': 'Protein'}}, + "MULTIPLEX_BEAD_ASSAY": {'description': 'Simultaneous detection of multiple analytes using antibody-conjugated beads', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, +} + +class ProteinEngineeringAssayEnum(RichEnum): + """ + Assays for protein engineering including binding kinetics, biophysical characterization, and display-based selection methods. + """ + # Enum members + SURFACE_PLASMON_RESONANCE = "SURFACE_PLASMON_RESONANCE" + BIOLAYER_INTERFEROMETRY = "BIOLAYER_INTERFEROMETRY" + THERMAL_SHIFT_ASSAY = "THERMAL_SHIFT_ASSAY" + CIRCULAR_DICHROISM = "CIRCULAR_DICHROISM" + PHAGE_DISPLAY = "PHAGE_DISPLAY" + YEAST_DISPLAY = "YEAST_DISPLAY" + DIRECTED_EVOLUTION_SCREEN = "DIRECTED_EVOLUTION_SCREEN" + +# Set metadata after class creation to avoid it becoming an enum member +ProteinEngineeringAssayEnum._metadata = { + "SURFACE_PLASMON_RESONANCE": {'description': 'Real-time label-free measurement of biomolecular binding kinetics', 'meaning': 'BAO:0000054', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['SPR']}, + "BIOLAYER_INTERFEROMETRY": {'description': 'Label-free measurement of biomolecular interactions via interference patterns', 'meaning': 'BAO:0000066', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['BLI', 'bio layer interferometry']}, + "THERMAL_SHIFT_ASSAY": {'description': 'Measurement of protein thermal stability via fluorescent dye binding', 'meaning': 'BAO:0010261', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['differential scanning fluorimetry', 'DSF']}, + "CIRCULAR_DICHROISM": {'description': 'Assessment of protein secondary and tertiary structure using polarized light', 'meaning': 'BAO:0000161', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['CD']}, + "PHAGE_DISPLAY": {'description': 'Selection of peptides or proteins displayed on bacteriophage surface', 'annotations': {'companion_enum_target_protein': 'Protein'}}, + "YEAST_DISPLAY": {'description': 'Selection of proteins displayed on yeast cell surface', 'annotations': {'companion_enum_target_protein': 'Protein'}}, + "DIRECTED_EVOLUTION_SCREEN": {'description': 'High-throughput screening of mutant protein libraries for improved function', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, +} + +class ToxicologyAssayEnum(RichEnum): + """ + Assays for evaluating toxicity, genotoxicity, and safety of compounds including cytotoxicity, mutagenicity, and ADME measurements. + """ + # Enum members + TOXICITY_ASSAY = "TOXICITY_ASSAY" + MTT_ASSAY = "MTT_ASSAY" + LDH_RELEASE_ASSAY = "LDH_RELEASE_ASSAY" + AMES_TEST = "AMES_TEST" + COMET_ASSAY = "COMET_ASSAY" + MICRONUCLEUS_ASSAY = "MICRONUCLEUS_ASSAY" + DOSE_RESPONSE = "DOSE_RESPONSE" + ADME_ASSAY = "ADME_ASSAY" + +# Set metadata after class creation to avoid it becoming an enum member +ToxicologyAssayEnum._metadata = { + "TOXICITY_ASSAY": {'description': 'General assay measuring degree of substance toxicity to living cells', 'meaning': 'BAO:0002189', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "MTT_ASSAY": {'description': 'Colorimetric assay measuring cell metabolic activity via MTT reduction', 'meaning': 'BAO:0002457', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}, 'aliases': ['MTT reduction assay']}, + "LDH_RELEASE_ASSAY": {'description': 'Cytotoxicity assay measuring lactate dehydrogenase release from damaged cells', 'meaning': 'BAO:0013056', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "AMES_TEST": {'description': 'Mutagenicity assay using bacterial reverse mutation in Salmonella strains', 'meaning': 'BAO:0013054', 'annotations': {'companion_enum_compound': 'ChemicalEntity'}}, + "COMET_ASSAY": {'description': 'Single cell gel electrophoresis assay measuring DNA strand breaks', 'meaning': 'OBI:0302736', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "MICRONUCLEUS_ASSAY": {'description': 'Genotoxicity assay detecting chromosomal damage via micronucleus formation', 'meaning': 'BAO:0013055', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "DOSE_RESPONSE": {'description': 'Measurement of biological response as a function of compound concentration', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "ADME_ASSAY": {'description': 'Absorption, distribution, metabolism, and excretion profiling', 'annotations': {'companion_enum_compound': 'ChemicalEntity'}}, +} + class BioticInteractionType(RichEnum): """ Types of biotic interactions between organisms, based on RO:0002437 (biotically interacts with). These represent ecological relationships where at least one partner is an organism. diff --git a/src/valuesets/enums/__init__.py b/src/valuesets/enums/__init__.py index 90606e58..d0c94158 100644 --- a/src/valuesets/enums/__init__.py +++ b/src/valuesets/enums/__init__.py @@ -22,7 +22,11 @@ from .analytical_chemistry.mass_spectrometry import RelativeTimeEnum, PresenceEnum, MassSpectrometerFileFormat, MassSpectrometerVendor, ChromatographyType, DerivatizationMethod, MetabolomicsAssayType, AnalyticalControlType # Bio domain -from .bio.assays import SequencingAssayEnum, ImagingAssayEnum, MassSpectrometryAssayEnum, CellBasedAssayEnum, ClinicalBehavioralAssayEnum +from .bio.assays.enzymology import EnzymologyAssayEnum +from .bio.assays.immunology import ImmunologyAssayEnum +from .bio.assays.nf_osi_assays import SequencingAssayEnum, ImagingAssayEnum, MassSpectrometryAssayEnum, CellBasedAssayEnum, ClinicalBehavioralAssayEnum +from .bio.assays.protein_engineering import ProteinEngineeringAssayEnum +from .bio.assays.toxicology import ToxicologyAssayEnum from .bio.bgc_categories import BgcCategoryEnum from .bio.biological_colors import EyeColorEnum, HairColorEnum, FlowerColorEnum, AnimalCoatColorEnum, SkinToneEnum, PlantLeafColorEnum from .bio.biosafety import BiosafetyLevelEnum @@ -421,6 +425,7 @@ "EnrichmentProcessEnum", "EnvironmentalImpact", "EnzymeClassEnum", + "EnzymologyAssayEnum", "EthnicityOMB1997Enum", "ExecutionModeEnum", "ExperimentalDesignMethodType", @@ -523,6 +528,7 @@ "ImageFileFormatEnum", "ImagingAssayEnum", "ImagingSystemPlatformEnum", + "ImmunologyAssayEnum", "InSituChemistryRegime", "IndustrialDyeEnum", "IndustryMaturityEnum", @@ -702,6 +708,7 @@ "ProductTypeEnum", "ProgrammingLanguageFileEnum", "ProjectMaturityLevel", + "ProteinEngineeringAssayEnum", "ProteinEvidenceForExistence", "ProteinModificationType", "ProtocolStateEnum", @@ -841,6 +848,7 @@ "TimeZoneEnum", "TissuePreservationEnum", "ToxicityClassificationEnum", + "ToxicologyAssayEnum", "TraditionalPigmentEnum", "TrafficLightColorEnum", "TrainingTypeEnum", diff --git a/src/valuesets/enums/bio/assays/__init__.py b/src/valuesets/enums/bio/assays/__init__.py new file mode 100644 index 00000000..633c553c --- /dev/null +++ b/src/valuesets/enums/bio/assays/__init__.py @@ -0,0 +1 @@ +"""Auto-generated package.""" diff --git a/src/valuesets/enums/bio/assays/enzymology.py b/src/valuesets/enums/bio/assays/enzymology.py new file mode 100644 index 00000000..748b8985 --- /dev/null +++ b/src/valuesets/enums/bio/assays/enzymology.py @@ -0,0 +1,43 @@ +""" +Enzymology Assay Value Sets + +Value sets for enzymology assays including enzyme activity, kinetics, inhibition, and substrate specificity measurements. + +Generated from: bio/assays/enzymology.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class EnzymologyAssayEnum(RichEnum): + """ + Assays for characterizing enzyme function including activity, kinetics, inhibition, and substrate specificity. + """ + # Enum members + ENZYME_ACTIVITY_ASSAY = "ENZYME_ACTIVITY_ASSAY" + MICHAELIS_MENTEN_KINETICS = "MICHAELIS_MENTEN_KINETICS" + INHIBITION_ASSAY = "INHIBITION_ASSAY" + SUBSTRATE_SPECIFICITY = "SUBSTRATE_SPECIFICITY" + FLUOROMETRIC_ENZYME_ASSAY = "FLUOROMETRIC_ENZYME_ASSAY" + COLORIMETRIC_ENZYME_ASSAY = "COLORIMETRIC_ENZYME_ASSAY" + COUPLED_ENZYME_ASSAY = "COUPLED_ENZYME_ASSAY" + CONTINUOUS_ENZYME_ASSAY = "CONTINUOUS_ENZYME_ASSAY" + ENDPOINT_ENZYME_ASSAY = "ENDPOINT_ENZYME_ASSAY" + +# Set metadata after class creation +EnzymologyAssayEnum._metadata = { + "ENZYME_ACTIVITY_ASSAY": {'description': 'Measures the effect of a perturbagen on enzyme activity', 'meaning': 'BAO:0002994', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "MICHAELIS_MENTEN_KINETICS": {'description': 'Enzyme kinetics assay measuring Km and Vmax parameters', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "INHIBITION_ASSAY": {'description': 'Assay to measure enzyme inhibition (IC50, Ki)', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "SUBSTRATE_SPECIFICITY": {'description': 'Assay to determine enzyme substrate preference and specificity', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "FLUOROMETRIC_ENZYME_ASSAY": {'description': 'Enzyme assay using fluorescent substrates or products for detection', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "COLORIMETRIC_ENZYME_ASSAY": {'description': 'Enzyme assay using chromogenic substrates for absorbance-based detection', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, + "COUPLED_ENZYME_ASSAY": {'description': 'Enzyme assay using a secondary enzyme reaction for signal generation', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "CONTINUOUS_ENZYME_ASSAY": {'description': 'Real-time monitoring of enzyme reaction progress', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, + "ENDPOINT_ENZYME_ASSAY": {'description': 'Single time-point measurement of enzyme reaction product', 'annotations': {'companion_enum_substrate': 'ChemicalEntity', 'companion_enum_enzyme': 'Protein'}}, +} + +__all__ = [ + "EnzymologyAssayEnum", +] \ No newline at end of file diff --git a/src/valuesets/enums/bio/assays/immunology.py b/src/valuesets/enums/bio/assays/immunology.py new file mode 100644 index 00000000..30678443 --- /dev/null +++ b/src/valuesets/enums/bio/assays/immunology.py @@ -0,0 +1,43 @@ +""" +Immunology Assay Value Sets + +Value sets for immunological assays including ELISA, immunoprecipitation, flow cytometry, western blot, and related methods. + +Generated from: bio/assays/immunology.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class ImmunologyAssayEnum(RichEnum): + """ + Assays for detecting and quantifying immune-related molecules including antibody-based detection, cell sorting, and blotting methods. + """ + # Enum members + ELISA = "ELISA" + SANDWICH_ELISA = "SANDWICH_ELISA" + IMMUNOPRECIPITATION = "IMMUNOPRECIPITATION" + FLOW_CYTOMETRY = "FLOW_CYTOMETRY" + WESTERN_BLOT = "WESTERN_BLOT" + CYTOKINE_SECRETION_ASSAY = "CYTOKINE_SECRETION_ASSAY" + IMMUNOBLOT = "IMMUNOBLOT" + COMPLEMENT_FIXATION = "COMPLEMENT_FIXATION" + MULTIPLEX_BEAD_ASSAY = "MULTIPLEX_BEAD_ASSAY" + +# Set metadata after class creation +ImmunologyAssayEnum._metadata = { + "ELISA": {'description': 'Enzyme-linked immunosorbent assay for detecting antigens or antibodies', 'meaning': 'BAO:0000134', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "SANDWICH_ELISA": {'description': 'Sandwich ELISA using capture and detection antibodies', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "IMMUNOPRECIPITATION": {'description': 'Precipitation of a protein antigen from solution using a specific antibody', 'meaning': 'BAO:0002508', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "FLOW_CYTOMETRY": {'description': 'Analysis of cell populations using fluorescent antibodies and light scattering', 'meaning': 'BAO:0000005', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "WESTERN_BLOT": {'description': 'Protein detection by gel electrophoresis, membrane transfer, and antibody staining', 'meaning': 'OBI:0000854', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}, 'aliases': ['western blot assay']}, + "CYTOKINE_SECRETION_ASSAY": {'description': 'Measurement of cytokine types and amounts released from cells', 'meaning': 'BAO:0003003', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "IMMUNOBLOT": {'description': 'Detection of proteins using antibodies on a membrane', 'meaning': 'BAO:0002422', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, + "COMPLEMENT_FIXATION": {'description': 'Serological assay detecting antibodies by complement consumption', 'annotations': {'companion_enum_antibody_target': 'Protein'}}, + "MULTIPLEX_BEAD_ASSAY": {'description': 'Simultaneous detection of multiple analytes using antibody-conjugated beads', 'annotations': {'companion_enum_antibody_target': 'Protein', 'companion_enum_detection_method': 'DetectionModeEnum'}}, +} + +__all__ = [ + "ImmunologyAssayEnum", +] \ No newline at end of file diff --git a/src/valuesets/enums/bio/assays/nf_osi_assays.py b/src/valuesets/enums/bio/assays/nf_osi_assays.py new file mode 100644 index 00000000..fd945f2c --- /dev/null +++ b/src/valuesets/enums/bio/assays/nf_osi_assays.py @@ -0,0 +1,411 @@ +""" +NF-OSI Biological Assay Value Sets + +Value sets for biological assays including sequencing, imaging, mass spectrometry, cell-based, and clinical/behavioral assays. Derived from NF-OSI metadata dictionary with ontology mappings to OBI, CHMO, BAO, and other relevant ontologies. + +Generated from: bio/assays/nf_osi_assays.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class SequencingAssayEnum(RichEnum): + """ + Sequencing-based assays including RNA-seq, DNA-seq, and related methods + """ + # Enum members + RNA_SEQ = "RNA_SEQ" + SINGLE_CELL_RNA_SEQ = "SINGLE_CELL_RNA_SEQ" + SINGLE_NUCLEUS_RNA_SEQ = "SINGLE_NUCLEUS_RNA_SEQ" + SPATIAL_TRANSCRIPTOMICS = "SPATIAL_TRANSCRIPTOMICS" + LNCRNA_SEQ = "LNCRNA_SEQ" + MIRNA_SEQ = "MIRNA_SEQ" + RIBO_SEQ = "RIBO_SEQ" + WHOLE_GENOME_SEQUENCING = "WHOLE_GENOME_SEQUENCING" + WHOLE_EXOME_SEQUENCING = "WHOLE_EXOME_SEQUENCING" + TARGETED_EXOME_SEQUENCING = "TARGETED_EXOME_SEQUENCING" + NEXT_GENERATION_TARGETED_SEQUENCING = "NEXT_GENERATION_TARGETED_SEQUENCING" + SANGER_SEQUENCING = "SANGER_SEQUENCING" + ATAC_SEQ = "ATAC_SEQ" + SINGLE_CELL_ATAC_SEQ = "SINGLE_CELL_ATAC_SEQ" + CHIP_SEQ = "CHIP_SEQ" + CUT_AND_RUN = "CUT_AND_RUN" + BISULFITE_SEQUENCING = "BISULFITE_SEQUENCING" + ERR_BISULFITE_SEQUENCING = "ERR_BISULFITE_SEQUENCING" + OXBS_SEQ = "OXBS_SEQ" + HI_C = "HI_C" + ISO_SEQ = "ISO_SEQ" + NOME_SEQ = "NOME_SEQ" + CAPP_SEQ = "CAPP_SEQ" + SAFER_SEQS = "SAFER_SEQS" + TCR_REPERTOIRE_SEQUENCING = "TCR_REPERTOIRE_SEQUENCING" + SCCGI_SEQ = "SCCGI_SEQ" + JUMPING_LIBRARY = "JUMPING_LIBRARY" + SNP_ARRAY = "SNP_ARRAY" + RNA_ARRAY = "RNA_ARRAY" + MIRNA_ARRAY = "MIRNA_ARRAY" + METHYLATION_ARRAY = "METHYLATION_ARRAY" + +# Set metadata after class creation +SequencingAssayEnum._metadata = { + "RNA_SEQ": {'description': 'RNA sequencing to profile transcriptome', 'meaning': 'OBI:0001271', 'aliases': ['RNA-seq']}, + "SINGLE_CELL_RNA_SEQ": {'description': 'Single-cell RNA sequencing', 'meaning': 'OBI:0002631', 'aliases': ['scRNA-seq']}, + "SINGLE_NUCLEUS_RNA_SEQ": {'description': 'Single-nucleus RNA sequencing', 'aliases': ['snRNA-seq']}, + "SPATIAL_TRANSCRIPTOMICS": {'description': 'Spatially resolved transcriptomics', 'meaning': 'EFO:0008992'}, + "LNCRNA_SEQ": {'description': 'Long non-coding RNA sequencing', 'aliases': ['lncRNA-seq']}, + "MIRNA_SEQ": {'description': 'MicroRNA sequencing', 'meaning': 'OBI:0002112', 'aliases': ['miRNA-seq']}, + "RIBO_SEQ": {'description': 'Ribosome profiling sequencing', 'aliases': ['Ribo-seq']}, + "WHOLE_GENOME_SEQUENCING": {'description': 'Whole genome sequencing', 'meaning': 'OBI:0002117', 'aliases': ['WGS']}, + "WHOLE_EXOME_SEQUENCING": {'description': 'Whole exome sequencing', 'meaning': 'OBI:0002118', 'aliases': ['WES']}, + "TARGETED_EXOME_SEQUENCING": {'description': 'Targeted exome sequencing panel'}, + "NEXT_GENERATION_TARGETED_SEQUENCING": {'description': 'Next generation targeted sequencing panel'}, + "SANGER_SEQUENCING": {'description': 'Sanger chain termination sequencing', 'meaning': 'OBI:0000695'}, + "ATAC_SEQ": {'description': 'Assay for Transposase-Accessible Chromatin sequencing', 'meaning': 'OBI:0002039', 'aliases': ['ATAC-seq']}, + "SINGLE_CELL_ATAC_SEQ": {'description': 'Single-cell ATAC-seq', 'aliases': ['scATAC-seq']}, + "CHIP_SEQ": {'description': 'Chromatin immunoprecipitation sequencing', 'meaning': 'OBI:0000716', 'aliases': ['ChIP-seq']}, + "CUT_AND_RUN": {'description': 'Cleavage Under Targets and Release Using Nuclease', 'aliases': ['CUT&RUN']}, + "BISULFITE_SEQUENCING": {'description': 'Bisulfite sequencing for DNA methylation', 'meaning': 'OBI:0000748', 'aliases': ['BS-seq']}, + "ERR_BISULFITE_SEQUENCING": {'description': 'Enzymatic methyl-seq (EM-seq) or similar error-reduced bisulfite sequencing'}, + "OXBS_SEQ": {'description': 'Oxidative bisulfite sequencing', 'aliases': ['oxBS-seq']}, + "HI_C": {'description': 'High-throughput chromosome conformation capture', 'meaning': 'OBI:0002042', 'aliases': ['Hi-C']}, + "ISO_SEQ": {'description': 'Isoform sequencing (PacBio long-read)', 'aliases': ['Iso-Seq']}, + "NOME_SEQ": {'description': 'Nucleosome Occupancy and Methylome Sequencing', 'aliases': ['NOMe-seq']}, + "CAPP_SEQ": {'description': 'CAncer Personalized Profiling by deep Sequencing', 'aliases': ['CAPP-Seq']}, + "SAFER_SEQS": {'description': 'Safe-Sequencing System'}, + "TCR_REPERTOIRE_SEQUENCING": {'description': 'T cell receptor repertoire sequencing', 'aliases': ['TCR-seq']}, + "SCCGI_SEQ": {'description': 'Single-cell CGI sequencing', 'aliases': ['scCGI-seq']}, + "JUMPING_LIBRARY": {'description': 'Jumping library sequencing for structural variants'}, + "SNP_ARRAY": {'description': 'SNP genotyping array', 'meaning': 'OBI:0001204'}, + "RNA_ARRAY": {'description': 'RNA expression array', 'meaning': 'OBI:0001463'}, + "MIRNA_ARRAY": {'description': 'MicroRNA array'}, + "METHYLATION_ARRAY": {'description': 'DNA methylation array', 'meaning': 'OBI:0001332'}, +} + +class ImagingAssayEnum(RichEnum): + """ + Imaging-based assays including microscopy, MRI, and related methods + """ + # Enum members + BRIGHTFIELD_MICROSCOPY = "BRIGHTFIELD_MICROSCOPY" + CONFOCAL_MICROSCOPY = "CONFOCAL_MICROSCOPY" + THREE_D_CONFOCAL_IMAGING = "THREE_D_CONFOCAL_IMAGING" + FLUORESCENCE_MICROSCOPY = "FLUORESCENCE_MICROSCOPY" + PHASE_CONTRAST_MICROSCOPY = "PHASE_CONTRAST_MICROSCOPY" + ATOMIC_FORCE_MICROSCOPY = "ATOMIC_FORCE_MICROSCOPY" + THREE_D_ELECTRON_MICROSCOPY = "THREE_D_ELECTRON_MICROSCOPY" + IMMUNOFLUORESCENCE = "IMMUNOFLUORESCENCE" + IMMUNOHISTOCHEMISTRY = "IMMUNOHISTOCHEMISTRY" + IMMUNOCYTOCHEMISTRY = "IMMUNOCYTOCHEMISTRY" + HISTOLOGY = "HISTOLOGY" + FISH = "FISH" + CODEX = "CODEX" + LIVE_IMAGING = "LIVE_IMAGING" + AUTORADIOGRAPHY = "AUTORADIOGRAPHY" + CONVENTIONAL_MRI = "CONVENTIONAL_MRI" + FUNCTIONAL_MRI = "FUNCTIONAL_MRI" + DIFFUSION_MRI = "DIFFUSION_MRI" + MPRAGE_MRI = "MPRAGE_MRI" + MAGNETIC_RESONANCE_SPECTROSCOPY = "MAGNETIC_RESONANCE_SPECTROSCOPY" + MAGNETIC_RESONANCE_ANGIOGRAPHY = "MAGNETIC_RESONANCE_ANGIOGRAPHY" + POSITRON_EMISSION_TOMOGRAPHY = "POSITRON_EMISSION_TOMOGRAPHY" + OPTICAL_COHERENCE_TOMOGRAPHY = "OPTICAL_COHERENCE_TOMOGRAPHY" + OPTICAL_TOMOGRAPHY = "OPTICAL_TOMOGRAPHY" + HIGH_FREQUENCY_ULTRASOUND = "HIGH_FREQUENCY_ULTRASOUND" + TRANSCRANIAL_DOPPLER = "TRANSCRANIAL_DOPPLER" + IN_VIVO_BIOLUMINESCENCE = "IN_VIVO_BIOLUMINESCENCE" + LASER_SPECKLE_IMAGING = "LASER_SPECKLE_IMAGING" + SPATIAL_FREQUENCY_DOMAIN_IMAGING = "SPATIAL_FREQUENCY_DOMAIN_IMAGING" + TRACTION_FORCE_MICROSCOPY = "TRACTION_FORCE_MICROSCOPY" + PHOTOGRAPH = "PHOTOGRAPH" + +# Set metadata after class creation +ImagingAssayEnum._metadata = { + "BRIGHTFIELD_MICROSCOPY": {'description': 'Brightfield microscopy imaging', 'meaning': 'CHMO:0000104'}, + "CONFOCAL_MICROSCOPY": {'description': 'Confocal laser scanning microscopy', 'meaning': 'CHMO:0000545'}, + "THREE_D_CONFOCAL_IMAGING": {'description': 'Three-dimensional confocal imaging', 'aliases': ['3D confocal imaging']}, + "FLUORESCENCE_MICROSCOPY": {'description': 'Fluorescence microscopy assay', 'meaning': 'CHMO:0000087'}, + "PHASE_CONTRAST_MICROSCOPY": {'description': 'Phase-contrast microscopy', 'meaning': 'CHMO:0000056'}, + "ATOMIC_FORCE_MICROSCOPY": {'description': 'Atomic force microscopy', 'meaning': 'CHMO:0000113', 'aliases': ['AFM']}, + "THREE_D_ELECTRON_MICROSCOPY": {'description': 'Three-dimensional electron microscopy', 'aliases': ['3D EM']}, + "IMMUNOFLUORESCENCE": {'description': 'Immunofluorescence staining and imaging', 'meaning': 'OBI:0003357'}, + "IMMUNOHISTOCHEMISTRY": {'description': 'Immunohistochemistry staining', 'meaning': 'OBI:0001986', 'aliases': ['IHC']}, + "IMMUNOCYTOCHEMISTRY": {'description': 'Immunocytochemistry staining', 'aliases': ['ICC']}, + "HISTOLOGY": {'description': 'Histological examination', 'meaning': 'OBI:0600020'}, + "FISH": {'description': 'Fluorescence In Situ Hybridization', 'meaning': 'OBI:0003094', 'aliases': ['Fluorescence In Situ Hybridization']}, + "CODEX": {'description': 'CO-Detection by indEXing imaging'}, + "LIVE_IMAGING": {'description': 'Live cell or tissue imaging'}, + "AUTORADIOGRAPHY": {'description': 'Autoradiography imaging', 'meaning': 'CHMO:0000812'}, + "CONVENTIONAL_MRI": {'description': 'Conventional magnetic resonance imaging', 'meaning': 'OBI:0002985'}, + "FUNCTIONAL_MRI": {'description': 'Functional magnetic resonance imaging', 'meaning': 'OBI:0001501', 'aliases': ['fMRI']}, + "DIFFUSION_MRI": {'description': 'Diffusion-weighted MRI', 'aliases': ['DWI']}, + "MPRAGE_MRI": {'description': 'Magnetization-Prepared Rapid Gradient Echo MRI', 'aliases': ['MPRAGE']}, + "MAGNETIC_RESONANCE_SPECTROSCOPY": {'description': 'Magnetic resonance spectroscopy', 'meaning': 'CHMO:0000566', 'aliases': ['MRS']}, + "MAGNETIC_RESONANCE_ANGIOGRAPHY": {'description': 'Magnetic resonance angiography', 'meaning': 'OBI:0002986', 'aliases': ['MRA']}, + "POSITRON_EMISSION_TOMOGRAPHY": {'description': 'Positron emission tomography', 'meaning': 'OBI:0001912', 'aliases': ['PET']}, + "OPTICAL_COHERENCE_TOMOGRAPHY": {'description': 'Optical coherence tomography', 'meaning': 'CHMO:0000896', 'aliases': ['OCT']}, + "OPTICAL_TOMOGRAPHY": {'description': 'Optical tomography'}, + "HIGH_FREQUENCY_ULTRASOUND": {'description': 'High frequency ultrasound imaging'}, + "TRANSCRANIAL_DOPPLER": {'description': 'Transcranial doppler ultrasonography'}, + "IN_VIVO_BIOLUMINESCENCE": {'description': 'In vivo bioluminescence imaging', 'meaning': 'OBI:0001503'}, + "LASER_SPECKLE_IMAGING": {'description': 'Laser speckle contrast imaging'}, + "SPATIAL_FREQUENCY_DOMAIN_IMAGING": {'description': 'Spatial frequency domain imaging'}, + "TRACTION_FORCE_MICROSCOPY": {'description': 'Traction force microscopy'}, + "PHOTOGRAPH": {'description': 'Photographic documentation'}, +} + +class MassSpectrometryAssayEnum(RichEnum): + """ + Mass spectrometry-based assays for proteomics and metabolomics + """ + # Enum members + MASS_SPECTROMETRY = "MASS_SPECTROMETRY" + LC_MS = "LC_MS" + LC_MS_MS = "LC_MS_MS" + HPLC_MS_MS = "HPLC_MS_MS" + UHPLC_MS_MS = "UHPLC_MS_MS" + FIA_MSMS = "FIA_MSMS" + LABEL_FREE_MS = "LABEL_FREE_MS" + TMT_QUANTITATION = "TMT_QUANTITATION" + MUDPIT = "MUDPIT" + MIB_MS = "MIB_MS" + LC_ECD = "LC_ECD" + FTIR_SPECTROSCOPY = "FTIR_SPECTROSCOPY" + RPPA = "RPPA" + PROXIMITY_EXTENSION_ASSAY = "PROXIMITY_EXTENSION_ASSAY" + +# Set metadata after class creation +MassSpectrometryAssayEnum._metadata = { + "MASS_SPECTROMETRY": {'description': 'General mass spectrometry', 'meaning': 'CHMO:0000470', 'aliases': ['MS']}, + "LC_MS": {'description': 'Liquid chromatography-mass spectrometry', 'meaning': 'CHMO:0000524', 'aliases': ['liquid chromatography/mass spectrometry']}, + "LC_MS_MS": {'description': 'Liquid chromatography-tandem mass spectrometry', 'meaning': 'CHMO:0000701', 'aliases': ['LC-MS/MS', 'liquid chromatography/tandem mass spectrometry']}, + "HPLC_MS_MS": {'description': 'High-performance liquid chromatography/tandem mass spectrometry', 'aliases': ['high-performance liquid chromatography/tandem mass spectrometry']}, + "UHPLC_MS_MS": {'description': 'Ultra high-performance liquid chromatography/tandem mass spectrometry', 'aliases': ['ultra high-performance liquid chromatography/tandem mass spectrometry']}, + "FIA_MSMS": {'description': 'Flow injection analysis tandem mass spectrometry', 'aliases': ['FIA-MSMS']}, + "LABEL_FREE_MS": {'description': 'Label-free mass spectrometry quantification', 'aliases': ['label free mass spectrometry']}, + "TMT_QUANTITATION": {'description': 'Tandem mass tag quantitation', 'aliases': ['TMT quantitation']}, + "MUDPIT": {'description': 'Multidimensional Protein Identification Technology', 'aliases': ['MudPIT']}, + "MIB_MS": {'description': 'Multiplexed Inhibitor Beads mass spectrometry', 'aliases': ['MIB/MS']}, + "LC_ECD": {'description': 'Liquid chromatography-electrochemical detection', 'aliases': ['liquid chromatography-electrochemical detection']}, + "FTIR_SPECTROSCOPY": {'description': 'Fourier-transform infrared spectroscopy', 'meaning': 'CHMO:0000817', 'aliases': ['FTIR spectroscopy']}, + "RPPA": {'description': 'Reverse Phase Protein Array', 'meaning': 'OBI:0001975', 'aliases': ['RPPA']}, + "PROXIMITY_EXTENSION_ASSAY": {'description': 'Proximity extension assay', 'aliases': ['PEA']}, +} + +class CellBasedAssayEnum(RichEnum): + """ + Cell-based assays including viability, proliferation, and functional assays + """ + # Enum members + CELL_VIABILITY_ASSAY = "CELL_VIABILITY_ASSAY" + CELL_PROLIFERATION_ASSAY = "CELL_PROLIFERATION_ASSAY" + CELL_COUNT = "CELL_COUNT" + ALAMAR_BLUE_ABSORBANCE = "ALAMAR_BLUE_ABSORBANCE" + ALAMAR_BLUE_FLUORESCENCE = "ALAMAR_BLUE_FLUORESCENCE" + THREE_D_MICROTISSUE_VIABILITY = "THREE_D_MICROTISSUE_VIABILITY" + BRDU_PROLIFERATION = "BRDU_PROLIFERATION" + EDU_PROLIFERATION = "EDU_PROLIFERATION" + ATPASE_ACTIVITY_ASSAY = "ATPASE_ACTIVITY_ASSAY" + CAMP_GLO_ASSAY = "CAMP_GLO_ASSAY" + FLOW_CYTOMETRY = "FLOW_CYTOMETRY" + ELISA = "ELISA" + SANDWICH_ELISA = "SANDWICH_ELISA" + WESTERN_BLOT = "WESTERN_BLOT" + IMMUNOASSAY = "IMMUNOASSAY" + PCR = "PCR" + QPCR = "QPCR" + NANOSTRING_NCOUNTER = "NANOSTRING_NCOUNTER" + MULTI_ELECTRODE_ARRAY = "MULTI_ELECTRODE_ARRAY" + CURRENT_CLAMP_ASSAY = "CURRENT_CLAMP_ASSAY" + WHOLE_CELL_PATCH_CLAMP = "WHOLE_CELL_PATCH_CLAMP" + LOCAL_FIELD_POTENTIAL = "LOCAL_FIELD_POTENTIAL" + LONG_TERM_POTENTIATION = "LONG_TERM_POTENTIATION" + MIGRATION_ASSAY = "MIGRATION_ASSAY" + IN_VITRO_TUMORIGENESIS = "IN_VITRO_TUMORIGENESIS" + IN_VIVO_TUMOR_GROWTH = "IN_VIVO_TUMOR_GROWTH" + IN_VIVO_PDX_VIABILITY = "IN_VIVO_PDX_VIABILITY" + MATRIGEL_TUMORIGENESIS = "MATRIGEL_TUMORIGENESIS" + HIGH_CONTENT_SCREEN = "HIGH_CONTENT_SCREEN" + CELL_PAINTING = "CELL_PAINTING" + COMPOUND_SCREEN = "COMPOUND_SCREEN" + COMBINATION_SCREEN = "COMBINATION_SCREEN" + SMALL_MOLECULE_LIBRARY_SCREEN = "SMALL_MOLECULE_LIBRARY_SCREEN" + REPORTER_GENE_ASSAY = "REPORTER_GENE_ASSAY" + MASSIVELY_PARALLEL_REPORTER_ASSAY = "MASSIVELY_PARALLEL_REPORTER_ASSAY" + SPLIT_GFP_ASSAY = "SPLIT_GFP_ASSAY" + FOCUS_FORMING_ASSAY = "FOCUS_FORMING_ASSAY" + OXYGEN_CONSUMPTION_ASSAY = "OXYGEN_CONSUMPTION_ASSAY" + ROS_ASSAY = "ROS_ASSAY" + CALCIUM_RETENTION_ASSAY = "CALCIUM_RETENTION_ASSAY" + TRANS_ENDOTHELIAL_RESISTANCE = "TRANS_ENDOTHELIAL_RESISTANCE" + CELL_PERMEABILITY_ASSAY = "CELL_PERMEABILITY_ASSAY" + PHARMACOKINETIC_ADME = "PHARMACOKINETIC_ADME" + ARRAY = "ARRAY" + HPLC = "HPLC" + ELECTROCHEMILUMINESCENCE = "ELECTROCHEMILUMINESCENCE" + STR_PROFILE = "STR_PROFILE" + TIDE = "TIDE" + SURVIVAL_ASSAY = "SURVIVAL_ASSAY" + +# Set metadata after class creation +CellBasedAssayEnum._metadata = { + "CELL_VIABILITY_ASSAY": {'description': 'Cell viability measurement assay', 'meaning': 'BAO:0003009'}, + "CELL_PROLIFERATION_ASSAY": {'description': 'Cell proliferation measurement', 'meaning': 'BAO:0002100'}, + "CELL_COUNT": {'description': 'Cell counting assay', 'meaning': 'BAO:0002097'}, + "ALAMAR_BLUE_ABSORBANCE": {'description': 'AlamarBlue absorbance assay (2D)', 'aliases': ['2D AlamarBlue absorbance']}, + "ALAMAR_BLUE_FLUORESCENCE": {'description': 'AlamarBlue fluorescence assay (2D)', 'aliases': ['2D AlamarBlue fluorescence']}, + "THREE_D_MICROTISSUE_VIABILITY": {'description': '3D microtissue viability assay', 'aliases': ['3D microtissue viability']}, + "BRDU_PROLIFERATION": {'description': 'BrdU incorporation proliferation assay', 'meaning': 'OBI:0001330', 'aliases': ['BrdU proliferation assay']}, + "EDU_PROLIFERATION": {'description': 'EdU incorporation proliferation assay', 'aliases': ['EdU proliferation assay']}, + "ATPASE_ACTIVITY_ASSAY": {'description': 'ATPase activity measurement'}, + "CAMP_GLO_ASSAY": {'description': 'cAMP-Glo Max Assay', 'aliases': ['cAMP-Glo Max Assay']}, + "FLOW_CYTOMETRY": {'description': 'Flow cytometry analysis', 'meaning': 'OBI:0000916'}, + "ELISA": {'description': 'Enzyme-linked immunosorbent assay', 'meaning': 'OBI:0000661'}, + "SANDWICH_ELISA": {'description': 'Sandwich ELISA'}, + "WESTERN_BLOT": {'description': 'Western blot analysis', 'meaning': 'OBI:0000714'}, + "IMMUNOASSAY": {'description': 'General immunoassay', 'meaning': 'OBI:0000717'}, + "PCR": {'description': 'Polymerase chain reaction', 'meaning': 'OBI:0000415', 'aliases': ['polymerase chain reaction']}, + "QPCR": {'description': 'Quantitative PCR', 'meaning': 'OBI:0000893', 'aliases': ['quantitative PCR']}, + "NANOSTRING_NCOUNTER": {'description': 'NanoString nCounter Analysis System'}, + "MULTI_ELECTRODE_ARRAY": {'description': 'Multi-electrode array recording', 'meaning': 'OBI:0002187'}, + "CURRENT_CLAMP_ASSAY": {'description': 'Current clamp electrophysiology'}, + "WHOLE_CELL_PATCH_CLAMP": {'description': 'Whole-cell patch clamp recording', 'meaning': 'OBI:0002179'}, + "LOCAL_FIELD_POTENTIAL": {'description': 'Local field potential recording'}, + "LONG_TERM_POTENTIATION": {'description': 'Long-term potentiation assay'}, + "MIGRATION_ASSAY": {'description': 'Cell migration assay', 'meaning': 'BAO:0002110'}, + "IN_VITRO_TUMORIGENESIS": {'description': 'In vitro tumorigenesis assay'}, + "IN_VIVO_TUMOR_GROWTH": {'description': 'In vivo tumor growth assay'}, + "IN_VIVO_PDX_VIABILITY": {'description': 'In vivo patient-derived xenograft viability'}, + "MATRIGEL_TUMORIGENESIS": {'description': 'Matrigel-based tumorigenesis assay', 'aliases': ['Matrigel-based tumorigenesis assay']}, + "HIGH_CONTENT_SCREEN": {'description': 'High content screening assay', 'meaning': 'BAO:0000514'}, + "CELL_PAINTING": {'description': 'Cell painting morphological profiling', 'meaning': 'BAO:0020000'}, + "COMPOUND_SCREEN": {'description': 'Compound library screening'}, + "COMBINATION_SCREEN": {'description': 'Drug combination screening'}, + "SMALL_MOLECULE_LIBRARY_SCREEN": {'description': 'Small molecule library screen'}, + "REPORTER_GENE_ASSAY": {'description': 'Reporter gene assay', 'meaning': 'BAO:0000098'}, + "MASSIVELY_PARALLEL_REPORTER_ASSAY": {'description': 'Massively parallel reporter assay', 'aliases': ['MPRA']}, + "SPLIT_GFP_ASSAY": {'description': 'Split-GFP protein interaction assay', 'aliases': ['split-GFP assay']}, + "FOCUS_FORMING_ASSAY": {'description': 'Focus forming assay'}, + "OXYGEN_CONSUMPTION_ASSAY": {'description': 'Oxygen consumption rate measurement', 'meaning': 'BAO:0003028'}, + "ROS_ASSAY": {'description': 'Reactive oxygen species assay', 'aliases': ['reactive oxygen species assay']}, + "CALCIUM_RETENTION_ASSAY": {'description': 'Calcium retention capacity assay'}, + "TRANS_ENDOTHELIAL_RESISTANCE": {'description': 'Trans-endothelial electrical resistance measurement', 'aliases': ['trans-endothelial electrical resistance']}, + "CELL_PERMEABILITY_ASSAY": {'description': 'Cell permeability assay'}, + "PHARMACOKINETIC_ADME": {'description': 'Pharmacokinetic ADME assay', 'aliases': ['pharmocokinetic ADME assay']}, + "ARRAY": {'description': 'General array-based assay'}, + "HPLC": {'description': 'High-performance liquid chromatography', 'meaning': 'CHMO:0001009'}, + "ELECTROCHEMILUMINESCENCE": {'description': 'Electrochemiluminescence detection'}, + "STR_PROFILE": {'description': 'Short tandem repeat profiling'}, + "TIDE": {'description': 'Tracking of Indels by Decomposition'}, + "SURVIVAL_ASSAY": {'description': 'Cell or organism survival assay'}, +} + +class ClinicalBehavioralAssayEnum(RichEnum): + """ + Clinical assessments and behavioral assays used in research + """ + # Enum members + CLINICAL_DATA = "CLINICAL_DATA" + QUESTIONNAIRE = "QUESTIONNAIRE" + INTERVIEW = "INTERVIEW" + FOCUS_GROUP = "FOCUS_GROUP" + SCALE = "SCALE" + NEUROPSYCHOLOGICAL_ASSESSMENT = "NEUROPSYCHOLOGICAL_ASSESSMENT" + COGNITIVE_ASSESSMENT = "COGNITIVE_ASSESSMENT" + NIH_TOOLBOX = "NIH_TOOLBOX" + PROMIS_COGNITIVE_FUNCTION = "PROMIS_COGNITIVE_FUNCTION" + N_BACK_TASK = "N_BACK_TASK" + CORSI_BLOCKS = "CORSI_BLOCKS" + CBCL_1_5_5 = "CBCL_1_5_5" + CBCL_6_18 = "CBCL_6_18" + SRS = "SRS" + SRS_2 = "SRS_2" + BLOOD_CHEMISTRY = "BLOOD_CHEMISTRY" + METABOLIC_SCREENING = "METABOLIC_SCREENING" + GENOTYPING = "GENOTYPING" + BODY_SIZE_MEASUREMENT = "BODY_SIZE_MEASUREMENT" + GAIT_MEASUREMENT = "GAIT_MEASUREMENT" + GRIP_STRENGTH = "GRIP_STRENGTH" + HAND_HELD_DYNAMOMETRY = "HAND_HELD_DYNAMOMETRY" + SIX_MINUTE_WALK_TEST = "SIX_MINUTE_WALK_TEST" + ACTIGRAPHY = "ACTIGRAPHY" + POLYSOMNOGRAPHY = "POLYSOMNOGRAPHY" + QUANTITATIVE_SENSORY_TESTING = "QUANTITATIVE_SENSORY_TESTING" + VON_FREY_TEST = "VON_FREY_TEST" + ALGOMETRX_NOCIOMETER = "ALGOMETRX_NOCIOMETER" + AUDITORY_BRAINSTEM_RESPONSE = "AUDITORY_BRAINSTEM_RESPONSE" + PURE_TONE_AVERAGE = "PURE_TONE_AVERAGE" + WORD_RECOGNITION_SCORE = "WORD_RECOGNITION_SCORE" + DPOE = "DPOE" + PATTERN_ERG = "PATTERN_ERG" + OPTOKINETIC_REFLEX = "OPTOKINETIC_REFLEX" + RICCARDI_ABLON_SCALES = "RICCARDI_ABLON_SCALES" + SKINDEX_16 = "SKINDEX_16" + CNF_SKINDEX = "CNF_SKINDEX" + CDLQI = "CDLQI" + FACEQ_DISTRESS = "FACEQ_DISTRESS" + OPEN_FIELD_TEST = "OPEN_FIELD_TEST" + ELEVATED_PLUS_MAZE = "ELEVATED_PLUS_MAZE" + ROTAROD_TEST = "ROTAROD_TEST" + ACTIVE_AVOIDANCE = "ACTIVE_AVOIDANCE" + CONTEXTUAL_CONDITIONING = "CONTEXTUAL_CONDITIONING" + NOVELTY_RESPONSE = "NOVELTY_RESPONSE" + FEEDING_ASSAY = "FEEDING_ASSAY" + +# Set metadata after class creation +ClinicalBehavioralAssayEnum._metadata = { + "CLINICAL_DATA": {'description': 'Clinical data collection'}, + "QUESTIONNAIRE": {'description': 'Questionnaire-based assessment', 'meaning': 'OBI:0001504'}, + "INTERVIEW": {'description': 'Clinical or research interview'}, + "FOCUS_GROUP": {'description': 'Focus group discussion'}, + "SCALE": {'description': 'Clinical rating scale'}, + "NEUROPSYCHOLOGICAL_ASSESSMENT": {'description': 'Neuropsychological testing', 'meaning': 'OBI:0002508'}, + "COGNITIVE_ASSESSMENT": {'description': 'Cognitive function assessment'}, + "NIH_TOOLBOX": {'description': 'NIH Toolbox assessment battery'}, + "PROMIS_COGNITIVE_FUNCTION": {'description': 'PROMIS Cognitive Function measures'}, + "N_BACK_TASK": {'description': 'N-back working memory task', 'aliases': ['n-back task']}, + "CORSI_BLOCKS": {'description': 'Corsi block-tapping task'}, + "CBCL_1_5_5": {'description': 'Child Behavior Checklist for Ages 1.5-5', 'aliases': ['Child Behavior Checklist for Ages 1.5-5']}, + "CBCL_6_18": {'description': 'Child Behavior Checklist for Ages 6-18', 'aliases': ['Child Behavior Checklist for Ages 6-18']}, + "SRS": {'description': 'Social Responsiveness Scale', 'aliases': ['Social Responsiveness Scale']}, + "SRS_2": {'description': 'Social Responsiveness Scale Second Edition', 'aliases': ['Social Responsiveness Scale Second Edition']}, + "BLOOD_CHEMISTRY": {'description': 'Blood chemistry measurement', 'aliases': ['blood chemistry measurement']}, + "METABOLIC_SCREENING": {'description': 'Metabolic screening panel'}, + "GENOTYPING": {'description': 'Genotyping assay', 'meaning': 'OBI:0000435'}, + "BODY_SIZE_MEASUREMENT": {'description': 'Body size trait measurement', 'meaning': 'MMO:0000013', 'aliases': ['body size trait measurement']}, + "GAIT_MEASUREMENT": {'description': 'Gait analysis measurement', 'aliases': ['gait measurement']}, + "GRIP_STRENGTH": {'description': 'Grip strength measurement'}, + "HAND_HELD_DYNAMOMETRY": {'description': 'Hand-held dynamometry'}, + "SIX_MINUTE_WALK_TEST": {'description': 'Six-minute walk test', 'aliases': ['six-minute walk test']}, + "ACTIGRAPHY": {'description': 'Actigraphy monitoring'}, + "POLYSOMNOGRAPHY": {'description': 'Polysomnography sleep study'}, + "QUANTITATIVE_SENSORY_TESTING": {'description': 'Quantitative sensory testing'}, + "VON_FREY_TEST": {'description': 'Von Frey filament test', 'aliases': ['Von Frey test']}, + "ALGOMETRX_NOCIOMETER": {'description': 'AlgometRx Nociometer assessment'}, + "AUDITORY_BRAINSTEM_RESPONSE": {'description': 'Auditory brainstem response testing', 'aliases': ['ABR']}, + "PURE_TONE_AVERAGE": {'description': 'Pure tone average audiometry'}, + "WORD_RECOGNITION_SCORE": {'description': 'Word recognition score'}, + "DPOE": {'description': 'Distortion product otoacoustic emissions', 'aliases': ['distortion product otoacoustic emissions']}, + "PATTERN_ERG": {'description': 'Pattern electroretinogram', 'aliases': ['pattern electroretinogram']}, + "OPTOKINETIC_REFLEX": {'description': 'Optokinetic reflex assay', 'aliases': ['optokinetic reflex assay']}, + "RICCARDI_ABLON_SCALES": {'description': 'Riccardi and Ablon clinical severity scales'}, + "SKINDEX_16": {'description': 'Skindex-16 dermatology questionnaire'}, + "CNF_SKINDEX": {'description': 'Cutaneous neurofibroma Skindex', 'aliases': ['cNF-Skindex']}, + "CDLQI": {'description': "Children's Dermatology Life Quality Index Questionnaire", 'aliases': ["Children's Dermatology Life Quality Index Questionnaire"]}, + "FACEQ_DISTRESS": {'description': 'FACE-Q Appearance-related Distress', 'aliases': ['FACE-Q Appearance-related Distress']}, + "OPEN_FIELD_TEST": {'description': 'Open field locomotor test', 'meaning': 'MMO:0000093'}, + "ELEVATED_PLUS_MAZE": {'description': 'Elevated plus maze anxiety test', 'meaning': 'MMO:0000292', 'aliases': ['elevated plus maze test']}, + "ROTAROD_TEST": {'description': 'Rotarod motor coordination test', 'meaning': 'MMO:0000091', 'aliases': ['rotarod performance test']}, + "ACTIVE_AVOIDANCE": {'description': 'Active avoidance learning behavior assay', 'aliases': ['active avoidance learning behavior assay']}, + "CONTEXTUAL_CONDITIONING": {'description': 'Contextual conditioning behavior assay', 'aliases': ['contextual conditioning behavior assay']}, + "NOVELTY_RESPONSE": {'description': 'Novelty response behavior assay', 'aliases': ['novelty response behavior assay']}, + "FEEDING_ASSAY": {'description': 'Feeding behavior assay'}, +} + +__all__ = [ + "SequencingAssayEnum", + "ImagingAssayEnum", + "MassSpectrometryAssayEnum", + "CellBasedAssayEnum", + "ClinicalBehavioralAssayEnum", +] \ No newline at end of file diff --git a/src/valuesets/enums/bio/assays/protein_engineering.py b/src/valuesets/enums/bio/assays/protein_engineering.py new file mode 100644 index 00000000..7c3f0320 --- /dev/null +++ b/src/valuesets/enums/bio/assays/protein_engineering.py @@ -0,0 +1,39 @@ +""" +Protein Engineering Assay Value Sets + +Value sets for protein engineering and characterization assays including binding kinetics, biophysical characterization, and display technologies. + +Generated from: bio/assays/protein_engineering.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class ProteinEngineeringAssayEnum(RichEnum): + """ + Assays for protein engineering including binding kinetics, biophysical characterization, and display-based selection methods. + """ + # Enum members + SURFACE_PLASMON_RESONANCE = "SURFACE_PLASMON_RESONANCE" + BIOLAYER_INTERFEROMETRY = "BIOLAYER_INTERFEROMETRY" + THERMAL_SHIFT_ASSAY = "THERMAL_SHIFT_ASSAY" + CIRCULAR_DICHROISM = "CIRCULAR_DICHROISM" + PHAGE_DISPLAY = "PHAGE_DISPLAY" + YEAST_DISPLAY = "YEAST_DISPLAY" + DIRECTED_EVOLUTION_SCREEN = "DIRECTED_EVOLUTION_SCREEN" + +# Set metadata after class creation +ProteinEngineeringAssayEnum._metadata = { + "SURFACE_PLASMON_RESONANCE": {'description': 'Real-time label-free measurement of biomolecular binding kinetics', 'meaning': 'BAO:0000054', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['SPR']}, + "BIOLAYER_INTERFEROMETRY": {'description': 'Label-free measurement of biomolecular interactions via interference patterns', 'meaning': 'BAO:0000066', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['BLI', 'bio layer interferometry']}, + "THERMAL_SHIFT_ASSAY": {'description': 'Measurement of protein thermal stability via fluorescent dye binding', 'meaning': 'BAO:0010261', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['differential scanning fluorimetry', 'DSF']}, + "CIRCULAR_DICHROISM": {'description': 'Assessment of protein secondary and tertiary structure using polarized light', 'meaning': 'BAO:0000161', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}, 'aliases': ['CD']}, + "PHAGE_DISPLAY": {'description': 'Selection of peptides or proteins displayed on bacteriophage surface', 'annotations': {'companion_enum_target_protein': 'Protein'}}, + "YEAST_DISPLAY": {'description': 'Selection of proteins displayed on yeast cell surface', 'annotations': {'companion_enum_target_protein': 'Protein'}}, + "DIRECTED_EVOLUTION_SCREEN": {'description': 'High-throughput screening of mutant protein libraries for improved function', 'annotations': {'companion_enum_target_protein': 'Protein', 'companion_enum_readout': 'DetectionModeEnum'}}, +} + +__all__ = [ + "ProteinEngineeringAssayEnum", +] \ No newline at end of file diff --git a/src/valuesets/enums/bio/assays/toxicology.py b/src/valuesets/enums/bio/assays/toxicology.py new file mode 100644 index 00000000..06940664 --- /dev/null +++ b/src/valuesets/enums/bio/assays/toxicology.py @@ -0,0 +1,41 @@ +""" +Toxicology Assay Value Sets + +Value sets for toxicological assays including cytotoxicity, genotoxicity, mutagenicity, and dose-response measurements. + +Generated from: bio/assays/toxicology.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class ToxicologyAssayEnum(RichEnum): + """ + Assays for evaluating toxicity, genotoxicity, and safety of compounds including cytotoxicity, mutagenicity, and ADME measurements. + """ + # Enum members + TOXICITY_ASSAY = "TOXICITY_ASSAY" + MTT_ASSAY = "MTT_ASSAY" + LDH_RELEASE_ASSAY = "LDH_RELEASE_ASSAY" + AMES_TEST = "AMES_TEST" + COMET_ASSAY = "COMET_ASSAY" + MICRONUCLEUS_ASSAY = "MICRONUCLEUS_ASSAY" + DOSE_RESPONSE = "DOSE_RESPONSE" + ADME_ASSAY = "ADME_ASSAY" + +# Set metadata after class creation +ToxicologyAssayEnum._metadata = { + "TOXICITY_ASSAY": {'description': 'General assay measuring degree of substance toxicity to living cells', 'meaning': 'BAO:0002189', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "MTT_ASSAY": {'description': 'Colorimetric assay measuring cell metabolic activity via MTT reduction', 'meaning': 'BAO:0002457', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}, 'aliases': ['MTT reduction assay']}, + "LDH_RELEASE_ASSAY": {'description': 'Cytotoxicity assay measuring lactate dehydrogenase release from damaged cells', 'meaning': 'BAO:0013056', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "AMES_TEST": {'description': 'Mutagenicity assay using bacterial reverse mutation in Salmonella strains', 'meaning': 'BAO:0013054', 'annotations': {'companion_enum_compound': 'ChemicalEntity'}}, + "COMET_ASSAY": {'description': 'Single cell gel electrophoresis assay measuring DNA strand breaks', 'meaning': 'OBI:0302736', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "MICRONUCLEUS_ASSAY": {'description': 'Genotoxicity assay detecting chromosomal damage via micronucleus formation', 'meaning': 'BAO:0013055', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "DOSE_RESPONSE": {'description': 'Measurement of biological response as a function of compound concentration', 'annotations': {'companion_enum_compound': 'ChemicalEntity', 'companion_enum_cell_line': 'CellType'}}, + "ADME_ASSAY": {'description': 'Absorption, distribution, metabolism, and excretion profiling', 'annotations': {'companion_enum_compound': 'ChemicalEntity'}}, +} + +__all__ = [ + "ToxicologyAssayEnum", +] \ No newline at end of file diff --git a/src/valuesets/merged/merged_hierarchy.yaml b/src/valuesets/merged/merged_hierarchy.yaml index 145a9379..96d6c368 100644 --- a/src/valuesets/merged/merged_hierarchy.yaml +++ b/src/valuesets/merged/merged_hierarchy.yaml @@ -6,6 +6,11 @@ license: MIT prefixes: linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ + ROR: https://ror.org/ + GRID: https://www.grid.ac/institutes/ + ISNI: https://isni.org/isni/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ DCMITYPE: http://purl.org/dc/dcmitype/ FABIO: http://purl.org/spar/fabio/ SPDX: https://spdx.org/licenses/ @@ -18,10 +23,15 @@ prefixes: MS: http://purl.obolibrary.org/obo/MS_ MSIO: http://purl.obolibrary.org/obo/MSIO_ CHMO: http://purl.obolibrary.org/obo/CHMO_ + OBI: http://purl.obolibrary.org/obo/OBI_ + BAO: http://www.bioassayontology.org/bao#BAO_ + EFO: http://www.ebi.ac.uk/efo/EFO_ + ERO: http://purl.obolibrary.org/obo/ERO_ + MMO: http://purl.obolibrary.org/obo/MMO_ + CHEBI: http://purl.obolibrary.org/obo/CHEBI_ UBERON: http://purl.obolibrary.org/obo/UBERON_ CL: http://purl.obolibrary.org/obo/CL_ MONDO: http://purl.obolibrary.org/obo/MONDO_ - CHEBI: http://purl.obolibrary.org/obo/CHEBI_ HP: http://purl.obolibrary.org/obo/HP_ GO: http://purl.obolibrary.org/obo/GO_ DOID: http://purl.obolibrary.org/obo/DOID_ @@ -35,35 +45,41 @@ prefixes: HEX: https://www.color-hex.com/color/ TO: http://purl.obolibrary.org/obo/TO_ VT: http://purl.obolibrary.org/obo/VT_ - CVS: https://w3id.org/common-value-sets/ + SNOMED: http://snomed.info/id/ + METPO: https://w3id.org/metpo/ HsapDv: http://purl.obolibrary.org/obo/HsapDv_ MmusDv: http://purl.obolibrary.org/obo/MmusDv_ - mixs: https://genomicsstandardsconsortium.github.io/mixs/ + MESH: http://id.nlm.nih.gov/mesh/ + STATO: http://purl.obolibrary.org/obo/STATO_ + UO: http://purl.obolibrary.org/obo/UO_ + EDAM: http://edamontology.org/ + MI: http://purl.obolibrary.org/obo/MI_ + mixs: http://purl.obolibrary.org/obo/MIXS_ ECO: http://purl.obolibrary.org/obo/ECO_ GO_REF: http://purl.obolibrary.org/obo/GO_REF_ insdc: https://www.insdc.org/controlled-vocabulary/geographic-location/ iso3166loc: http://id.loc.gov/vocabulary/countries/ geonames: http://sws.geonames.org/ - OBI: http://purl.obolibrary.org/obo/OBI_ SLM: https://swisslipids.org/rdf/SLM_ GSSO: http://purl.obolibrary.org/obo/GSSO_ ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_ + PECO: http://purl.obolibrary.org/obo/PECO_ PRIDE: http://purl.obolibrary.org/obo/PRIDE_ - UO: http://purl.obolibrary.org/obo/UO_ - cvs: https://w3id.org/common-value-sets/ - MI: http://purl.obolibrary.org/obo/MI_ OMP: http://purl.obolibrary.org/obo/OMP_ MICRO: http://purl.obolibrary.org/obo/MICRO_ - EDAM: http://edamontology.org/ GENO: http://purl.obolibrary.org/obo/GENO_ IUPAC: http://purl.obolibrary.org/obo/IUPAC_ + MOP: http://purl.obolibrary.org/obo/MOP_ + MOD: http://purl.obolibrary.org/obo/MOD_ + FBbi: http://purl.obolibrary.org/obo/FBbi_ TAXRANK: http://purl.obolibrary.org/obo/TAXRANK_ BTO: http://purl.obolibrary.org/obo/BTO_ uniprot.proteome: http://purl.uniprot.org/proteomes/ - BAO: http://www.bioassayontology.org/bao#BAO_ + AGRO: http://purl.obolibrary.org/obo/AGRO_ + FOODON: http://purl.obolibrary.org/obo/FOODON_ + PROCO: http://purl.obolibrary.org/obo/PROCO_ SBO: http://biomodels.net/SBO/SBO_ mesh: http://id.nlm.nih.gov/mesh/ - FOODON: http://purl.obolibrary.org/obo/FOODON_ SHRM: https://www.shrm.org/ BLS: https://www.bls.gov/ FLSA: https://www.dol.gov/agencies/whd/flsa/ @@ -83,63 +99,85 @@ prefixes: CSCMP: https://cscmp.org/ ISM: https://www.ismworld.org/ RXNO: http://purl.obolibrary.org/obo/RXNO_ - MOP: http://purl.obolibrary.org/obo/MOP_ goldbook: https://goldbook.iupac.org/terms/view/ gc: http://purl.org/gc/ damlpt: http://www.daml.org/2003/01/periodictable/PeriodicTable# pdg: https://pdgapi.lbl.gov/summaries/ REX: http://purl.obolibrary.org/obo/REX_ EC: https://enzyme.expasy.org/EC/ + rdfs: http://www.w3.org/2000/01/rdf-schema# OMRSE: http://purl.obolibrary.org/obo/OMRSE_ + ExO: http://purl.obolibrary.org/obo/ExO_ LOINC: https://loinc.org/ UCUM: http://unitsofmeasure.org/ + schema: http://schema.org/ + xsd: http://www.w3.org/2001/XMLSchema# + spdx: https://spdx.org/licenses/ + brick: https://brickschema.org/schema/Brick# SWO: http://purl.obolibrary.org/obo/SWO_ iana: https://www.iana.org/assignments/media-types/ + owl: http://www.w3.org/2002/07/owl# fhir: http://hl7.org/fhir/ fhir_data_absent_reason: http://terminology.hl7.org/CodeSystem/data-absent-reason - STATO: http://purl.obolibrary.org/obo/STATO_ + DUO: http://purl.obolibrary.org/obo/DUO_ + dcat: http://www.w3.org/ns/dcat# + adms: http://www.w3.org/ns/adms# + euvoc: http://publications.europa.eu/resource/authority/ + DataCite: https://datacite.org/schema/kernel-4/ + marcrel: http://id.loc.gov/vocabulary/relators/ + cito: http://purl.org/spar/cito/ + prov: http://www.w3.org/ns/prov# MFOEM: http://purl.obolibrary.org/obo/MFOEM_ QUDT: http://qudt.org/vocab/unit/ + OEO: http://openenergy-platform.org/ontology/oeo/OEO_ + sweet: http://sweetontology.net/ + wikidata: http://www.wikidata.org/entity/ + IAEA: https://www.iaea.org/ + WNA: https://world-nuclear.org/ + NRC: https://www.nrc.gov/ + INES: https://www.iaea.org/resources/databases/ines + IEEE: https://standards.ieee.org/ + CFR: https://www.ecfr.gov/ + ECTO: http://purl.obolibrary.org/obo/ECTO_ biolink: https://w3id.org/biolink/ - schema: http://schema.org/ VO: http://purl.obolibrary.org/obo/VO_ - ExO: http://purl.obolibrary.org/obo/ExO_ MINMOD: https://minmod.isi.edu/resource/ ANSI: https://www.ansi.org/ OSHA: https://www.osha.gov/ EMMO: http://emmo.info/emmo# ENM: http://purl.enanomapper.org/onto/ENM_ - PROCO: http://purl.obolibrary.org/obo/PROCO_ SRAO: http://www.fairsharing.org/ontology/subject/SRAO_ - SNOMED: http://snomed.info/id/ NCIt: http://purl.obolibrary.org/obo/NCIT_ ICD10: http://purl.bioontology.org/ontology/ICD10/ RxNorm: http://purl.bioontology.org/ontology/RXNORM/ + HL7: http://terminology.hl7.org/CodeSystem/ DICOM: http://dicom.nema.org/dcm/ - MMO: http://purl.obolibrary.org/obo/MMO_ + caDSR: https://cadsr.cancer.gov/onedata/cde/ + ICDO: http://purl.obolibrary.org/obo/ICDO_ + seer: https://seer.cancer.gov/ AFO: http://purl.allotrope.org/ontologies/quality# + premis: http://id.loc.gov/vocabulary/preservation/ + arxiv: https://arxiv.org/abs/ CIO: http://purl.obolibrary.org/obo/CIO_ OBCS: http://purl.obolibrary.org/obo/OBCS_ - DataCite: https://purl.org/datacite/ BFO: http://purl.obolibrary.org/obo/BFO_ - rdfs: http://www.w3.org/2000/01/rdf-schema# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# bibo: http://purl.org/ontology/bibo/ oboe-core: http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# omopschema: http://example.org/omop/ wgs84: http://www.w3.org/2003/01/geo/wgs84_pos# om: http://www.opengis.net/om/2.0 - prov: http://www.w3.org/ns/prov# example: http://example.org/ _base: http://example.org/ ucum: http://unitsofmeasure.org/ - HL7: http://terminology.hl7.org/CodeSystem/ + COB: http://purl.obolibrary.org/obo/COB_ fibo.commons.PartiesAndSituations: https://spec.edmcouncil.org/fibo/ontology/FBC/ommons/PartiesAndSituations/ BSPO: http://purl.obolibrary.org/obo/BSPO_ TIME: http://www.w3.org/2006/time# greg: http://www.w3.org/ns/time/gregorian# OPMI: http://purl.obolibrary.org/obo/OPMI_ SI: http://www.bipm.org/en/si/ + quantitykind: http://qudt.org/vocab/quantitykind/ X11: https://en.wikipedia.org/wiki/X11_color_names# CSS: https://www.w3.org/TR/css-color-3/# default_prefix: valuesets @@ -153,6 +191,586 @@ enums: description: Domain-level enum for academic value sets is_a: ValueSetEnum abstract: true + OrganizationsSchemaEnum: + description: Schema-level enum for organizations in academic + is_a: AcademicDomainEnum + abstract: true + annotations: + source_file: academic/organizations.yaml + USDOENationalLaboratoryEnum: + title: USDOE National Laboratory + description: 'United States Department of Energy National Laboratories. + + + The DOE operates 17 National Laboratories that serve as powerhouses of science and technology, + + tackling critical scientific challenges and conducting cutting-edge research across multiple disciplines. + + + These laboratories are managed by contractors and stewarded by various DOE program offices, + + with the Office of Science stewarding 10 of the 17 laboratories. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + comments: + - All organization names mapped to ROR (Research Organization Registry) identifiers + - See https://www.energy.gov/national-laboratories for official information + permissible_values: + AMES_LABORATORY: + title: Ames National Laboratory + description: National laboratory focused on materials science and chemistry research + meaning: ROR:041m9xr71 + annotations: + location: Ames, Iowa + established: 1947 + stewarding_office: Office of Science + website: https://www.ameslab.gov/ + ARGONNE_NATIONAL_LABORATORY: + title: Argonne National Laboratory + description: Multidisciplinary science and engineering research center + meaning: ROR:05gvnxz63 + annotations: + location: Lemont, Illinois + established: 1946 + stewarding_office: Office of Science + website: https://www.anl.gov/ + BROOKHAVEN_NATIONAL_LABORATORY: + title: Brookhaven National Laboratory + description: Research center for nuclear and high-energy physics + meaning: ROR:02ex6cf31 + annotations: + location: Upton, New York + established: 1947 + stewarding_office: Office of Science + website: https://www.bnl.gov/ + FERMI_NATIONAL_ACCELERATOR_LABORATORY: + title: Fermi National Accelerator Laboratory + description: Particle physics and accelerator research laboratory + meaning: ROR:020hgte69 + aliases: + - Fermilab + annotations: + location: Batavia, Illinois + established: 1967 + stewarding_office: Office of Science + website: https://www.fnal.gov/ + IDAHO_NATIONAL_LABORATORY: + title: Idaho National Laboratory + description: Nuclear energy research and national security laboratory + meaning: ROR:00ty2a548 + annotations: + location: Idaho Falls, Idaho + established: 1949 + stewarding_office: Office of Nuclear Energy + website: https://inl.gov/ + LAWRENCE_BERKELEY_NATIONAL_LABORATORY: + title: Lawrence Berkeley National Laboratory + description: Multidisciplinary research laboratory + meaning: ROR:02jbv0t02 + aliases: + - Berkeley Lab + - LBNL + annotations: + location: Berkeley, California + established: 1931 + stewarding_office: Office of Science + website: https://www.lbl.gov/ + LAWRENCE_LIVERMORE_NATIONAL_LABORATORY: + title: Lawrence Livermore National Laboratory + description: National security laboratory focused on nuclear weapons and advanced technology + meaning: ROR:041nk4h53 + aliases: + - LLNL + annotations: + location: Livermore, California + established: 1952 + stewarding_office: National Nuclear Security Administration + website: https://www.llnl.gov/ + LOS_ALAMOS_NATIONAL_LABORATORY: + title: Los Alamos National Laboratory + description: Multidisciplinary research institution for national security + meaning: ROR:01e41cf67 + aliases: + - LANL + annotations: + location: Los Alamos, New Mexico + established: 1943 + stewarding_office: National Nuclear Security Administration + website: https://www.lanl.gov/ + NATIONAL_ENERGY_TECHNOLOGY_LABORATORY: + title: National Energy Technology Laboratory + description: Federal research laboratory focused on energy and environmental technology + meaning: ROR:01x26mz03 + aliases: + - NETL + annotations: + location: Pittsburgh, Pennsylvania and Morgantown, West Virginia + established: 1910 + stewarding_office: Office of Fossil Energy and Carbon Management + website: https://www.netl.doe.gov/ + NATIONAL_RENEWABLE_ENERGY_LABORATORY: + title: National Renewable Energy Laboratory + description: Research and development laboratory focused on renewable energy and energy efficiency + meaning: ROR:036266993 + aliases: + - NREL + annotations: + location: Golden, Colorado + established: 1977 + stewarding_office: Office of Energy Efficiency and Renewable Energy + website: https://www.nrel.gov/ + OAK_RIDGE_NATIONAL_LABORATORY: + title: Oak Ridge National Laboratory + description: Multidisciplinary science and technology laboratory + meaning: ROR:01qz5mb56 + aliases: + - ORNL + annotations: + location: Oak Ridge, Tennessee + established: 1943 + stewarding_office: Office of Science + website: https://www.ornl.gov/ + PACIFIC_NORTHWEST_NATIONAL_LABORATORY: + title: Pacific Northwest National Laboratory + description: Research laboratory focused on energy, environment, and national security + meaning: ROR:05h992307 + aliases: + - PNNL + annotations: + location: Richland, Washington + established: 1965 + stewarding_office: Office of Science + website: https://www.pnnl.gov/ + PRINCETON_PLASMA_PHYSICS_LABORATORY: + title: Princeton Plasma Physics Laboratory + description: Plasma physics and fusion energy research laboratory + meaning: ROR:03vn1ts68 + aliases: + - PPPL + annotations: + location: Princeton, New Jersey + established: 1951 + stewarding_office: Office of Science + website: https://www.pppl.gov/ + SANDIA_NATIONAL_LABORATORIES: + title: Sandia National Laboratories + description: Multimission laboratory for national security and technology innovation + meaning: ROR:01apwpt12 + aliases: + - Sandia + - SNL + annotations: + location: Albuquerque, New Mexico and Livermore, California + established: 1949 + stewarding_office: National Nuclear Security Administration + website: https://www.sandia.gov/ + SAVANNAH_RIVER_NATIONAL_LABORATORY: + title: Savannah River National Laboratory + description: Applied research laboratory for environmental and national security missions + meaning: ROR:05vc7qy59 + aliases: + - SRNL + annotations: + location: Aiken, South Carolina + established: 1951 + stewarding_office: Office of Environmental Management + website: https://www.srnl.gov/ + SLAC_NATIONAL_ACCELERATOR_LABORATORY: + title: SLAC National Accelerator Laboratory + description: Particle physics and photon science research laboratory + meaning: ROR:05gzmn429 + aliases: + - SLAC + annotations: + location: Menlo Park, California + established: 1962 + stewarding_office: Office of Science + website: https://www6.slac.stanford.edu/ + THOMAS_JEFFERSON_NATIONAL_ACCELERATOR_FACILITY: + title: Thomas Jefferson National Accelerator Facility + description: Nuclear physics research laboratory with particle accelerator + meaning: ROR:02vwzrd76 + aliases: + - Jefferson Lab + - JLab + annotations: + location: Newport News, Virginia + established: 1984 + stewarding_office: Office of Science + website: https://www.jlab.org/ + is_a: OrganizationsSchemaEnum + annotations: + source_domain: academic + source_schema: organizations + USFederalFundingAgencyEnum: + title: US Federal Funding Agency + description: 'Major United States Federal Research Funding Agencies. + + + These agencies provide funding for basic and applied research across various scientific disciplines, + + supporting universities, national laboratories, and other research institutions. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + comments: + - All agency names mapped to ROR (Research Organization Registry) identifiers + - Includes primary research funding agencies + permissible_values: + NIH: + title: National Institutes of Health + description: Primary federal agency for biomedical and public health research + meaning: ROR:01cwqze88 + aliases: + - National Institutes of Health + annotations: + parent_department: Department of Health and Human Services + website: https://www.nih.gov/ + established: 1887 + NSF: + title: U.S. National Science Foundation + description: Federal agency supporting fundamental research and education in non-medical fields + meaning: ROR:021nxhr62 + aliases: + - National Science Foundation + annotations: + website: https://www.nsf.gov/ + established: 1950 + DOE: + title: United States Department of Energy + description: Federal department overseeing energy policy and nuclear weapons program + meaning: ROR:01bj3aw27 + aliases: + - Department of Energy + - U.S. Department of Energy + annotations: + website: https://www.energy.gov/ + established: 1977 + NASA: + title: National Aeronautics and Space Administration + description: Federal agency responsible for civil space program and aeronautics research + meaning: ROR:027ka1x80 + annotations: + website: https://www.nasa.gov/ + established: 1958 + EPA: + title: Environmental Protection Agency + description: Federal agency protecting human health and the environment + meaning: ROR:03tns0030 + aliases: + - U.S. Environmental Protection Agency + annotations: + website: https://www.epa.gov/ + established: 1970 + NOAA: + title: National Oceanic and Atmospheric Administration + description: Federal agency focused on ocean, atmosphere, and coastal research + meaning: ROR:02z5nhe81 + annotations: + parent_department: Department of Commerce + website: https://www.noaa.gov/ + established: 1970 + NIST: + title: National Institute of Standards and Technology + description: Federal agency promoting innovation and industrial competitiveness + meaning: ROR:05xpvk416 + annotations: + parent_department: Department of Commerce + website: https://www.nist.gov/ + established: 1901 + USDA_ARS: + title: Agricultural Research Service + description: Principal research agency of the U.S. Department of Agriculture + meaning: ROR:02d2m2044 + aliases: + - USDA ARS + annotations: + parent_department: Department of Agriculture + website: https://www.ars.usda.gov/ + established: 1953 + DOD: + title: United States Department of Defense + description: Federal department responsible for military research and development + meaning: ROR:0447fe631 + aliases: + - Department of Defense + - U.S. Department of Defense + annotations: + website: https://www.defense.gov/ + established: 1947 + USGS: + title: United States Geological Survey + description: Federal agency for earth science research and monitoring + meaning: ROR:035a68863 + annotations: + parent_department: Department of the Interior + website: https://www.usgs.gov/ + established: 1879 + is_a: OrganizationsSchemaEnum + annotations: + source_domain: academic + source_schema: organizations + NIHInstituteCenterEnum: + title: NIH Institute Center + description: 'National Institutes of Health (NIH) Institutes and Centers. + + + NIH comprises 27 Institutes and Centers, each with a specific research agenda focused on particular + + diseases or body systems. These are the major NIH ICs that fund extramural research. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + comments: + - All mapped to ROR (Research Organization Registry) identifiers + - Focuses on major funding institutes + permissible_values: + NCI: + title: National Cancer Institute + description: NIH institute for cancer research and training + meaning: ROR:02t771148 + aliases: + - National Cancer Institute + annotations: + parent_organization: National Institutes of Health + website: https://www.cancer.gov/ + established: 1937 + NHLBI: + title: National Heart Lung and Blood Institute + description: NIH institute for heart, lung, and blood diseases research + meaning: ROR:012pb6c26 + aliases: + - National Heart, Lung, and Blood Institute + annotations: + parent_organization: National Institutes of Health + website: https://www.nhlbi.nih.gov/ + established: 1948 + NIAID: + title: National Institute of Allergy and Infectious Diseases + description: NIH institute for infectious, immunologic, and allergic diseases research + meaning: ROR:043z4tv69 + annotations: + parent_organization: National Institutes of Health + website: https://www.niaid.nih.gov/ + established: 1948 + NIMH: + title: National Institute of Mental Health + description: NIH institute for mental health research + meaning: ROR:04t0s7x83 + annotations: + parent_organization: National Institutes of Health + website: https://www.nimh.nih.gov/ + established: 1949 + NINDS: + title: National Institute of Neurological Disorders and Stroke + description: NIH institute for neurological disorders research + meaning: ROR:01s5ya894 + annotations: + parent_organization: National Institutes of Health + website: https://www.ninds.nih.gov/ + established: 1950 + NIDDK: + title: National Institute of Diabetes and Digestive and Kidney Diseases + description: NIH institute for diabetes, digestive, and kidney diseases research + meaning: ROR:00adh9b73 + annotations: + parent_organization: National Institutes of Health + website: https://www.niddk.nih.gov/ + established: 1950 + NHGRI: + title: National Human Genome Research Institute + description: NIH institute for genomics and genetics research + meaning: ROR:00baak391 + annotations: + parent_organization: National Institutes of Health + website: https://www.genome.gov/ + established: 1989 + NIGMS: + title: National Institute of General Medical Sciences + description: NIH institute supporting basic biomedical research + meaning: ROR:04q48ey07 + annotations: + parent_organization: National Institutes of Health + website: https://www.nigms.nih.gov/ + established: 1962 + NIEHS: + title: National Institute of Environmental Health Sciences + description: NIH institute for environmental health sciences research + meaning: ROR:00j4k1h63 + annotations: + parent_organization: National Institutes of Health + website: https://www.niehs.nih.gov/ + established: 1966 + NEI: + title: National Eye Institute + description: NIH institute for vision and eye disease research + meaning: ROR:03wkg3b53 + annotations: + parent_organization: National Institutes of Health + website: https://www.nei.nih.gov/ + established: 1968 + NIA: + title: National Institute on Aging + description: NIH institute for aging research + meaning: ROR:049v75w11 + annotations: + parent_organization: National Institutes of Health + website: https://www.nia.nih.gov/ + established: 1974 + NLM: + title: United States National Library of Medicine + description: World's largest biomedical library and NIH component + meaning: ROR:0060t0j89 + aliases: + - National Library of Medicine + annotations: + parent_organization: National Institutes of Health + website: https://www.nlm.nih.gov/ + established: 1956 + is_a: OrganizationsSchemaEnum + annotations: + source_domain: academic + source_schema: organizations + StandardsOrganizationEnum: + title: Standards Organization + description: 'Major International Standards Development Organizations. + + + These organizations develop technical standards, specifications, and guidelines used globally + + across various industries including information technology, healthcare, and engineering. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + comments: + - All mapped to ROR (Research Organization Registry) identifiers where available + - Includes standards bodies commonly referenced in research + permissible_values: + ISO: + title: International Organization for Standardization + description: International standard-setting body for industrial and commercial standards + meaning: ROR:004s85t07 + annotations: + website: https://www.iso.org/ + established: 1947 + headquarters: Geneva, Switzerland + W3C: + title: World Wide Web Consortium + description: International standards organization for World Wide Web standards + meaning: ROR:0059y1582 + annotations: + website: https://www.w3.org/ + established: 1994 + headquarters: Cambridge, Massachusetts + IEEE: + title: Institute of Electrical and Electronics Engineers + description: Professional association for electronic and electrical engineering + meaning: ROR:01n002310 + annotations: + website: https://www.ieee.org/ + established: 1963 + headquarters: New York, USA + HL7: + title: Health Level Seven International + description: Standards development organization for healthcare information exchange + meaning: ROR:029ga8k16 + aliases: + - Health Level Seven + annotations: + website: https://www.hl7.org/ + established: 1987 + headquarters: Ann Arbor, Michigan + is_a: OrganizationsSchemaEnum + annotations: + source_domain: academic + source_schema: organizations + UNSpecializedAgencyEnum: + title: UN Specialized Agency + description: 'United Nations Specialized Agencies. + + + UN specialized agencies are autonomous international organizations that coordinate their work + + with the UN through negotiated agreements. They address international issues in their respective fields. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + comments: + - All mapped to ROR (Research Organization Registry) identifiers + - Includes major UN agencies relevant to research and development + permissible_values: + WHO: + title: World Health Organization + description: UN agency for international public health + meaning: ROR:01f80g185 + annotations: + website: https://www.who.int/ + established: 1948 + headquarters: Geneva, Switzerland + UNESCO: + title: UNESCO + description: UN Educational, Scientific and Cultural Organization + meaning: ROR:04h4z8k05 + aliases: + - United Nations Educational, Scientific and Cultural Organization + annotations: + website: https://www.unesco.org/ + established: 1945 + headquarters: Paris, France + IAEA: + title: International Atomic Energy Agency + description: International organization promoting peaceful use of nuclear energy + meaning: ROR:00gtfax65 + annotations: + website: https://www.iaea.org/ + established: 1957 + headquarters: Vienna, Austria + WMO: + title: World Meteorological Organization + description: UN agency for weather, climate and water resources + meaning: ROR:011pjwf87 + annotations: + website: https://public.wmo.int/ + established: 1950 + headquarters: Geneva, Switzerland + UNEP: + title: United Nations Environment Programme + description: UN program coordinating environmental activities + meaning: ROR:015z29x25 + annotations: + website: https://www.unep.org/ + established: 1972 + headquarters: Nairobi, Kenya + is_a: OrganizationsSchemaEnum + annotations: + source_domain: academic + source_schema: organizations ResearchSchemaEnum: description: Schema-level enum for research in academic is_a: AcademicDomainEnum @@ -162,6 +780,12 @@ enums: PublicationType: title: Publication Type description: Types of academic and research publications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JOURNAL_ARTICLE: description: Peer-reviewed journal article @@ -314,7 +938,14 @@ enums: source_domain: academic source_schema: research PeerReviewStatus: + title: Peer Review Status description: Status of peer review process + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NOT_PEER_REVIEWED: description: Not peer reviewed @@ -349,7 +980,14 @@ enums: source_domain: academic source_schema: research AcademicDegree: + title: Academic Degree description: Academic degrees and qualifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BA: title: Bachelor of Arts @@ -521,7 +1159,14 @@ enums: source_domain: academic source_schema: research LicenseType: + title: License Type description: Common software and content licenses + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MIT: description: MIT License @@ -586,7 +1231,14 @@ enums: source_domain: academic source_schema: research ResearchField: + title: Research Field description: Major research fields and disciplines + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PHYSICS: description: Physics @@ -675,7 +1327,14 @@ enums: source_domain: academic source_schema: research FundingType: + title: Funding Type description: Types of research funding + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GRANT: description: Research grant @@ -704,7 +1363,14 @@ enums: source_domain: academic source_schema: research ManuscriptSection: + title: Manuscript Section description: Sections of a scientific manuscript or publication + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TITLE: title: document title @@ -938,7 +1604,14 @@ enums: source_domain: academic source_schema: research ResearchRole: + title: Research Role description: Roles in research and authorship + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CONCEPTUALIZATION: description: Ideas; formulation of research goals @@ -1010,7 +1683,14 @@ enums: source_domain: academic source_schema: research OpenAccessType: + title: Open Access Type description: Types of open access publishing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GOLD: description: Gold open access (published OA) @@ -1031,7 +1711,14 @@ enums: source_domain: academic source_schema: research CitationStyle: + title: Citation Style description: Common citation and reference styles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: APA: description: American Psychological Association @@ -1070,7 +1757,14 @@ enums: annotations: source_file: analytical_chemistry/mass_spectrometry.yaml MassSpectrometerFileFormat: + title: Mass Spectrometer File Format description: Standard file formats used in mass spectrometry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MZML: title: mzML format @@ -1141,7 +1835,14 @@ enums: source_domain: analytical_chemistry source_schema: mass_spectrometry MassSpectrometerVendor: + title: Mass Spectrometer Vendor description: Major mass spectrometer manufacturers + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: THERMO_FISHER_SCIENTIFIC: title: Thermo Fisher Scientific instrument model @@ -1176,7 +1877,14 @@ enums: source_domain: analytical_chemistry source_schema: mass_spectrometry ChromatographyType: + title: Chromatography Type description: Types of chromatographic separation methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GAS_CHROMATOGRAPHY: description: Gas chromatography @@ -1201,7 +1909,14 @@ enums: source_domain: analytical_chemistry source_schema: mass_spectrometry DerivatizationMethod: + title: Derivatization Method description: Chemical derivatization methods for sample preparation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SILYLATION: description: Addition of silyl groups for improved volatility @@ -1226,7 +1941,14 @@ enums: source_domain: analytical_chemistry source_schema: mass_spectrometry MetabolomicsAssayType: + title: Metabolomics Assay Type description: Types of metabolomics assays and profiling approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TARGETED_METABOLITE_PROFILING: title: targeted metabolite profiling @@ -1245,7 +1967,14 @@ enums: source_domain: analytical_chemistry source_schema: mass_spectrometry AnalyticalControlType: + title: Analytical Control Type description: Types of control samples used in analytical chemistry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INTERNAL_STANDARD: title: internal standard role @@ -1279,6 +2008,733 @@ enums: description: Domain-level enum for bio value sets is_a: ValueSetEnum abstract: true + AssaysSchemaEnum: + description: Schema-level enum for assays in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/assays.yaml + SequencingAssayEnum: + title: Sequencing Assay Types + description: Sequencing-based assays including RNA-seq, DNA-seq, and related methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + RNA_SEQ: + description: RNA sequencing to profile transcriptome + meaning: OBI:0001271 + aliases: + - RNA-seq + SINGLE_CELL_RNA_SEQ: + description: Single-cell RNA sequencing + meaning: OBI:0002631 + aliases: + - scRNA-seq + SINGLE_NUCLEUS_RNA_SEQ: + description: Single-nucleus RNA sequencing + aliases: + - snRNA-seq + SPATIAL_TRANSCRIPTOMICS: + description: Spatially resolved transcriptomics + meaning: EFO:0008992 + LNCRNA_SEQ: + description: Long non-coding RNA sequencing + aliases: + - lncRNA-seq + MIRNA_SEQ: + description: MicroRNA sequencing + meaning: OBI:0002112 + aliases: + - miRNA-seq + RIBO_SEQ: + description: Ribosome profiling sequencing + aliases: + - Ribo-seq + WHOLE_GENOME_SEQUENCING: + description: Whole genome sequencing + meaning: OBI:0002117 + aliases: + - WGS + WHOLE_EXOME_SEQUENCING: + description: Whole exome sequencing + meaning: OBI:0002118 + aliases: + - WES + TARGETED_EXOME_SEQUENCING: + description: Targeted exome sequencing panel + NEXT_GENERATION_TARGETED_SEQUENCING: + description: Next generation targeted sequencing panel + SANGER_SEQUENCING: + description: Sanger chain termination sequencing + meaning: OBI:0000695 + ATAC_SEQ: + description: Assay for Transposase-Accessible Chromatin sequencing + meaning: OBI:0002039 + aliases: + - ATAC-seq + SINGLE_CELL_ATAC_SEQ: + description: Single-cell ATAC-seq + aliases: + - scATAC-seq + CHIP_SEQ: + description: Chromatin immunoprecipitation sequencing + meaning: OBI:0000716 + aliases: + - ChIP-seq + CUT_AND_RUN: + description: Cleavage Under Targets and Release Using Nuclease + aliases: + - CUT&RUN + BISULFITE_SEQUENCING: + description: Bisulfite sequencing for DNA methylation + meaning: OBI:0000748 + aliases: + - BS-seq + ERR_BISULFITE_SEQUENCING: + description: Enzymatic methyl-seq (EM-seq) or similar error-reduced bisulfite sequencing + OXBS_SEQ: + description: Oxidative bisulfite sequencing + aliases: + - oxBS-seq + HI_C: + description: High-throughput chromosome conformation capture + meaning: OBI:0002042 + aliases: + - Hi-C + ISO_SEQ: + description: Isoform sequencing (PacBio long-read) + aliases: + - Iso-Seq + NOME_SEQ: + description: Nucleosome Occupancy and Methylome Sequencing + aliases: + - NOMe-seq + CAPP_SEQ: + description: CAncer Personalized Profiling by deep Sequencing + aliases: + - CAPP-Seq + SAFER_SEQS: + description: Safe-Sequencing System + TCR_REPERTOIRE_SEQUENCING: + description: T cell receptor repertoire sequencing + aliases: + - TCR-seq + SCCGI_SEQ: + description: Single-cell CGI sequencing + aliases: + - scCGI-seq + JUMPING_LIBRARY: + description: Jumping library sequencing for structural variants + SNP_ARRAY: + description: SNP genotyping array + meaning: OBI:0001204 + RNA_ARRAY: + description: RNA expression array + meaning: OBI:0001463 + MIRNA_ARRAY: + description: MicroRNA array + METHYLATION_ARRAY: + description: DNA methylation array + meaning: OBI:0001332 + is_a: AssaysSchemaEnum + annotations: + source_domain: bio + source_schema: assays + ImagingAssayEnum: + title: Imaging Assay Types + description: Imaging-based assays including microscopy, MRI, and related methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BRIGHTFIELD_MICROSCOPY: + description: Brightfield microscopy imaging + meaning: CHMO:0000104 + CONFOCAL_MICROSCOPY: + description: Confocal laser scanning microscopy + meaning: CHMO:0000545 + THREE_D_CONFOCAL_IMAGING: + description: Three-dimensional confocal imaging + aliases: + - 3D confocal imaging + FLUORESCENCE_MICROSCOPY: + description: Fluorescence microscopy assay + meaning: CHMO:0000087 + PHASE_CONTRAST_MICROSCOPY: + description: Phase-contrast microscopy + meaning: CHMO:0000056 + ATOMIC_FORCE_MICROSCOPY: + description: Atomic force microscopy + meaning: CHMO:0000113 + aliases: + - AFM + THREE_D_ELECTRON_MICROSCOPY: + description: Three-dimensional electron microscopy + aliases: + - 3D EM + IMMUNOFLUORESCENCE: + description: Immunofluorescence staining and imaging + meaning: OBI:0003357 + IMMUNOHISTOCHEMISTRY: + description: Immunohistochemistry staining + meaning: OBI:0001986 + aliases: + - IHC + IMMUNOCYTOCHEMISTRY: + description: Immunocytochemistry staining + aliases: + - ICC + HISTOLOGY: + description: Histological examination + meaning: OBI:0600020 + FISH: + description: Fluorescence In Situ Hybridization + meaning: OBI:0003094 + aliases: + - Fluorescence In Situ Hybridization + CODEX: + description: CO-Detection by indEXing imaging + LIVE_IMAGING: + description: Live cell or tissue imaging + AUTORADIOGRAPHY: + description: Autoradiography imaging + meaning: CHMO:0000812 + CONVENTIONAL_MRI: + description: Conventional magnetic resonance imaging + meaning: OBI:0002985 + FUNCTIONAL_MRI: + description: Functional magnetic resonance imaging + meaning: OBI:0001501 + aliases: + - fMRI + DIFFUSION_MRI: + description: Diffusion-weighted MRI + aliases: + - DWI + MPRAGE_MRI: + description: Magnetization-Prepared Rapid Gradient Echo MRI + aliases: + - MPRAGE + MAGNETIC_RESONANCE_SPECTROSCOPY: + description: Magnetic resonance spectroscopy + meaning: CHMO:0000566 + aliases: + - MRS + MAGNETIC_RESONANCE_ANGIOGRAPHY: + description: Magnetic resonance angiography + meaning: OBI:0002986 + aliases: + - MRA + POSITRON_EMISSION_TOMOGRAPHY: + description: Positron emission tomography + meaning: OBI:0001912 + aliases: + - PET + OPTICAL_COHERENCE_TOMOGRAPHY: + description: Optical coherence tomography + meaning: CHMO:0000896 + aliases: + - OCT + OPTICAL_TOMOGRAPHY: + description: Optical tomography + HIGH_FREQUENCY_ULTRASOUND: + description: High frequency ultrasound imaging + TRANSCRANIAL_DOPPLER: + description: Transcranial doppler ultrasonography + IN_VIVO_BIOLUMINESCENCE: + description: In vivo bioluminescence imaging + meaning: OBI:0001503 + LASER_SPECKLE_IMAGING: + description: Laser speckle contrast imaging + SPATIAL_FREQUENCY_DOMAIN_IMAGING: + description: Spatial frequency domain imaging + TRACTION_FORCE_MICROSCOPY: + description: Traction force microscopy + PHOTOGRAPH: + description: Photographic documentation + is_a: AssaysSchemaEnum + annotations: + source_domain: bio + source_schema: assays + MassSpectrometryAssayEnum: + title: Mass Spectrometry Assay Types + description: Mass spectrometry-based assays for proteomics and metabolomics + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MASS_SPECTROMETRY: + description: General mass spectrometry + meaning: CHMO:0000470 + aliases: + - MS + LC_MS: + description: Liquid chromatography-mass spectrometry + meaning: CHMO:0000524 + aliases: + - liquid chromatography/mass spectrometry + LC_MS_MS: + description: Liquid chromatography-tandem mass spectrometry + meaning: CHMO:0000701 + aliases: + - LC-MS/MS + - liquid chromatography/tandem mass spectrometry + HPLC_MS_MS: + description: High-performance liquid chromatography/tandem mass spectrometry + aliases: + - high-performance liquid chromatography/tandem mass spectrometry + UHPLC_MS_MS: + description: Ultra high-performance liquid chromatography/tandem mass spectrometry + aliases: + - ultra high-performance liquid chromatography/tandem mass spectrometry + FIA_MSMS: + description: Flow injection analysis tandem mass spectrometry + aliases: + - FIA-MSMS + LABEL_FREE_MS: + description: Label-free mass spectrometry quantification + aliases: + - label free mass spectrometry + TMT_QUANTITATION: + description: Tandem mass tag quantitation + aliases: + - TMT quantitation + MUDPIT: + description: Multidimensional Protein Identification Technology + aliases: + - MudPIT + MIB_MS: + description: Multiplexed Inhibitor Beads mass spectrometry + aliases: + - MIB/MS + LC_ECD: + description: Liquid chromatography-electrochemical detection + aliases: + - liquid chromatography-electrochemical detection + FTIR_SPECTROSCOPY: + description: Fourier-transform infrared spectroscopy + meaning: CHMO:0000817 + aliases: + - FTIR spectroscopy + RPPA: + description: Reverse Phase Protein Array + meaning: OBI:0001975 + aliases: + - RPPA + PROXIMITY_EXTENSION_ASSAY: + description: Proximity extension assay + aliases: + - PEA + is_a: AssaysSchemaEnum + annotations: + source_domain: bio + source_schema: assays + CellBasedAssayEnum: + title: Cell-Based Assay Types + description: Cell-based assays including viability, proliferation, and functional assays + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CELL_VIABILITY_ASSAY: + description: Cell viability measurement assay + meaning: BAO:0003009 + CELL_PROLIFERATION_ASSAY: + description: Cell proliferation measurement + meaning: BAO:0002100 + CELL_COUNT: + description: Cell counting assay + meaning: BAO:0002097 + ALAMAR_BLUE_ABSORBANCE: + description: AlamarBlue absorbance assay (2D) + aliases: + - 2D AlamarBlue absorbance + ALAMAR_BLUE_FLUORESCENCE: + description: AlamarBlue fluorescence assay (2D) + aliases: + - 2D AlamarBlue fluorescence + THREE_D_MICROTISSUE_VIABILITY: + description: 3D microtissue viability assay + aliases: + - 3D microtissue viability + BRDU_PROLIFERATION: + description: BrdU incorporation proliferation assay + meaning: OBI:0001330 + aliases: + - BrdU proliferation assay + EDU_PROLIFERATION: + description: EdU incorporation proliferation assay + aliases: + - EdU proliferation assay + ATPASE_ACTIVITY_ASSAY: + description: ATPase activity measurement + CAMP_GLO_ASSAY: + description: cAMP-Glo Max Assay + aliases: + - cAMP-Glo Max Assay + FLOW_CYTOMETRY: + description: Flow cytometry analysis + meaning: OBI:0000916 + ELISA: + description: Enzyme-linked immunosorbent assay + meaning: OBI:0000661 + SANDWICH_ELISA: + description: Sandwich ELISA + WESTERN_BLOT: + description: Western blot analysis + meaning: OBI:0000714 + IMMUNOASSAY: + description: General immunoassay + meaning: OBI:0000717 + PCR: + description: Polymerase chain reaction + meaning: OBI:0000415 + aliases: + - polymerase chain reaction + QPCR: + description: Quantitative PCR + meaning: OBI:0000893 + aliases: + - quantitative PCR + NANOSTRING_NCOUNTER: + description: NanoString nCounter Analysis System + MULTI_ELECTRODE_ARRAY: + description: Multi-electrode array recording + meaning: OBI:0002187 + CURRENT_CLAMP_ASSAY: + description: Current clamp electrophysiology + WHOLE_CELL_PATCH_CLAMP: + description: Whole-cell patch clamp recording + meaning: OBI:0002179 + LOCAL_FIELD_POTENTIAL: + description: Local field potential recording + LONG_TERM_POTENTIATION: + description: Long-term potentiation assay + MIGRATION_ASSAY: + description: Cell migration assay + meaning: BAO:0002110 + IN_VITRO_TUMORIGENESIS: + description: In vitro tumorigenesis assay + IN_VIVO_TUMOR_GROWTH: + description: In vivo tumor growth assay + IN_VIVO_PDX_VIABILITY: + description: In vivo patient-derived xenograft viability + MATRIGEL_TUMORIGENESIS: + description: Matrigel-based tumorigenesis assay + aliases: + - Matrigel-based tumorigenesis assay + HIGH_CONTENT_SCREEN: + description: High content screening assay + meaning: BAO:0000514 + CELL_PAINTING: + description: Cell painting morphological profiling + meaning: BAO:0020000 + COMPOUND_SCREEN: + description: Compound library screening + COMBINATION_SCREEN: + description: Drug combination screening + SMALL_MOLECULE_LIBRARY_SCREEN: + description: Small molecule library screen + REPORTER_GENE_ASSAY: + description: Reporter gene assay + meaning: BAO:0000098 + MASSIVELY_PARALLEL_REPORTER_ASSAY: + description: Massively parallel reporter assay + aliases: + - MPRA + SPLIT_GFP_ASSAY: + description: Split-GFP protein interaction assay + aliases: + - split-GFP assay + FOCUS_FORMING_ASSAY: + description: Focus forming assay + OXYGEN_CONSUMPTION_ASSAY: + description: Oxygen consumption rate measurement + meaning: BAO:0003028 + ROS_ASSAY: + description: Reactive oxygen species assay + aliases: + - reactive oxygen species assay + CALCIUM_RETENTION_ASSAY: + description: Calcium retention capacity assay + TRANS_ENDOTHELIAL_RESISTANCE: + description: Trans-endothelial electrical resistance measurement + aliases: + - trans-endothelial electrical resistance + CELL_PERMEABILITY_ASSAY: + description: Cell permeability assay + PHARMACOKINETIC_ADME: + description: Pharmacokinetic ADME assay + aliases: + - pharmocokinetic ADME assay + ARRAY: + description: General array-based assay + HPLC: + description: High-performance liquid chromatography + meaning: CHMO:0001009 + ELECTROCHEMILUMINESCENCE: + description: Electrochemiluminescence detection + STR_PROFILE: + description: Short tandem repeat profiling + TIDE: + description: Tracking of Indels by Decomposition + SURVIVAL_ASSAY: + description: Cell or organism survival assay + is_a: AssaysSchemaEnum + annotations: + source_domain: bio + source_schema: assays + ClinicalBehavioralAssayEnum: + title: Clinical and Behavioral Assay Types + description: Clinical assessments and behavioral assays used in research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CLINICAL_DATA: + description: Clinical data collection + QUESTIONNAIRE: + description: Questionnaire-based assessment + meaning: OBI:0001504 + INTERVIEW: + description: Clinical or research interview + FOCUS_GROUP: + description: Focus group discussion + SCALE: + description: Clinical rating scale + NEUROPSYCHOLOGICAL_ASSESSMENT: + description: Neuropsychological testing + meaning: OBI:0002508 + COGNITIVE_ASSESSMENT: + description: Cognitive function assessment + NIH_TOOLBOX: + description: NIH Toolbox assessment battery + PROMIS_COGNITIVE_FUNCTION: + description: PROMIS Cognitive Function measures + N_BACK_TASK: + description: N-back working memory task + aliases: + - n-back task + CORSI_BLOCKS: + description: Corsi block-tapping task + CBCL_1_5_5: + description: Child Behavior Checklist for Ages 1.5-5 + aliases: + - Child Behavior Checklist for Ages 1.5-5 + CBCL_6_18: + description: Child Behavior Checklist for Ages 6-18 + aliases: + - Child Behavior Checklist for Ages 6-18 + SRS: + description: Social Responsiveness Scale + aliases: + - Social Responsiveness Scale + SRS_2: + description: Social Responsiveness Scale Second Edition + aliases: + - Social Responsiveness Scale Second Edition + BLOOD_CHEMISTRY: + description: Blood chemistry measurement + aliases: + - blood chemistry measurement + METABOLIC_SCREENING: + description: Metabolic screening panel + GENOTYPING: + description: Genotyping assay + meaning: OBI:0000435 + BODY_SIZE_MEASUREMENT: + description: Body size trait measurement + meaning: MMO:0000013 + aliases: + - body size trait measurement + GAIT_MEASUREMENT: + description: Gait analysis measurement + aliases: + - gait measurement + GRIP_STRENGTH: + description: Grip strength measurement + HAND_HELD_DYNAMOMETRY: + description: Hand-held dynamometry + SIX_MINUTE_WALK_TEST: + description: Six-minute walk test + aliases: + - six-minute walk test + ACTIGRAPHY: + description: Actigraphy monitoring + POLYSOMNOGRAPHY: + description: Polysomnography sleep study + QUANTITATIVE_SENSORY_TESTING: + description: Quantitative sensory testing + VON_FREY_TEST: + description: Von Frey filament test + aliases: + - Von Frey test + ALGOMETRX_NOCIOMETER: + description: AlgometRx Nociometer assessment + AUDITORY_BRAINSTEM_RESPONSE: + description: Auditory brainstem response testing + aliases: + - ABR + PURE_TONE_AVERAGE: + description: Pure tone average audiometry + WORD_RECOGNITION_SCORE: + description: Word recognition score + DPOE: + description: Distortion product otoacoustic emissions + aliases: + - distortion product otoacoustic emissions + PATTERN_ERG: + description: Pattern electroretinogram + aliases: + - pattern electroretinogram + OPTOKINETIC_REFLEX: + description: Optokinetic reflex assay + aliases: + - optokinetic reflex assay + RICCARDI_ABLON_SCALES: + description: Riccardi and Ablon clinical severity scales + SKINDEX_16: + description: Skindex-16 dermatology questionnaire + CNF_SKINDEX: + description: Cutaneous neurofibroma Skindex + aliases: + - cNF-Skindex + CDLQI: + description: Children's Dermatology Life Quality Index Questionnaire + aliases: + - Children's Dermatology Life Quality Index Questionnaire + FACEQ_DISTRESS: + description: FACE-Q Appearance-related Distress + aliases: + - FACE-Q Appearance-related Distress + OPEN_FIELD_TEST: + description: Open field locomotor test + meaning: MMO:0000093 + ELEVATED_PLUS_MAZE: + description: Elevated plus maze anxiety test + meaning: MMO:0000292 + aliases: + - elevated plus maze test + ROTAROD_TEST: + description: Rotarod motor coordination test + meaning: MMO:0000091 + aliases: + - rotarod performance test + ACTIVE_AVOIDANCE: + description: Active avoidance learning behavior assay + aliases: + - active avoidance learning behavior assay + CONTEXTUAL_CONDITIONING: + description: Contextual conditioning behavior assay + aliases: + - contextual conditioning behavior assay + NOVELTY_RESPONSE: + description: Novelty response behavior assay + aliases: + - novelty response behavior assay + FEEDING_ASSAY: + description: Feeding behavior assay + is_a: AssaysSchemaEnum + annotations: + source_domain: bio + source_schema: assays + BgcCategoriesSchemaEnum: + description: Schema-level enum for bgc_categories in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/bgc_categories.yaml + BgcCategoryEnum: + title: BGC Category + description: 'Categories of biosynthetic gene clusters based on the type of secondary metabolite produced. + + These categories are used in genome mining and natural product discovery.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + POLYKETIDE: + description: Polyketide biosynthetic gene clusters + meaning: CHEBI:26188 + annotations: + definition: Natural products containing alternating carbonyl and methylene groups + biosynthetic_enzyme: Polyketide synthase (PKS) + examples: Erythromycin, lovastatin, rapamycin + NRP: + title: Non-ribosomal peptide + description: Non-ribosomal peptide biosynthetic gene clusters + annotations: + definition: Peptides synthesized by non-ribosomal peptide synthetases + biosynthetic_enzyme: Non-ribosomal peptide synthetase (NRPS) + examples: Penicillin, vancomycin, cyclosporin + RIPP: + title: Ribosomally synthesized and post-translationally modified peptide + description: RiPP biosynthetic gene clusters + annotations: + definition: Ribosomally synthesized peptides with extensive post-translational modifications + biosynthetic_enzyme: Various modifying enzymes + examples: Nisin, thiopeptides, lanthipeptides + related_chebi: CHEBI:71629 (nisin) + TERPENE: + description: Terpene biosynthetic gene clusters + meaning: CHEBI:35186 + annotations: + definition: Hydrocarbons derived from isoprene units + biosynthetic_enzyme: Terpene synthase + examples: Limonene, carotenoids, taxol + ALKALOID: + description: Alkaloid biosynthetic gene clusters + meaning: CHEBI:22315 + annotations: + definition: Nitrogen-containing organic compounds with diverse structures + biosynthetic_enzyme: Various enzymes + examples: Morphine, caffeine, nicotine + SACCHARIDE: + title: polysaccharide + description: Saccharide/polysaccharide biosynthetic gene clusters + meaning: CHEBI:18154 + annotations: + definition: Carbohydrate polymers and oligomers + biosynthetic_enzyme: Glycosyltransferases + examples: Cellulose, chitin, bacterial capsular polysaccharides + OTHER: + description: Other or unclassified biosynthetic gene clusters + annotations: + definition: BGCs that do not fit into standard categories or are of unknown type + examples: Novel or hybrid BGCs + is_a: BgcCategoriesSchemaEnum + annotations: + source_domain: bio + source_schema: bgc_categories BioEntitiesSchemaEnum: description: Schema-level enum for bio_entities in bio is_a: BioDomainEnum @@ -1286,9 +2742,16 @@ enums: annotations: source_file: bio/bio_entities.yaml MetazoanAnatomicalStructure: + title: Metazoan Anatomical Structure description: 'Any anatomical structure found in metazoan organisms, including organs, tissues, and body parts' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:uberon source_nodes: @@ -1301,7 +2764,14 @@ enums: source_domain: bio source_schema: bio_entities HumanAnatomicalStructure: + title: Human Anatomical Structure description: Anatomical structures specific to humans (Homo sapiens) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:uberon source_nodes: @@ -1314,7 +2784,14 @@ enums: source_domain: bio source_schema: bio_entities PlantAnatomicalStructure: + title: Plant Anatomical Structure description: Any anatomical structure found in plant organisms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:po source_nodes: @@ -1327,9 +2804,16 @@ enums: source_domain: bio source_schema: bio_entities CellType: + title: Cell Type description: 'Any cell type from the Cell Ontology (CL), including native and experimentally modified cells' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -1342,7 +2826,14 @@ enums: source_domain: bio source_schema: bio_entities NeuronType: + title: Neuron Type description: Neuron cell types from the Cell Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -1355,7 +2846,14 @@ enums: source_domain: bio source_schema: bio_entities ImmuneCell: + title: Immune Cell description: Immune system cell types (leukocytes and their subtypes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -1368,7 +2866,14 @@ enums: source_domain: bio source_schema: bio_entities StemCell: + title: Stem Cell description: Stem cell types and progenitor cells + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -1382,7 +2887,14 @@ enums: source_domain: bio source_schema: bio_entities Disease: + title: Disease description: Human diseases from the Mondo Disease Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -1395,7 +2907,14 @@ enums: source_domain: bio source_schema: bio_entities InfectiousDisease: + title: Infectious Disease description: Infectious diseases caused by pathogenic organisms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -1408,7 +2927,14 @@ enums: source_domain: bio source_schema: bio_entities Cancer: + title: Cancer description: Neoplastic and cancerous diseases + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -1422,7 +2948,14 @@ enums: source_domain: bio source_schema: bio_entities GeneticDisease: + title: Genetic Disease description: Hereditary and genetic diseases + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -1436,7 +2969,14 @@ enums: source_domain: bio source_schema: bio_entities ChemicalEntity: + title: Chemical Entity description: Any chemical entity from ChEBI ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:chebi source_nodes: @@ -1449,7 +2989,14 @@ enums: source_domain: bio source_schema: bio_entities Drug: + title: Drug description: Pharmaceutical drugs and medications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:chebi source_nodes: @@ -1463,7 +3010,14 @@ enums: source_domain: bio source_schema: bio_entities Metabolite: + title: Metabolite description: Metabolites and metabolic intermediates + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:chebi source_nodes: @@ -1476,7 +3030,14 @@ enums: source_domain: bio source_schema: bio_entities Protein: + title: Protein description: Proteins and protein complexes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:pr source_nodes: @@ -1489,7 +3050,14 @@ enums: source_domain: bio source_schema: bio_entities Phenotype: + title: Phenotype description: Phenotypic abnormalities from Human Phenotype Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:hp source_nodes: @@ -1502,7 +3070,14 @@ enums: source_domain: bio source_schema: bio_entities ClinicalFinding: + title: Clinical Finding description: Clinical findings and observations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:hp source_nodes: @@ -1515,7 +3090,14 @@ enums: source_domain: bio source_schema: bio_entities BiologicalProcess: + title: Biological Process description: Biological processes from Gene Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -1528,7 +3110,14 @@ enums: source_domain: bio source_schema: bio_entities MetabolicProcess: + title: Metabolic Process description: Metabolic processes and pathways + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -1541,7 +3130,14 @@ enums: source_domain: bio source_schema: bio_entities MolecularFunction: + title: Molecular Function description: Molecular functions from Gene Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -1554,7 +3150,14 @@ enums: source_domain: bio source_schema: bio_entities CellularComponent: + title: Cellular Component description: Cellular components and locations from Gene Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -1567,7 +3170,14 @@ enums: source_domain: bio source_schema: bio_entities SequenceFeature: + title: Sequence Feature description: Sequence features from the Sequence Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:so source_nodes: @@ -1580,7 +3190,14 @@ enums: source_domain: bio source_schema: bio_entities GeneFeature: + title: Gene Feature description: Gene-related sequence features + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:so source_nodes: @@ -1593,7 +3210,14 @@ enums: source_domain: bio source_schema: bio_entities Environment: + title: Environment description: Environmental systems and biomes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:envo source_nodes: @@ -1607,7 +3231,14 @@ enums: source_domain: bio source_schema: bio_entities EnvironmentalMaterial: + title: Environmental Material description: Environmental materials and substances + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:envo source_nodes: @@ -1620,7 +3251,14 @@ enums: source_domain: bio source_schema: bio_entities Quality: + title: Quality description: Phenotypic qualities and attributes from PATO + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:pato source_nodes: @@ -1633,7 +3271,14 @@ enums: source_domain: bio source_schema: bio_entities PhysicalQuality: + title: Physical Quality description: Physical qualities like size, shape, color + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:pato source_nodes: @@ -1652,7 +3297,14 @@ enums: annotations: source_file: bio/biological_colors.yaml EyeColorEnum: + title: Eye Color description: Human eye color phenotypes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BROWN: description: Brown eyes @@ -1708,7 +3360,14 @@ enums: source_domain: bio source_schema: biological_colors HairColorEnum: + title: Hair Color description: Human hair color phenotypes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLACK: description: Black hair @@ -1785,7 +3444,14 @@ enums: source_domain: bio source_schema: biological_colors FlowerColorEnum: + title: Flower Color description: Common flower colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED: description: Red flowers @@ -1870,7 +3536,14 @@ enums: source_domain: bio source_schema: biological_colors AnimalCoatColorEnum: + title: Animal Coat Color description: Animal coat/fur colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLACK: description: Black coat @@ -1963,7 +3636,14 @@ enums: source_domain: bio source_schema: biological_colors SkinToneEnum: + title: Skin Tone description: Human skin tone classifications (Fitzpatrick scale based) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TYPE_I: description: Very pale white skin @@ -2006,7 +3686,14 @@ enums: source_domain: bio source_schema: biological_colors PlantLeafColorEnum: + title: Plant Leaf Color description: Plant leaf colors (including seasonal changes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GREEN: description: Green leaves (healthy/summer) @@ -2071,6 +3758,51 @@ enums: annotations: source_domain: bio source_schema: biological_colors + BiosafetySchemaEnum: + description: Schema-level enum for biosafety in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/biosafety.yaml + BiosafetyLevelEnum: + title: Biosafety Level + description: Biosafety levels (BSL) defining containment requirements for biological agents + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BSL1: + description: Suitable for well-characterized agents not known to consistently cause disease in healthy adults + meaning: SNOMED:409600007 + exact_mappings: + - METPO:1001102 + title: biosafety level 1 + BSL2: + description: Suitable for agents that pose moderate hazards to personnel and the environment + meaning: SNOMED:409603009 + exact_mappings: + - METPO:1001103 + title: biosafety level 2 + BSL3: + description: Suitable for indigenous or exotic agents that may cause serious or potentially lethal disease through + inhalation + meaning: SNOMED:409604003 + exact_mappings: + - METPO:1001104 + title: biosafety level 3 + BSL4: + description: Suitable for dangerous and exotic agents that pose high risk of life-threatening disease + meaning: SNOMED:409605002 + exact_mappings: + - METPO:1001105 + title: biosafety level 4 + is_a: BiosafetySchemaEnum + annotations: + source_domain: bio + source_schema: biosafety CellCycleSchemaEnum: description: Schema-level enum for cell_cycle in bio is_a: BioDomainEnum @@ -2078,7 +3810,14 @@ enums: annotations: source_file: bio/cell_cycle.yaml CellCyclePhase: + title: Cell Cycle Phase description: Major phases of the eukaryotic cell cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: G0: description: G0 phase (quiescent/resting phase) @@ -2124,7 +3863,14 @@ enums: source_domain: bio source_schema: cell_cycle MitoticPhase: + title: Mitotic Phase description: Stages of mitosis (M phase) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROPHASE: description: Prophase @@ -2168,7 +3914,14 @@ enums: source_domain: bio source_schema: cell_cycle CellCycleCheckpoint: + title: Cell Cycle Checkpoint description: Cell cycle checkpoints that regulate progression + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: G1_S_CHECKPOINT: description: G1/S checkpoint (Restriction point) @@ -2204,35 +3957,48 @@ enums: source_domain: bio source_schema: cell_cycle MeioticPhase: + title: Meiotic Phase description: Phases specific to meiotic cell division + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MEIOSIS_I: description: Meiosis I (reductional division) meaning: GO:0007127 annotations: result: reduction from diploid to haploid + succeeded_by: MEIOSIS_II PROPHASE_I: description: Prophase I meaning: GO:0007128 title: meiotic prophase I annotations: substages: leptotene, zygotene, pachytene, diplotene, diakinesis + succeeded_by: METAPHASE_I METAPHASE_I: description: Metaphase I meaning: GO:0007132 title: meiotic metaphase I annotations: feature: homologous pairs align + succeeded_by: ANAPHASE_I ANAPHASE_I: description: Anaphase I meaning: GO:0007133 title: meiotic anaphase I annotations: feature: homologous chromosomes separate + succeeded_by: TELOPHASE_I TELOPHASE_I: description: Telophase I meaning: GO:0007134 title: meiotic telophase I + annotations: + succeeded_by: PROPHASE_II MEIOSIS_II: description: Meiosis II (equational division) meaning: GO:0007135 @@ -2242,16 +4008,21 @@ enums: description: Prophase II meaning: GO:0007136 title: meiotic prophase II + annotations: + succeeded_by: METAPHASE_II METAPHASE_II: description: Metaphase II meaning: GO:0007137 title: meiotic metaphase II + annotations: + succeeded_by: ANAPHASE_II ANAPHASE_II: description: Anaphase II meaning: GO:0007138 title: meiotic anaphase II annotations: feature: sister chromatids separate + succeeded_by: TELOPHASE_II TELOPHASE_II: description: Telophase II meaning: GO:0007139 @@ -2261,7 +4032,14 @@ enums: source_domain: bio source_schema: cell_cycle CellCycleRegulator: + title: Cell Cycle Regulator description: Types of cell cycle regulatory molecules + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CYCLIN: description: Cyclin proteins @@ -2311,7 +4089,14 @@ enums: source_domain: bio source_schema: cell_cycle CellProliferationState: + title: Cell Proliferation State description: Cell proliferation and growth states + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROLIFERATING: description: Actively proliferating cells @@ -2354,7 +4139,14 @@ enums: source_domain: bio source_schema: cell_cycle DNADamageResponse: + title: DNA Damage Response description: DNA damage response pathways during cell cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CELL_CYCLE_ARREST: description: Cell cycle arrest @@ -2388,8 +4180,15 @@ enums: annotations: source_file: bio/currency_chemicals.yaml CurrencyChemical: + title: Currency Chemical description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron donors/acceptors, and group transfer agents in cellular metabolism. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ATP: description: Adenosine triphosphate - primary energy currency molecule in cells @@ -2449,6 +4248,13 @@ enums: annotations: source_file: bio/developmental_stages.yaml HumanDevelopmentalStage: + title: Human Developmental Stage + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZYGOTE_STAGE: text: ZYGOTE_STAGE @@ -2560,6 +4366,13 @@ enums: source_domain: bio source_schema: developmental_stages MouseDevelopmentalStage: + title: Mouse Developmental Stage + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZYGOTE_STAGE: text: ZYGOTE_STAGE @@ -2660,66 +4473,734 @@ enums: annotations: source_domain: bio source_schema: developmental_stages - GenomeFeaturesSchemaEnum: - description: Schema-level enum for genome_features in bio + HumanAgeGroupEnum: + title: Human Age Group Categories + description: Simplified human age group categories based on MeSH classifications. Useful for cohort stratification and + demographic reporting. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + INFANT: + description: A child between 1 and 23 months of age + meaning: MESH:D007223 + aliases: + - Infant + annotations: + age_range: 1-23 months + CHILD: + description: A person 2 to 12 years of age + meaning: MESH:D002648 + aliases: + - Child + annotations: + age_range: 2-12 years + ADOLESCENT: + description: A person 13 to 18 years of age + meaning: MESH:D000293 + aliases: + - Adolescent + - Teenager + annotations: + age_range: 13-18 years + ADULT: + description: A person having attained full growth or maturity. Adults are of 19 to 120 years of age + meaning: MESH:D000328 + aliases: + - Adult + annotations: + age_range: 19-120 years + is_a: DevelopmentalStagesSchemaEnum + annotations: + source_domain: bio + source_schema: developmental_stages + MousePostnatalAgeGroupEnum: + title: Mouse Postnatal Age Groups + description: Postnatal mouse age groups using postnatal day (P) notation. Common categories used in laboratory research + for developmental studies. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + P0_P3_NEONATAL: + description: Neonatal stage from birth through postnatal day 3 + aliases: + - P0-P3 Neonatal + annotations: + postnatal_days: P0-P3 + approximate_age: birth to day 3 + P4_P21_PREWEANING: + description: Pre-weaning stage from postnatal days 4-21 (typical weaning age) + aliases: + - P4-P21 Pre-weaning + annotations: + postnatal_days: P4-P21 + approximate_age: days 4-21 + P21_P60_YOUNG_ADULT: + description: Young adult stage from postnatal days 21-60 (3 weeks to 2 months) + aliases: + - P21-P60 Young Adult + annotations: + postnatal_days: P21-P60 + approximate_age: 3 weeks to 2 months + P60_P180_ADULT: + description: Adult stage from postnatal days 60-180 (2 to 6 months) + aliases: + - P60-P180 Adult + annotations: + postnatal_days: P60-P180 + approximate_age: 2 to 6 months + P180_P365_MIDDLE_AGED: + description: Middle-aged stage from postnatal days 180-365 (6 to 12 months) + aliases: + - P180-P365 Middle-Aged + annotations: + postnatal_days: P180-P365 + approximate_age: 6 to 12 months + P365_PLUS_AGED: + description: Aged stage from postnatal day 365 onwards (12+ months) + aliases: + - P365+ Aged + annotations: + postnatal_days: P365+ + approximate_age: 12+ months + is_a: DevelopmentalStagesSchemaEnum + annotations: + source_domain: bio + source_schema: developmental_stages + ExpressionUnitsSchemaEnum: + description: Schema-level enum for expression_units in bio is_a: BioDomainEnum abstract: true annotations: - source_file: bio/genome_features.yaml - GenomeFeatureType: - description: 'Genome feature types from SOFA (Sequence Ontology Feature Annotation). - - This is the subset of Sequence Ontology terms used in GFF3 files. - - Organized hierarchically following the Sequence Ontology structure.' + source_file: bio/expression_units.yaml + ExpressionUnitEnum: + title: Gene Expression Units + description: Quantification units for gene expression data from RNA-seq and microarray experiments. Includes raw counts + and various normalization methods. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + RAW_COUNTS: + description: Raw read counts of transcripts without normalization + aliases: + - Raw Counts + - raw counts + annotations: + normalization: none + use: within-sample comparisons only + NORMALIZED_COUNTS: + description: Counts normalized by a method such as DESeq2 or edgeR + aliases: + - Normalized Counts + annotations: + normalization: library size + use: differential expression + COUNTS: + description: General read counts category + aliases: + - Counts + TPM: + description: Transcripts per million - normalized for gene length and sequencing depth + meaning: NCIT:C181327 + aliases: + - Transcript per million + annotations: + normalization: length and depth + use: within and between sample comparisons + formula: (reads/gene_length_kb) / sum(reads/gene_length_kb) * 1e6 + FPKM: + description: Fragments per kilobase of transcript per million reads mapped + meaning: STATO:0000172 + aliases: + - Fragments per kilobase of transcript per million reads mapped + annotations: + normalization: length and depth + use: within-sample comparisons + library_type: paired-end + RPKM: + description: Reads per kilobase of transcript per million reads mapped + meaning: STATO:0000206 + aliases: + - Reads per kilobase of transcript per million reads mapped + annotations: + normalization: length and depth + use: within-sample comparisons + library_type: single-end + CPM: + description: Counts per million reads + aliases: + - Counts per million + annotations: + normalization: depth only + RPKM_UQ: + description: RPKM with upper quartile normalization + annotations: + normalization: length, depth, and upper quartile + VST: + description: Variance stabilizing transformation values + annotations: + method: DESeq2 + use: visualization, clustering + RLOG: + description: Regularized log transformation values + aliases: + - rlog + annotations: + method: DESeq2 + use: visualization, clustering + LOG2_RATIO: + description: Log2 fold change ratio + annotations: + use: differential expression + Z_SCORE: + description: Z-score normalized expression + annotations: + use: cross-gene comparisons + is_a: ExpressionUnitsSchemaEnum + annotations: + source_domain: bio + source_schema: expression_units + ConcentrationUnitEnum: + title: Concentration Unit + description: Units of concentration measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - REGION: - description: A sequence feature with an extent greater than zero - meaning: SO:0000001 - BIOLOGICAL_REGION: - description: A region defined by its biological properties - meaning: SO:0001411 - is_a: REGION - GENE: - description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript - meaning: SO:0000704 - is_a: BIOLOGICAL_REGION - TRANSCRIPT: - description: An RNA synthesized on a DNA or RNA template by an RNA polymerase - meaning: SO:0000673 - is_a: BIOLOGICAL_REGION - PRIMARY_TRANSCRIPT: - description: A transcript that has not been processed - meaning: SO:0000185 - is_a: TRANSCRIPT - MRNA: - description: Messenger RNA; includes 5'UTR, coding sequences and 3'UTR - meaning: SO:0000234 - is_a: TRANSCRIPT - EXON: - description: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript - by RNA splicing - meaning: SO:0000147 - is_a: BIOLOGICAL_REGION - CDS: - description: Coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein - meaning: SO:0000316 - is_a: BIOLOGICAL_REGION - INTRON: - description: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing - meaning: SO:0000188 - is_a: BIOLOGICAL_REGION - FIVE_PRIME_UTR: - description: 5' untranslated region - meaning: SO:0000204 - is_a: BIOLOGICAL_REGION - THREE_PRIME_UTR: - description: 3' untranslated region - meaning: SO:0000205 - is_a: BIOLOGICAL_REGION - NCRNA: - description: Non-protein coding RNA - meaning: SO:0000655 + MOLAR: + description: Molar (moles per liter) + meaning: UO:0000062 + annotations: + symbol: M + definition: mol/L + MILLIMOLAR: + description: Millimolar (10^-3 molar) + meaning: UO:0000063 + annotations: + symbol: mM + conversion_to_molar: '0.001' + MICROMOLAR: + description: Micromolar (10^-6 molar) + meaning: UO:0000064 + annotations: + symbol: μM + conversion_to_molar: 1e-6 + NANOMOLAR: + description: Nanomolar (10^-9 molar) + meaning: UO:0000065 + annotations: + symbol: nM + conversion_to_molar: 1e-9 + PICOMOLAR: + description: Picomolar (10^-12 molar) + meaning: UO:0000066 + annotations: + symbol: pM + conversion_to_molar: 1e-12 + MG_PER_ML: + title: milligram per milliliter + description: Milligrams per milliliter + meaning: UO:0000176 + annotations: + symbol: mg/mL + UG_PER_ML: + title: microgram per milliliter + description: Micrograms per milliliter + meaning: UO:0000274 + annotations: + symbol: μg/mL + NG_PER_ML: + title: nanogram per milliliter + description: Nanograms per milliliter + meaning: UO:0000275 + annotations: + symbol: ng/mL + PERCENT: + description: Percent (parts per hundred) + meaning: UO:0000187 + annotations: + symbol: '%' + conversion_to_fraction: '0.01' + PPM: + title: parts per million + description: Parts per million + meaning: UO:0000169 + annotations: + symbol: ppm + conversion_to_fraction: 1e-6 + PPB: + title: parts per billion + description: Parts per billion + meaning: UO:0000170 + annotations: + symbol: ppb + conversion_to_fraction: 1e-9 + is_a: MeasurementsSchemaEnum + annotations: + source_domain: units + source_schema: measurements + TimeUnitEnum: + title: Time Unit + description: Units of time measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SECOND: + description: Second (SI base unit) + meaning: UO:0000010 + annotations: + symbol: s + system: SI + MILLISECOND: + description: Millisecond (0.001 second) + meaning: UO:0000028 + annotations: + symbol: ms + conversion_to_second: '0.001' + MICROSECOND: + description: Microsecond (10^-6 second) + meaning: UO:0000029 + annotations: + symbol: μs + conversion_to_second: 1e-6 + NANOSECOND: + title: nanosecond + description: Nanosecond (10^-9 second) + meaning: UO:0000150 + annotations: + symbol: ns + conversion_to_second: 1e-9 + MINUTE: + description: Minute (60 seconds) + meaning: UO:0000031 + annotations: + symbol: min + conversion_to_second: '60' + HOUR: + description: Hour (3600 seconds) + meaning: UO:0000032 + annotations: + symbol: h + conversion_to_second: '3600' + DAY: + description: Day (86400 seconds) + meaning: UO:0000033 + annotations: + symbol: d + conversion_to_second: '86400' + WEEK: + description: Week (7 days) + meaning: UO:0000034 + annotations: + symbol: wk + conversion_to_second: '604800' + MONTH: + description: Month (approximately 30 days) + meaning: UO:0000035 + annotations: + symbol: mo + conversion_to_second: '2592000' + note: approximate, varies by month + YEAR: + description: Year (365.25 days) + meaning: UO:0000036 + annotations: + symbol: yr + conversion_to_second: '31557600' + note: accounts for leap years + is_a: MeasurementsSchemaEnum + annotations: + source_domain: units + source_schema: measurements + GenePerturbationSchemaEnum: + description: Schema-level enum for gene_perturbation in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/gene_perturbation.yaml + GenePerturbationMethodEnum: + title: Gene Perturbation Methods + description: Methods for perturbing or modifying gene expression and function. Includes gene editing, silencing, and overexpression + approaches. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CRISPR: + description: CRISPR/Cas9 gene editing technology + meaning: BAO:0010249 + aliases: + - CRISPR/Cas9 + - CRISPR-Cas9 + annotations: + mechanism: DNA cleavage and repair + CRISPR_ACTIVATION: + description: CRISPR activation (CRISPRa) for gene upregulation + aliases: + - CRISPRa + annotations: + mechanism: transcriptional activation + effect: overexpression + CRISPR_INTERFERENCE: + description: CRISPR interference (CRISPRi) for gene silencing + aliases: + - CRISPRi + annotations: + mechanism: transcriptional repression + effect: knockdown + CRISPR_BASE_EDITING: + description: CRISPR base editing for precise nucleotide changes + aliases: + - base editing + annotations: + mechanism: nucleotide conversion + CRISPR_PRIME_EDITING: + description: CRISPR prime editing for versatile sequence changes + aliases: + - prime editing + annotations: + mechanism: search-and-replace + CRAFT: + description: CRISPR Assisted mRNA Fragment Trans-splicing + aliases: + - CRISPR Assisted mRNA Fragment Trans-splicing + annotations: + mechanism: RNA trans-splicing + RNAI: + description: RNA interference for post-transcriptional gene silencing + meaning: NCIT:C20153 + aliases: + - RNAi + - RNA interference + annotations: + mechanism: mRNA degradation + effect: knockdown + SIRNA: + description: Small interfering RNA for transient gene silencing + meaning: NCIT:C2191 + aliases: + - siRNA + annotations: + duration: transient + delivery: transfection + SHRNA: + description: Short hairpin RNA for stable gene silencing + meaning: NCIT:C111906 + aliases: + - shRNA + annotations: + duration: stable + delivery: viral transduction + ANTISENSE_OLIGONUCLEOTIDE: + description: Antisense oligonucleotides for gene silencing + meaning: NCIT:C1653 + aliases: + - ASO + - antisense + annotations: + mechanism: RNase H activation or steric blocking + MORPHOLINO: + description: Morpholino oligomers for gene knockdown + meaning: NCIT:C96280 + annotations: + mechanism: steric blocking + use: developmental biology + CRE_RECOMBINASE: + description: Cre-lox recombination system for conditional gene modification + meaning: NCIT:C17285 + aliases: + - Cre-lox + - CRE Recombinase + annotations: + mechanism: site-specific recombination + use: conditional knockout + FLPE_RECOMBINASE: + description: Flp-FRT recombination system + aliases: + - Flp-FRT + annotations: + mechanism: site-specific recombination + TALEN: + description: Transcription Activator-Like Effector Nucleases + meaning: NCIT:C111903 + aliases: + - TALENs + annotations: + mechanism: DNA cleavage + ZINC_FINGER_NUCLEASE: + description: Zinc finger nucleases for gene editing + meaning: NCIT:C111904 + aliases: + - ZFN + annotations: + mechanism: DNA cleavage + TRANSPOSON_MUTAGENESIS: + description: Transposon-mediated insertional mutagenesis + meaning: OBI:0001187 + aliases: + - transposon insertion + annotations: + mechanism: random insertion + CHEMICAL_MUTAGENESIS: + description: Chemical mutagen-induced mutagenesis + meaning: OBI:0001183 + aliases: + - ENU mutagenesis + - EMS mutagenesis + annotations: + mechanism: base modification + OVEREXPRESSION: + description: Transgene overexpression + meaning: OBI:0002452 + aliases: + - transgene expression + annotations: + effect: gain of function + is_a: GenePerturbationSchemaEnum + annotations: + source_domain: bio + source_schema: gene_perturbation + GeneKnockoutMethodEnum: + title: Gene Knockout Methods + description: Specific methods for creating gene knockouts in model systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + HOMOLOGOUS_RECOMBINATION: + description: Traditional homologous recombination-based knockout + meaning: OBI:0001186 + annotations: + use: ES cell targeting + CRISPR_KNOCKOUT: + description: CRISPR-mediated gene knockout + aliases: + - CRISPR KO + annotations: + mechanism: indel formation + CONDITIONAL_KNOCKOUT: + description: Conditional/inducible gene knockout (Cre-lox or similar) + aliases: + - cKO + - floxed + annotations: + mechanism: Cre-lox recombination + CONSTITUTIVE_KNOCKOUT: + description: Constitutive whole-body gene knockout + aliases: + - germline knockout + TISSUE_SPECIFIC_KNOCKOUT: + description: Tissue or cell type-specific gene knockout + annotations: + mechanism: tissue-specific Cre + INDUCIBLE_KNOCKOUT: + description: Temporally inducible gene knockout + aliases: + - tamoxifen-inducible + annotations: + mechanism: CreERT2 + is_a: GenePerturbationSchemaEnum + annotations: + source_domain: bio + source_schema: gene_perturbation + GenotypeEnum: + title: Genotype States + description: Allelic states for genotype description + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + HOMOZYGOUS_WILDTYPE: + description: Homozygous wild-type alleles + aliases: + - +/+ + - wild-type + - WT + HETEROZYGOUS: + description: Heterozygous for mutation or deletion + aliases: + - +/- + - het + HOMOZYGOUS_MUTANT: + description: Homozygous for mutation or deletion + aliases: + - -/- + - null + - KO + HEMIZYGOUS: + description: Hemizygous (single allele, X-linked or deletion) + aliases: + - -/Y + COMPOUND_HETEROZYGOUS: + description: Compound heterozygous (two different mutant alleles) + aliases: + - compound het + is_a: GenePerturbationSchemaEnum + annotations: + source_domain: bio + source_schema: gene_perturbation + VectorTypeEnum: + title: Gene Delivery Vector Types + description: Types of vectors used for gene delivery in research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LENTIVIRAL: + description: Lentiviral vector + meaning: NCIT:C73481 + annotations: + integration: integrating + RETROVIRAL: + description: Retroviral vector (gamma-retrovirus) + meaning: NCIT:C16886 + annotations: + integration: integrating + ADENOVIRAL: + description: Adenoviral vector + meaning: NCIT:C73475 + annotations: + integration: non-integrating + AAV: + description: Adeno-associated viral vector + meaning: NCIT:C73476 + aliases: + - adeno-associated virus + annotations: + integration: non-integrating (episomal) + PLASMID: + description: Plasmid DNA vector + meaning: NCIT:C730 + annotations: + delivery: transfection + duration: transient + MRNA: + description: mRNA delivery + meaning: NCIT:C813 + annotations: + duration: transient + LNP: + description: Lipid nanoparticle delivery + aliases: + - lipid nanoparticle + annotations: + cargo: mRNA, siRNA + ELECTROPORATION: + description: Electroporation-based delivery + meaning: OBI:0001937 + annotations: + method: physical + is_a: GenePerturbationSchemaEnum + annotations: + source_domain: bio + source_schema: gene_perturbation + GenomeFeaturesSchemaEnum: + description: Schema-level enum for genome_features in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/genome_features.yaml + GenomeFeatureType: + title: Genome Feature Type + description: 'Genome feature types from SOFA (Sequence Ontology Feature Annotation). + + This is the subset of Sequence Ontology terms used in GFF3 files. + + Organized hierarchically following the Sequence Ontology structure.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + REGION: + description: A sequence feature with an extent greater than zero + meaning: SO:0000001 + BIOLOGICAL_REGION: + description: A region defined by its biological properties + meaning: SO:0001411 + is_a: REGION + GENE: + description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript + meaning: SO:0000704 + is_a: BIOLOGICAL_REGION + TRANSCRIPT: + description: An RNA synthesized on a DNA or RNA template by an RNA polymerase + meaning: SO:0000673 + is_a: BIOLOGICAL_REGION + PRIMARY_TRANSCRIPT: + description: A transcript that has not been processed + meaning: SO:0000185 + is_a: TRANSCRIPT + MRNA: + description: Messenger RNA; includes 5'UTR, coding sequences and 3'UTR + meaning: SO:0000234 + is_a: TRANSCRIPT + EXON: + description: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript + by RNA splicing + meaning: SO:0000147 + is_a: BIOLOGICAL_REGION + CDS: + description: Coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein + meaning: SO:0000316 + is_a: BIOLOGICAL_REGION + INTRON: + description: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing + meaning: SO:0000188 + is_a: BIOLOGICAL_REGION + FIVE_PRIME_UTR: + description: 5' untranslated region + meaning: SO:0000204 + is_a: BIOLOGICAL_REGION + THREE_PRIME_UTR: + description: 3' untranslated region + meaning: SO:0000205 + is_a: BIOLOGICAL_REGION + NCRNA: + description: Non-protein coding RNA + meaning: SO:0000655 is_a: TRANSCRIPT RRNA: description: Ribosomal RNA @@ -2999,9 +5480,16 @@ enums: annotations: source_file: bio/genomics.yaml CdsPhaseType: + title: Cds Phase Type description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PHASE_0: description: Zero bases from reading frame to feature start. @@ -3017,9 +5505,16 @@ enums: source_domain: bio source_schema: genomics ContigCollectionType: + title: Contig Collection Type description: The type of the contig set; the type of the 'omics data set. Terms are taken from the Genomics Standards Consortium where possible. See the GSC checklists at https://genomicsstandardsconsortium.github.io/mixs/ for the controlled vocabularies used. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ISOLATE: description: 'Sequences assembled from DNA of isolated organism. Bacteria/Archaea: https://genomicsstandardsconsortium.github.io/mixs/0010003/ @@ -3029,27 +5524,25 @@ enums: description: Sequences assembled from DNA of mixed community and binned. MAGs are likely to represent a single taxonomic origin. See checkm2 scores for quality assessment. meaning: mixs:0010011 - title: Metagenome-Assembled Genome + title: Mimag aliases: - - Mimag + - Metagenome-Assembled Genome METAGENOME: description: Sequences assembled from DNA of mixed community. meaning: mixs:0010007 - aliases: - - Mims + title: Mims METATRANSCRIPTOME: description: Sequences assembled from RNA of mixed community. Currently not represented by GSC. SAG: description: Sequences assembled from DNA of single cell. meaning: mixs:0010010 - title: Single Amplified Genome + title: Misag aliases: - - Misag + - Single Amplified Genome VIRUS: description: Sequences assembled from uncultivated virus genome (DNA/RNA). meaning: mixs:0010012 - aliases: - - Miuvig + title: Miuvig MARKER: description: 'Sequences from targeted region of DNA; see protocol for information on targeted region. specimen: https://genomicsstandardsconsortium.github.io/mixs/0010009/ survey: https://genomicsstandardsconsortium.github.io/mixs/0010008/' @@ -3058,7 +5551,14 @@ enums: source_domain: bio source_schema: genomics StrandType: + title: Strand Type description: The strand that a feature appears on relative to a landmark. Also encompasses unknown or irrelevant strandedness. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NEGATIVE: description: Represented by "-" in a GFF file; the strand is negative wrt the landmark. @@ -3077,7 +5577,14 @@ enums: source_domain: bio source_schema: genomics SequenceType: + title: Sequence Type description: The type of sequence being represented. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NUCLEIC_ACID: description: A nucleic acid sequence, as found in an FNA file. @@ -3094,7 +5601,19 @@ enums: annotations: source_file: bio/go_aspect.yaml GOAspect: + title: GO Aspect description: The three main aspects (namespaces) of Gene Ontology + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org + source_domain: bio + source_schema: go_aspect permissible_values: F: title: Molecular Function @@ -3118,9 +5637,6 @@ enums: - CC meaning: GO:0005575 is_a: GoAspectSchemaEnum - annotations: - source_domain: bio - source_schema: go_aspect GoCausalitySchemaEnum: description: Schema-level enum for go_causality in bio is_a: BioDomainEnum @@ -3128,8 +5644,20 @@ enums: annotations: source_file: bio/go_causality.yaml CausalPredicateEnum: + title: Causal Predicate description: A term describing the causal relationship between two activities. All terms are drawn from the "causally upstream or within" (RO:0002418) branch of the Relation Ontology (RO). + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org + source_domain: bio + source_schema: go_causality permissible_values: CONSTITUTIVELY_UPSTREAM_OF: title: constitutively upstream of @@ -3231,9 +5759,6 @@ enums: annotations: direction: NEGATIVE is_a: GoCausalitySchemaEnum - annotations: - source_domain: bio - source_schema: go_causality GoEvidenceSchemaEnum: description: Schema-level enum for go_evidence in bio is_a: BioDomainEnum @@ -3241,144 +5766,312 @@ enums: annotations: source_file: bio/go_evidence.yaml GOEvidenceCode: - description: Gene Ontology evidence codes mapped to Evidence and Conclusion Ontology (ECO) terms + title: GO Evidence Code + description: Gene Ontology evidence codes used to describe the type of support for GO annotations. Each code maps to the + Evidence and Conclusion Ontology (ECO). Evidence codes are categorized by whether they represent experimental evidence, + computational analysis, phylogenetic inference, author statements, or electronic annotation. All codes except IEA represent + manual curation. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org + source_domain: bio + source_schema: go_evidence permissible_values: EXP: title: Inferred from Experiment + description: General experimental evidence supporting a GO annotation aliases: - experimental evidence used in manual assertion meaning: ECO:0000269 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: false IDA: title: Inferred from Direct Assay + description: Evidence from a direct assay for the presence or activity of a gene product aliases: - direct assay evidence used in manual assertion meaning: ECO:0000314 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: false IPI: title: Inferred from Physical Interaction + description: Evidence from physical interaction between gene products aliases: - physical interaction evidence used in manual assertion meaning: ECO:0000353 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: false IMP: title: Inferred from Mutant Phenotype + description: Evidence from the phenotype of a mutant allele aliases: - mutant phenotype evidence used in manual assertion meaning: ECO:0000315 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: false IGI: title: Inferred from Genetic Interaction + description: Evidence from genetic interaction between genes aliases: - genetic interaction evidence used in manual assertion meaning: ECO:0000316 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: false IEP: title: Inferred from Expression Pattern + description: Evidence from gene expression pattern data aliases: - expression pattern evidence used in manual assertion meaning: ECO:0000270 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: false HTP: title: Inferred from High Throughput Experiment + description: Evidence from high-throughput experimental methods aliases: - high throughput evidence used in manual assertion meaning: ECO:0006056 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: true HDA: title: Inferred from High Throughput Direct Assay + description: Evidence from high-throughput direct assay experiments aliases: - high throughput direct assay evidence used in manual assertion meaning: ECO:0007005 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: true HMP: title: Inferred from High Throughput Mutant Phenotype + description: Evidence from high-throughput mutant phenotype screening aliases: - high throughput mutant phenotypic evidence used in manual assertion meaning: ECO:0007001 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: true HGI: title: Inferred from High Throughput Genetic Interaction + description: Evidence from high-throughput genetic interaction screening aliases: - high throughput genetic interaction phenotypic evidence used in manual assertion meaning: ECO:0007003 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: true HEP: title: Inferred from High Throughput Expression Pattern + description: Evidence from high-throughput expression profiling aliases: - high throughput expression pattern evidence used in manual assertion meaning: ECO:0007007 + annotations: + is_experimental: true + is_manual: true + is_high_throughput: true IBA: title: Inferred from Biological aspect of Ancestor + description: Evidence from conservation of biological aspect in an ancestral sequence aliases: - biological aspect of ancestor evidence used in manual assertion meaning: ECO:0000318 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_phylogenetic: true IBD: title: Inferred from Biological aspect of Descendant + description: Evidence from conservation of biological aspect in a descendant sequence aliases: - biological aspect of descendant evidence used in manual assertion meaning: ECO:0000319 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_phylogenetic: true IKR: title: Inferred from Key Residues + description: Evidence from phylogenetic analysis showing loss of key residues aliases: - phylogenetic determination of loss of key residues evidence used in manual assertion meaning: ECO:0000320 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_phylogenetic: true IRD: title: Inferred from Rapid Divergence + description: Evidence from rapid divergence from ancestral sequence aliases: - rapid divergence from ancestral sequence evidence used in manual assertion meaning: ECO:0000321 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_phylogenetic: true ISS: title: Inferred from Sequence or structural Similarity + description: Evidence from sequence or structural similarity to another annotated gene product aliases: - sequence similarity evidence used in manual assertion meaning: ECO:0000250 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_computational: true ISO: title: Inferred from Sequence Orthology + description: Evidence from orthology to an experimentally characterized gene product aliases: - sequence orthology evidence used in manual assertion meaning: ECO:0000266 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_computational: true ISA: title: Inferred from Sequence Alignment + description: Evidence from sequence alignment to an annotated gene product aliases: - sequence alignment evidence used in manual assertion meaning: ECO:0000247 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_computational: true ISM: title: Inferred from Sequence Model + description: Evidence from match to a sequence model (e.g., HMM, profile) aliases: - match to sequence model evidence used in manual assertion meaning: ECO:0000255 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_computational: true IGC: title: Inferred from Genomic Context + description: Evidence from genomic context such as synteny or gene neighborhood aliases: - genomic context evidence used in manual assertion meaning: ECO:0000317 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_computational: true RCA: title: Inferred from Reviewed Computational Analysis + description: Evidence from computational analysis that has been reviewed by a curator aliases: - automatically integrated combinatorial evidence used in manual assertion meaning: ECO:0000245 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_computational: true TAS: title: Traceable Author Statement + description: Evidence from an author statement in a published paper that can be traced to the original source aliases: - author statement supported by traceable reference used in manual assertion meaning: ECO:0000304 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_author_statement: true NAS: title: Non-traceable Author Statement + description: Evidence from an author statement that cannot be traced to the experimental source aliases: - author statement without traceable support used in manual assertion meaning: ECO:0000303 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_author_statement: true IC: title: Inferred by Curator + description: Evidence inferred by a curator based on existing annotations and biological knowledge aliases: - curator inference used in manual assertion meaning: ECO:0000305 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false + is_curator_inference: true ND: title: No biological Data available + description: Indicates that no biological data is available to support an annotation aliases: - no evidence data found used in manual assertion meaning: ECO:0000307 + annotations: + is_experimental: false + is_manual: true + is_high_throughput: false IEA: title: Inferred from Electronic Annotation + description: Evidence from automated electronic annotation pipelines without manual curation aliases: - evidence used in automatic assertion meaning: ECO:0000501 + annotations: + is_experimental: false + is_manual: false + is_high_throughput: false + is_electronic: true is_a: GoEvidenceSchemaEnum - annotations: - source_domain: bio - source_schema: go_evidence GOElectronicMethods: + title: GO Electronic Methods description: Electronic annotation methods used in Gene Ontology, identified by GO_REF codes + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org + source_domain: bio + source_schema: go_evidence permissible_values: INTERPRO2GO: title: Gene Ontology annotation based on InterPro classification @@ -3441,9 +6134,6 @@ enums: title: Gene Ontology annotation based on MetaCyc pathways meaning: GO_REF:0000112 is_a: GoEvidenceSchemaEnum - annotations: - source_domain: bio - source_schema: go_evidence InsdcGeographicLocationsSchemaEnum: description: Schema-level enum for insdc_geographic_locations in bio is_a: BioDomainEnum @@ -3451,11 +6141,23 @@ enums: annotations: source_file: bio/insdc_geographic_locations.yaml InsdcGeographicLocationEnum: + title: Insdc Geographic Location description: 'INSDC controlled vocabulary for geographic locations of collected samples. Includes countries, oceans, seas, and other geographic regions as defined by INSDC. Countries use ISO 3166-1 alpha-2 codes from Library of Congress as canonical identifiers.' + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://gensc.org + publishers: https://www.insdc.org + source_domain: bio + source_schema: insdc_geographic_locations permissible_values: AFGHANISTAN: description: Afghanistan @@ -4336,9 +7038,6 @@ enums: description: Zimbabwe meaning: iso3166loc:zw is_a: InsdcGeographicLocationsSchemaEnum - annotations: - source_domain: bio - source_schema: insdc_geographic_locations InsdcMissingValuesSchemaEnum: description: Schema-level enum for insdc_missing_values in bio is_a: BioDomainEnum @@ -4346,8 +7045,20 @@ enums: annotations: source_file: bio/insdc_missing_values.yaml InsdcMissingValueEnum: + title: Insdc Missing Value description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values in sequence records + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://gensc.org + publishers: https://www.insdc.org + source_domain: bio + source_schema: insdc_missing_values permissible_values: NOT_APPLICABLE: description: Information is inappropriate to report, can indicate that the standard itself fails to model or represent @@ -4415,9 +7126,6 @@ enums: annotations: note: No specific ontology term for data withheld due to human identifiability is_a: InsdcMissingValuesSchemaEnum - annotations: - source_domain: bio - source_schema: insdc_missing_values LipidCategoriesSchemaEnum: description: Schema-level enum for lipid_categories in bio is_a: BioDomainEnum @@ -4427,6 +7135,12 @@ enums: LipidCategory: title: Lipid Category description: Major categories of lipids based on SwissLipids classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIPID: description: Lipid @@ -4490,9 +7204,16 @@ enums: annotations: source_file: bio/plant_biology.yaml PlantSexualSystem: + title: Plant Sexual System description: 'Sexual systems in plants, describing the distribution and types of reproductive organs (flowers) within and among individual plants.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANDRODIOECIOUS: text: ANDRODIOECIOUS @@ -4603,8 +7324,15 @@ enums: annotations: source_file: bio/plant_developmental_stages.yaml PlantDevelopmentalStage: + title: Plant Developmental Stage description: Major developmental stages in the plant life cycle, from seed germination through senescence. Based on the Plant Ontology (PO) standardized stages. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SEED_GERMINATION_STAGE: description: Stage beginning with seed imbibition and ending with radicle emergence @@ -4665,6 +7393,201 @@ enums: annotations: source_domain: bio source_schema: plant_developmental_stages + PlantExperimentalConditionsSchemaEnum: + description: Schema-level enum for plant_experimental_conditions in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/plant_experimental_conditions.yaml + PlantExposureEnum: + title: Plant Exposure + description: A plant experimental condition describing the application of an abiotic (chemical, physical) or biotic (pathogen, + insect, plant) exposure. Dynamically populated from PECO. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + reachable_from: + source_ontology: obo:peco + source_nodes: + - PECO:0001001 + include_self: true + relationship_types: + - rdfs:subClassOf + is_a: PlantExperimentalConditionsSchemaEnum + annotations: + source_domain: bio + source_schema: plant_experimental_conditions + PlantStudyConditionEnum: + title: Plant Study Condition + description: The type of plant growth facility used in an experiment, describing whether plants were grown in a field, + greenhouse, growth chamber, or laboratory. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FIELD_STUDY: + title: field study + description: Plants were grown outdoors under field conditions + meaning: PECO:0007256 + GREENHOUSE_STUDY: + title: greenhouse study + description: Plants were grown under greenhouse conditions + meaning: PECO:0007248 + GROWTH_CHAMBER_STUDY: + title: growth chamber study + description: Plants were grown in growth chambers under controlled light and temperature conditions + meaning: PECO:0007269 + LABORATORY_STUDY: + title: laboratory study + description: Plants were grown under in vitro growth conditions in a laboratory + meaning: PECO:0007255 + is_a: PlantExperimentalConditionsSchemaEnum + annotations: + source_domain: bio + source_schema: plant_experimental_conditions + SeasonalEnvironmentExposureEnum: + title: Seasonal Environment Exposure + description: Seasonal conditions during plant growth, including standard seasons and regional agricultural seasons (e.g., + kharif, rabi in South Asia). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SPRING_SEASON: + title: spring season exposure + description: Growth during the spring season + meaning: PECO:0007037 + SUMMER_SEASON: + title: summer season exposure + description: Growth during the summer season + meaning: PECO:0007036 + AUTUMN_SEASON: + title: autumn season exposure + description: Growth during the autumn season + meaning: PECO:0007038 + WINTER_SEASON: + title: winter season exposure + description: Growth during the winter season + meaning: PECO:0007035 + DRY_SEASON: + title: dry season exposure + description: Growth during the dry season + meaning: PECO:0007286 + RAINY_SEASON: + title: rainy season exposure + description: Growth during the wet or rainy season + meaning: PECO:0007285 + KHARIF_SEASON: + title: kharif season exposure + description: Growth during the kharif crop season (May-October) as practiced in South Asia + meaning: PECO:0007034 + RABI_SEASON: + title: rabi season exposure + description: Growth during the rabi crop season (October-March) as practiced in South Asia + meaning: PECO:0007033 + is_a: PlantExperimentalConditionsSchemaEnum + annotations: + source_domain: bio + source_schema: plant_experimental_conditions + EcologicalEnvironmentExposureEnum: + title: Ecological Environment Exposure + description: Ecological or geographical environment conditions during plant growth, including climate zones, altitude, + atmospheric pressure, and land characteristics. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ALTITUDE: + title: altitude exposure + description: Growth at a given elevation or height above sea level + meaning: PECO:0007176 + ATMOSPHERIC_PRESSURE: + title: atmospheric pressure exposure + description: Growth at a given air pressure + meaning: PECO:0007178 + TROPICAL_REGION: + title: tropical region exposure + description: Growth in the geographical region between the Tropics of Cancer and Capricorn + meaning: PECO:0007061 + SUB_TROPICAL_REGION: + title: sub-tropical region exposure + description: Growth in regions adjacent to the tropics (roughly 25-40 degrees latitude) + meaning: PECO:0007398 + TEMPERATE_REGION: + title: temperate region exposure + description: Growth in regions with temperate climate, characterized by roughly equal winters and summers + meaning: PECO:0007003 + DESERT_LIKE_REGION: + title: desert-like region exposure + description: Growth in biome characterized by low moisture and infrequent precipitation + meaning: PECO:0007394 + SEMIARID_REGION: + title: semiarid region exposure + description: Growth in regions with 25-50cm (10-20 inches) annual rainfall + meaning: PECO:0007401 + LOWLAND_REGION: + title: lowland region exposure + description: Growth in slightly steep regions with noncontinuous flooding and alternating aerobic/anaerobic soil + meaning: PECO:0007391 + UPLAND_REGION: + title: upland region exposure + description: Growth in steep regions that are rarely flooded with aerobic soil + meaning: PECO:0007392 + FLOOD_PRONE_REGION: + title: flood-prone region exposure + description: Growth in conditions susceptible to inundation by water + meaning: PECO:0007396 + IRRIGATED_LAND_REGION: + title: irrigated land region exposure + description: Growth in leveled land with water control and shallow flooding + meaning: PECO:0007385 + is_a: PlantExperimentalConditionsSchemaEnum + annotations: + source_domain: bio + source_schema: plant_experimental_conditions + PlantGrowthMediumExposureEnum: + title: Plant Growth Medium Exposure + description: The type of growth medium or substrate used for plant cultivation, including soil, hydroponic, aeroponic, + and in vitro media. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SOIL_ENVIRONMENT: + title: soil environment exposure + description: Growing plants in soil growth media with varying contents + meaning: PECO:0007049 + HYDROPONIC_CULTURE: + title: hydroponic plant culture media exposure + description: Growing plants in liquid growth media + meaning: PECO:0007067 + AEROPONIC_GROWTH: + title: aeroponic plant growth media exposure + description: Growing plants in air and/or mist environment without soil or aggregate medium + meaning: PECO:0001073 + IN_VITRO_GROWTH_MEDIUM: + title: in vitro growth medium exposure + description: In vitro culture using solid or liquid substrate with nutrients and amendments + meaning: PECO:0007266 + is_a: PlantExperimentalConditionsSchemaEnum + annotations: + source_domain: bio + source_schema: plant_experimental_conditions PlantSexSchemaEnum: description: Schema-level enum for plant_sex in bio is_a: BioDomainEnum @@ -4672,7 +7595,14 @@ enums: annotations: source_file: bio/plant_sex.yaml PlantSexEnum: + title: Plant Sex description: Plant reproductive and sexual system types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANDRODIOECIOUS: description: Having male and hermaphrodite flowers on separate plants @@ -4700,7 +7630,6 @@ enums: title: Diclinous DIOECIOUS: description: Having male and female flowers on separate plants - meaning: GSSO:011872 title: Dioecious GYNODIOECIOUS: description: Having female and hermaphrodite flowers on separate plants @@ -4712,9 +7641,9 @@ enums: description: Having female and hermaphrodite flowers on the same plant title: Gynomonoecious HERMAPHRODITIC: + title: hermaphrodite description: Having both male and female reproductive organs - meaning: UBERON:0007197 - title: hermaphroditic organism + meaning: PATO:0001340 IMPERFECT: description: Flower lacking either male or female reproductive organs title: Imperfect @@ -4723,7 +7652,6 @@ enums: title: Monoclinous MONOECIOUS: description: Having male and female flowers on the same plant - meaning: GSSO:011868 title: Monoecious PERFECT: description: Flower having both male and female reproductive organs @@ -4775,8 +7703,15 @@ enums: annotations: source_file: bio/protein_evidence.yaml ProteinEvidenceForExistence: + title: Protein Evidence For Existence description: The evidence for the existence of a biological entity. See https://www.uniprot.org/help/protein_existence and https://www.ncbi.nlm.nih.gov/genbank/evidence/. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL: description: Indicates that there is clear experimental evidence for the existence of the protein. The criteria include @@ -4797,7 +7732,14 @@ enums: source_domain: bio source_schema: protein_evidence RefSeqStatusType: + title: Ref Seq Status Type description: RefSeq status codes, taken from https://www.ncbi.nlm.nih.gov/genbank/evidence/. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MODEL: description: The RefSeq record is provided by the NCBI Genome Annotation pipeline and is not subject to individual @@ -4834,6 +7776,12 @@ enums: PeakAnnotationSeriesLabel: title: Peak Annotation Series Label description: Types of peak annotations in mass spectrometry data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PEPTIDE: description: Peptide fragment ion @@ -4868,6 +7816,12 @@ enums: PeptideIonSeries: title: Peptide Ion Series description: Types of peptide fragment ion series in mass spectrometry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: B: description: B ion series - N-terminal fragment with CO @@ -4916,6 +7870,12 @@ enums: MassErrorUnit: title: Mass Error Unit description: Units for expressing mass error in mass spectrometry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PPM: description: Parts per million - relative mass error @@ -4942,6 +7902,12 @@ enums: InteractionDetectionMethod: title: Interaction Detection Method description: Methods used to detect molecular interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/mi.owl conforms_to: HUPO-PSI annotations: @@ -5011,6 +7977,12 @@ enums: InteractionType: title: Interaction Type description: Types of molecular interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/mi.owl conforms_to: HUPO-PSI permissible_values: @@ -5062,6 +8034,12 @@ enums: ExperimentalRole: title: Experimental Role description: Role played by a participant in the experiment + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/mi.owl conforms_to: HUPO-PSI permissible_values: @@ -5107,49 +8085,35 @@ enums: source_schema: psi_mi BiologicalRole: title: Biological Role - description: Physiological role of an interactor - source: http://purl.obolibrary.org/obo/mi.owl - conforms_to: HUPO-PSI - permissible_values: - ENZYME: - description: Catalytically active molecule - meaning: MI:0501 - ENZYME_TARGET: - description: Substrate of enzymatic activity - meaning: MI:0502 - ELECTRON_DONOR: - description: Donates electrons in reaction - meaning: MI:0579 - ELECTRON_ACCEPTOR: - description: Accepts electrons in reaction - meaning: MI:0580 - INHIBITOR: - description: Inhibits activity or interaction - meaning: MI:0586 - COFACTOR: - description: Required for activity - meaning: MI:0682 - LIGAND: - description: Small molecule binding partner - AGONIST: - description: Activates receptor - meaning: MI:0625 - ANTAGONIST: - description: Blocks receptor activation - meaning: MI:0626 - PHOSPHATE_DONOR: - description: Provides phosphate group - meaning: MI:0842 - PHOSPHATE_ACCEPTOR: - description: Receives phosphate group - meaning: MI:0843 - is_a: PsiMiSchemaEnum - annotations: - source_domain: bio - source_schema: psi_mi + description: Roles played by molecular entities within a biological context, dynamically populated from ChEBI. Includes + biochemical roles, pharmacological roles, physiological roles, and other biological functions. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.ebi.ac.uk/chebi + publishers: https://www.ebi.ac.uk/chebi + source_domain: chemistry + source_schema: roles + reachable_from: + source_nodes: + - CHEBI:24432 + is_direct: false + relationship_types: + - rdfs:subClassOf + is_a: RolesSchemaEnum ParticipantIdentificationMethod: title: Participant Identification Method description: Methods to identify interaction participants + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MASS_SPECTROMETRY: description: MS-based protein identification @@ -5186,6 +8150,12 @@ enums: FeatureType: title: Feature Type description: Molecular features affecting interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BINDING_SITE: description: Region involved in binding @@ -5233,6 +8203,12 @@ enums: InteractorType: title: Interactor Type description: Types of molecular species in interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROTEIN: description: Polypeptide molecule @@ -5283,6 +8259,12 @@ enums: ConfidenceScore: title: Confidence Score Types description: Types of confidence scoring methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INTACT_MISCORE: description: IntAct molecular interaction score @@ -5302,6 +8284,12 @@ enums: ExperimentalPreparation: title: Experimental Preparation description: Sample preparation methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RECOMBINANT_EXPRESSION: description: Expressed in heterologous system @@ -5334,7 +8322,14 @@ enums: annotations: source_file: bio/relationship_to_oxygen.yaml RelToOxygenEnum: + title: Rel To Oxygen description: Organism's relationship to oxygen for growth and survival + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AEROBE: description: Organism that can survive and grow in an oxygenated environment @@ -5376,7 +8371,14 @@ enums: annotations: source_file: bio/sequence_alphabets.yaml DNABaseEnum: + title: DNA Base description: Standard DNA nucleotide bases (canonical) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -5419,7 +8421,14 @@ enums: source_domain: bio source_schema: sequence_alphabets DNABaseExtendedEnum: + title: DNA Base Extended description: Extended DNA alphabet with IUPAC ambiguity codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -5516,7 +8525,14 @@ enums: source_domain: bio source_schema: sequence_alphabets RNABaseEnum: + title: RNA Base description: Standard RNA nucleotide bases (canonical) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -5559,7 +8575,14 @@ enums: source_domain: bio source_schema: sequence_alphabets RNABaseExtendedEnum: + title: RNA Base Extended description: Extended RNA alphabet with IUPAC ambiguity codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -5654,7 +8677,14 @@ enums: source_domain: bio source_schema: sequence_alphabets AminoAcidEnum: + title: Amino Acid description: Standard amino acid single letter codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Alanine @@ -5880,7 +8910,14 @@ enums: source_domain: bio source_schema: sequence_alphabets AminoAcidExtendedEnum: + title: Amino Acid Extended description: Extended amino acid alphabet with ambiguity codes and special characters + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Alanine @@ -6086,7 +9123,14 @@ enums: source_domain: bio source_schema: sequence_alphabets CodonEnum: + title: Codon description: Standard genetic code codons (DNA) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TTT: title: Phenylalanine codon @@ -6417,7 +9461,14 @@ enums: source_domain: bio source_schema: sequence_alphabets NucleotideModificationEnum: + title: Nucleotide Modification description: Common nucleotide modifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FIVE_METHYL_C: title: 5-methylcytosine @@ -6485,7 +9536,14 @@ enums: source_domain: bio source_schema: sequence_alphabets SequenceQualityEnum: + title: Sequence Quality description: Sequence quality indicators (Phred scores) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: Q0: description: Phred quality 0 (100% error probability) @@ -6544,6 +9602,12 @@ enums: description: 'Complete IUPAC nucleotide codes including ambiguous bases for DNA/RNA sequences. Used in FASTA and other sequence formats to represent uncertain nucleotides.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: A @@ -6594,6 +9658,12 @@ enums: StandardAminoAcid: title: Standard Amino Acids description: The 20 standard proteinogenic amino acids with IUPAC single-letter codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: A @@ -6664,6 +9734,12 @@ enums: description: 'Complete IUPAC amino acid codes including standard amino acids, rare amino acids, and ambiguity codes' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: A @@ -6756,6 +9832,12 @@ enums: SequenceAlphabet: title: Sequence Alphabet Types description: Types of sequence alphabets used in bioinformatics + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DNA: description: Deoxyribonucleic acid alphabet (A, T, G, C) @@ -6784,6 +9866,12 @@ enums: description: 'Quality score encoding standards used in FASTQ files and sequencing data. Different platforms and software versions use different ASCII offsets.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SANGER: description: Sanger/Phred+33 (PHRED scores, ASCII offset 33) @@ -6824,6 +9912,12 @@ enums: description: 'NCBI genetic code translation tables for different organisms. Table 1 is the universal genetic code used by most organisms.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TABLE_1: description: Standard genetic code (universal) @@ -6952,6 +10046,12 @@ enums: SequenceStrand: title: DNA/RNA Strand Orientation description: Strand orientation for nucleic acid sequences + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PLUS: title: PLUS @@ -6970,6 +10070,12 @@ enums: SequenceTopology: title: Sequence Topology description: Topological structure of nucleic acid molecules + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LINEAR: description: Linear sequence molecule @@ -6988,6 +10094,12 @@ enums: SequenceModality: title: Sequence Data Modality description: Types of sequence data based on experimental method + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE_CELL: description: Single-cell sequencing data @@ -7018,6 +10130,12 @@ enums: SequencingPlatform: title: Sequencing Platforms and Instruments description: Major DNA/RNA sequencing platforms and instruments used in genomics research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ILLUMINA_HISEQ_2000: description: Illumina HiSeq 2000 @@ -7231,6 +10349,12 @@ enums: SequencingChemistry: title: Sequencing Chemistry Methods description: Fundamental chemical methods used for DNA/RNA sequencing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SEQUENCING_BY_SYNTHESIS: title: SEQUENCING_BY_SYNTHESIS @@ -7272,6 +10396,12 @@ enums: LibraryPreparation: title: Library Preparation Methods description: Methods for preparing sequencing libraries from nucleic acid samples + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GENOMIC_DNA: description: Genomic DNA library preparation @@ -7318,6 +10448,12 @@ enums: SequencingApplication: title: Sequencing Applications description: Primary applications or assays using DNA/RNA sequencing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: WHOLE_GENOME_SEQUENCING: title: WHOLE_GENOME_SEQUENCING @@ -7380,6 +10516,12 @@ enums: ReadType: title: Sequencing Read Types description: Configuration of sequencing reads generated by different platforms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE_END: title: SINGLE_END @@ -7402,6 +10544,12 @@ enums: SequenceFileFormat: title: Sequence File Formats description: Standard file formats used for storing sequence data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FASTA: description: FASTA sequence format @@ -7498,6 +10646,12 @@ enums: DataProcessingLevel: title: Sequence Data Processing Levels description: Levels of processing applied to raw sequencing data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RAW: description: Raw unprocessed sequencing reads @@ -7523,6 +10677,614 @@ enums: annotations: source_domain: bio source_schema: sequencing_platforms + SpecimenProcessingSchemaEnum: + description: Schema-level enum for specimen_processing in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/specimen_processing.yaml + SpecimenPreparationMethodEnum: + title: Specimen Preparation Methods + description: Methods for preparing and preserving biological specimens for analysis. Sourced from NF-OSI metadata dictionary + and Human Cell Atlas standards. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + - https://data.humancellatlas.org/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FFPE: + description: Formalin-fixed, paraffin-embedded tissue preservation + meaning: NCIT:C143028 + aliases: + - Formalin-fixed paraffin-embedded + - formalin-fixed, paraffin-embedded + - FFPE Tissue Block + annotations: + fixative: formalin + embedding: paraffin + FORMALIN_FIXED: + description: Tissue fixed with formalin without paraffin embedding + aliases: + - formalin-fixed + annotations: + fixative: formalin + CRYOPRESERVED: + description: Specimen preserved by freezing with cryoprotectant + meaning: NCIT:C16475 + aliases: + - Cryopreserved + - Cryopreservation + annotations: + temperature: ultra-low + VIABLY_FROZEN: + description: Specimen frozen while maintaining cell viability + aliases: + - Viably frozen + annotations: + viability: preserved + FLASH_FROZEN: + description: Rapid freezing to preserve molecular integrity + aliases: + - Flash frozen + - snap frozen + annotations: + method: rapid freezing + FRESH_COLLECTED: + description: Freshly collected specimen without preservation + aliases: + - Fresh collected + - fresh + annotations: + preservation: none + OCT_EMBEDDED: + description: Tissue embedded in optimal cutting temperature compound + aliases: + - OCT + - OCT embedded + annotations: + embedding: OCT compound + purpose: cryosectioning + RNALATER: + description: Storage in reagent that stabilizes and protects cellular RNA + aliases: + - RNAlater + annotations: + purpose: RNA stabilization + manufacturer: Thermo Fisher + ETHANOL_PRESERVED: + description: Specimen preserved in ethanol + aliases: + - ethanol + annotations: + preservative: ethanol + METHANOL_FIXED: + description: Specimen fixed with methanol + aliases: + - methanol + annotations: + fixative: methanol + ACETONE_FIXED: + description: Specimen fixed with acetone + annotations: + fixative: acetone + PAXgene_FIXED: + description: Tissue fixed using PAXgene tissue system + annotations: + purpose: RNA and DNA preservation + DRIED: + description: Air-dried or desiccated specimen + aliases: + - air-dried + LYOPHILIZED: + description: Freeze-dried specimen + meaning: NCIT:C28150 + aliases: + - freeze-dried + - lyophilization + - Freeze-Drying + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + TissuePreservationEnum: + title: Tissue Preservation Methods + description: Broader categorization of tissue preservation approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FROZEN: + description: Tissue preserved by freezing + meaning: NCIT:C70717 + aliases: + - Frozen Specimen + FIXED: + description: Tissue preserved by chemical fixation + meaning: NCIT:C25219 + aliases: + - Fixation + FRESH: + description: Fresh unfixed tissue + EMBEDDED: + description: Tissue embedded in medium (paraffin, OCT, etc.) + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SpecimenCollectionMethodEnum: + title: Specimen Collection Methods + description: Methods for collecting biological specimens + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BIOPSY: + description: Tissue sample obtained by biopsy + meaning: NCIT:C15189 + aliases: + - Biopsy Procedure + SURGICAL_RESECTION: + description: Tissue obtained during surgical resection + meaning: NCIT:C15329 + aliases: + - Surgical Procedure + AUTOPSY: + description: Specimen obtained at autopsy + meaning: NCIT:C25153 + aliases: + - Autopsy + FINE_NEEDLE_ASPIRATE: + description: Sample obtained by fine needle aspiration + meaning: NCIT:C15361 + aliases: + - FNA + - Fine-Needle Aspiration + CORE_NEEDLE_BIOPSY: + description: Sample obtained by core needle biopsy + meaning: NCIT:C15190 + aliases: + - Needle Biopsy + PUNCH_BIOPSY: + description: Sample obtained by punch biopsy + SWAB: + description: Sample collected by swabbing + VENIPUNCTURE: + description: Blood sample obtained by venipuncture + meaning: NCIT:C28221 + aliases: + - Phlebotomy + LUMBAR_PUNCTURE: + description: CSF sample obtained by lumbar puncture + meaning: NCIT:C15327 + aliases: + - spinal tap + - Lumbar Puncture + LAVAGE: + description: Sample obtained by lavage (washing) + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SpecimenTypeEnum: + title: Biological Specimen Types + description: Types of biological specimens used in research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TISSUE: + description: Solid tissue specimen + meaning: NCIT:C12801 + aliases: + - Tissue + BLOOD: + description: Whole blood specimen + meaning: NCIT:C12434 + aliases: + - Blood + PLASMA: + description: Blood plasma specimen + meaning: NCIT:C13356 + aliases: + - Plasma + SERUM: + description: Blood serum specimen + meaning: NCIT:C13325 + aliases: + - Serum + BUFFY_COAT: + description: Leukocyte-enriched blood fraction + meaning: NCIT:C84507 + aliases: + - Buffy Coat + URINE: + description: Urine specimen + meaning: NCIT:C13283 + aliases: + - Urine + SALIVA: + description: Saliva specimen + meaning: NCIT:C13275 + aliases: + - Saliva + STOOL: + description: Stool/fecal specimen + meaning: NCIT:C13234 + aliases: + - Feces + - fecal + CSF: + description: Cerebrospinal fluid specimen + meaning: NCIT:C12692 + aliases: + - cerebrospinal fluid + - Cerebrospinal Fluid + SWEAT: + description: Sweat specimen + MUCUS: + description: Mucus specimen + BONE_MARROW: + description: Bone marrow specimen + meaning: NCIT:C12431 + aliases: + - Bone Marrow + PRIMARY_TUMOR: + description: Primary tumor tissue specimen + meaning: NCIT:C8509 + aliases: + - Primary Neoplasm + METASTATIC_TUMOR: + description: Metastatic tumor tissue specimen + meaning: NCIT:C3261 + aliases: + - Metastatic Neoplasm + TUMOR_ADJACENT_NORMAL: + description: Normal tissue adjacent to tumor + meaning: NCIT:C164032 + aliases: + - Tumor-Adjacent Normal Specimen + ORGANOID: + description: Organoid specimen + meaning: NCIT:C172259 + aliases: + - Organoid + SPHEROID: + description: Cell spheroid specimen + MICROTISSUE: + description: Engineered microtissue specimen + PDX_TISSUE: + description: Patient-derived xenograft tissue + meaning: NCIT:C122936 + aliases: + - PDX tissue + - Patient Derived Xenograft + CDX_TISSUE: + description: Cell line-derived xenograft tissue + aliases: + - CDX tissue + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + AnalyteTypeEnum: + title: Analyte Types + description: Types of analytes that can be extracted from biological specimens for molecular analysis. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://github.com/RTIInternational/NHLBI-BDC-DMC-HM + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + DNA: + description: Deoxyribonucleic acid + meaning: NCIT:C198567 + aliases: + - DNA Specimen + RNA: + description: Ribonucleic acid + meaning: NCIT:C198568 + aliases: + - RNA Specimen + TOTAL_RNA: + description: Total RNA including all RNA species + FFPE_DNA: + description: DNA extracted from formalin-fixed paraffin-embedded tissue + aliases: + - Formalin-Fixed Paraffin-Embedded DNA + FFPE_RNA: + description: RNA extracted from formalin-fixed paraffin-embedded tissue + aliases: + - Formalin-Fixed Paraffin-Embedded RNA + cfDNA: + description: Cell-free DNA found in blood plasma + meaning: NCIT:C128274 + aliases: + - Circulating Cell-Free DNA + - cell-free DNA + PROTEIN: + description: Protein analyte + meaning: NCIT:C17021 + aliases: + - Protein + NUCLEI_RNA: + description: RNA isolated from cell nuclei + REPLI_G_DNA: + description: Whole genome amplified DNA using Repli-G technology + aliases: + - Repli-G (Qiagen) DNA + REPLI_G_X_DNA: + description: Whole genome amplified DNA using Repli-G X technology + aliases: + - Repli-G X (Qiagen) DNA + REPLI_G_POOLED_DNA: + description: Pooled whole genome amplified DNA using Repli-G + aliases: + - Repli-G Pooled (Qiagen) DNA + GENOMEPLEX_DNA: + description: Whole genome amplified DNA using GenomePlex technology + aliases: + - GenomePlex (Rubicon) Amplified DNA + EBV_IMMORTALIZED: + description: DNA/cells from EBV immortalized cell lines + aliases: + - EBV Immortalized Normal + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SourceMaterialTypeEnum: + title: Source Material Types + description: Types of source materials from which specimens are derived, particularly relevant for cancer and tissue banking + research. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://github.com/RTIInternational/NHLBI-BDC-DMC-HM + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PRIMARY_TUMOR: + description: Primary tumor tissue + meaning: NCIT:C8509 + aliases: + - Primary Neoplasm + METASTATIC: + description: Metastatic tumor tissue + meaning: NCIT:C3261 + aliases: + - Metastatic Neoplasm + RECURRENT_TUMOR: + description: Recurrent tumor tissue + meaning: NCIT:C4798 + aliases: + - Recurrent Neoplasm + BLOOD_DERIVED_NORMAL: + description: Normal cells derived from blood + BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: + description: Cancer cells from peripheral blood + BLOOD_DERIVED_CANCER_BONE_MARROW: + description: Cancer cells from bone marrow + BONE_MARROW_NORMAL: + description: Normal bone marrow cells + SOLID_TISSUE_NORMAL: + description: Normal solid tissue + BUCCAL_CELL_NORMAL: + description: Normal buccal (cheek) cells + NORMAL_ADJACENT_TISSUE: + description: Normal tissue adjacent to tumor + meaning: NCIT:C164032 + aliases: + - Tumor-Adjacent Normal Specimen + CELL_LINES: + description: Established cell lines + meaning: NCIT:C16403 + aliases: + - Cell Line + PRIMARY_XENOGRAFT_TISSUE: + description: Tissue from primary xenograft + XENOGRAFT_TISSUE: + description: Tissue derived from xenograft models + NEXT_GENERATION_CANCER_MODEL: + description: Tissue from next-generation cancer models + PLEURAL_EFFUSION: + description: Fluid from pleural effusion + meaning: NCIT:C3331 + aliases: + - Pleural Effusion + SALIVA: + description: Saliva specimen + meaning: NCIT:C13275 + aliases: + - Saliva + GRANULOCYTES: + description: Granulocyte cells + meaning: NCIT:C12530 + aliases: + - Granulocyte + EBV_IMMORTALIZED_NORMAL: + description: EBV immortalized normal cells + CONTROL_ANALYTE: + description: Control analyte material + FFPE_SCROLLS: + description: FFPE tissue scrolls + FFPE_RECURRENT: + description: FFPE tissue from recurrent tumor + NOT_REPORTED: + description: Source material type not reported + UNKNOWN: + description: Unknown source material type + meaning: NCIT:C17998 + aliases: + - Unknown + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SpecimenCreationActivityTypeEnum: + title: Specimen Creation Activity Types + description: High-level types of activities through which specimens are generated, either by collection from source or + derivation from existing specimens. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + COLLECTION_FROM_SOURCE: + description: Activity that collects an initial sample directly from a subject or source + meaning: OBI:0000659 + aliases: + - specimen collection process + DERIVATION_FROM_SPECIMEN: + description: Activity that derives a new specimen from an existing one + meaning: OBI:0000094 + aliases: + - material processing + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SpecimenProcessingActivityTypeEnum: + title: Specimen Processing Activity Types + description: High-level types of specimen processing activities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FIXATION: + description: Chemical preservation to maintain structural and molecular features + meaning: NCIT:C25219 + aliases: + - Fixation + FREEZING: + description: Processing activity that freezes a specimen + meaning: NCIT:C70717 + aliases: + - Frozen Specimen + MOUNTING: + description: Securing a specimen in place for examination + PRESERVATION: + description: Processing activity that preserves a specimen for storage + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SpecimenQualityObservationTypeEnum: + title: Specimen Quality Observation Types + description: Types of measurements that reflect specimen quality or suitability for use + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + A260_A280_RATIO: + description: Ratio of absorbance at 260nm to 280nm wavelength for nucleic acid purity + RIBOSOMAL_RNA_28S_16S_RATIO: + description: Ratio of 28S to 16S ribosomal RNA for RNA integrity + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SpecimenQualityObservationMethodEnum: + title: Specimen Quality Observation Methods + description: Methods used for determining specimen quality + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + UV_SPEC: + description: UV-Vis spectrophotometry measuring absorbance across UV and visible ranges + meaning: NCIT:C116701 + aliases: + - Spectrophotometry + PICO_GREEN: + description: Fluorescent dye assay for quantifying double-stranded DNA + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SpecimenQuantityObservationTypeEnum: + title: Specimen Quantity Observation Types + description: Types of quantity measurements for specimens + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + WEIGHT: + description: Current weight of the specimen + meaning: NCIT:C25208 + aliases: + - Weight + VOLUME: + description: Current volume of the specimen + meaning: NCIT:C25335 + aliases: + - Volume + CONCENTRATION: + description: Concentration of extracted analyte in specimen + meaning: NCIT:C41185 + aliases: + - Concentration + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing + SectionLocationEnum: + title: Section Location + description: Location in a parent specimen from which a section was excised + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TOP: + description: The top portion of a specimen per orientation criteria + BOTTOM: + description: The bottom portion of a specimen per orientation criteria + UNKNOWN: + description: Unknown location on a specimen + meaning: NCIT:C17998 + aliases: + - Unknown + is_a: SpecimenProcessingSchemaEnum + annotations: + source_domain: bio + source_schema: specimen_processing StructuralBiologySchemaEnum: description: Schema-level enum for structural_biology in bio is_a: BioDomainEnum @@ -7530,30 +11292,54 @@ enums: annotations: source_file: bio/structural_biology.yaml SampleType: + title: Sample Type description: Types of biological samples used in structural biology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROTEIN: description: Purified protein sample + meaning: NCIT:C17021 NUCLEIC_ACID: + title: Nucleic Acids description: Nucleic acid sample (DNA or RNA) + meaning: NCIT:C706 PROTEIN_COMPLEX: + title: protein-containing complex description: Protein-protein or protein-nucleic acid complex + meaning: GO:0032991 MEMBRANE_PROTEIN: description: Membrane-associated protein sample + meaning: NCIT:C16837 VIRUS: description: Viral particle or capsid + meaning: NCIT:C14283 ORGANELLE: description: Cellular organelle (mitochondria, chloroplast, etc.) + meaning: GO:0043226 CELL: description: Whole cell sample + meaning: NCIT:C12508 TISSUE: description: Tissue sample + meaning: NCIT:C12801 is_a: StructuralBiologySchemaEnum annotations: source_domain: bio source_schema: structural_biology StructuralBiologyTechnique: + title: Structural Biology Technique description: Structural biology experimental techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CRYO_EM: title: cryogenic electron microscopy @@ -7563,7 +11349,9 @@ enums: resolution_range: 2-30 Å typical aliases: cryoEM, electron cryo-microscopy CRYO_ET: + title: electron tomography description: Cryo-electron tomography + meaning: MI:2338 annotations: resolution_range: 20-100 Å typical aliases: cryoET, electron cryo-tomography @@ -7575,7 +11363,9 @@ enums: resolution_range: 1-4 Å typical aliases: XRC, macromolecular crystallography NEUTRON_CRYSTALLOGRAPHY: + title: neutron diffraction description: Neutron crystallography + meaning: CHMO:0000698 annotations: advantages: hydrogen positions, deuteration studies SAXS: @@ -7585,11 +11375,15 @@ enums: annotations: information: low-resolution structure, conformational changes SANS: + title: small-angle neutron scattering description: Small-angle neutron scattering + meaning: CHMO:0000184 annotations: advantages: contrast variation with deuteration WAXS: + title: wide-angle X-ray scattering description: Wide-angle X-ray scattering + meaning: CHMO:0000207 NMR: title: nuclear magnetic resonance spectroscopy description: Nuclear magnetic resonance spectroscopy @@ -7602,7 +11396,9 @@ enums: annotations: applications: native MS, crosslinking, HDX NEGATIVE_STAIN_EM: + title: negative staining description: Negative stain electron microscopy + meaning: FBbi:00000399 annotations: resolution_range: 15-30 Å typical is_a: StructuralBiologySchemaEnum @@ -7610,7 +11406,14 @@ enums: source_domain: bio source_schema: structural_biology CryoEMPreparationType: + title: Cryo EM Preparation Type description: Types of cryo-EM sample preparation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VITREOUS_ICE: description: Sample embedded in vitreous ice @@ -7625,7 +11428,14 @@ enums: source_domain: bio source_schema: structural_biology CryoEMGridType: + title: Cryo EM Grid Type description: Types of electron microscopy grids + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: C_FLAT: description: C-flat holey carbon grid @@ -7658,7 +11468,14 @@ enums: source_domain: bio source_schema: structural_biology VitrificationMethod: + title: Vitrification Method description: Methods for sample vitrification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PLUNGE_FREEZING: description: Plunge freezing in liquid ethane @@ -7683,7 +11500,14 @@ enums: source_domain: bio source_schema: structural_biology CrystallizationMethod: + title: Crystallization Method description: Methods for protein crystallization + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VAPOR_DIFFUSION_HANGING: description: Vapor diffusion hanging drop method @@ -7717,10 +11541,20 @@ enums: source_domain: bio source_schema: structural_biology XRaySource: + title: X Ray Source description: Types of X-ray sources + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SYNCHROTRON: description: Synchrotron radiation source + meaning: CHMO:0001810 + exact_mappings: + - NCIT:C48205 annotations: advantages: high intensity, tunable wavelength brightness: 10^15-10^18 photons/s/mm²/mrad² @@ -7744,7 +11578,14 @@ enums: source_domain: bio source_schema: structural_biology Detector: + title: Detector description: Types of detectors for structural biology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DIRECT_ELECTRON: description: Direct electron detector (DED) @@ -7752,7 +11593,9 @@ enums: examples: K2, K3, Falcon, DE-series advantages: high DQE, fast readout CCD: + title: charge-coupled-device detector description: Charge-coupled device camera + meaning: CHMO:0002245 annotations: applications: legacy EM, some crystallography CMOS: @@ -7773,7 +11616,14 @@ enums: source_domain: bio source_schema: structural_biology WorkflowType: + title: Workflow Type description: Types of computational processing workflows + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MOTION_CORRECTION: description: Motion correction for cryo-EM movies @@ -7829,7 +11679,14 @@ enums: source_domain: bio source_schema: structural_biology FileFormat: + title: File Format description: File formats used in structural biology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MRC: description: MRC format for EM density maps @@ -7838,11 +11695,13 @@ enums: applications: EM volumes, tomograms TIFF: description: Tagged Image File Format + meaning: EDAM:format_3591 annotations: extension: .tif, .tiff applications: micrographs, general imaging HDF5: description: Hierarchical Data Format 5 + meaning: EDAM:format_3590 annotations: extension: .h5, .hdf5 applications: large datasets, metadata storage @@ -7853,11 +11712,17 @@ enums: applications: RELION metadata, particle parameters PDB: description: Protein Data Bank coordinate format + meaning: EDAM:format_1476 + exact_mappings: + - OBI:0001525 annotations: extension: .pdb applications: atomic coordinates, legacy format MMCIF: description: Macromolecular Crystallographic Information File + meaning: EDAM:format_1477 + exact_mappings: + - NCIT:C133997 annotations: extension: .cif applications: atomic coordinates, modern PDB format @@ -7886,7 +11751,14 @@ enums: source_domain: bio source_schema: structural_biology DataType: + title: Data Type description: Types of structural biology data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MICROGRAPH: description: Electron micrograph image @@ -7929,7 +11801,14 @@ enums: source_domain: bio source_schema: structural_biology ProcessingStatus: + title: Processing Status description: Status of data processing workflows + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RAW: description: Raw unprocessed data @@ -7951,6 +11830,178 @@ enums: annotations: source_domain: bio source_schema: structural_biology + CoordinationGeometry: + title: Coordination Geometry + description: Coordination geometry of metal centers in protein structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LINEAR: + description: Linear coordination geometry (2 ligands at 180°) + annotations: + coordination_number: '2' + TRIGONAL_PLANAR: + description: Trigonal planar coordination geometry (3 ligands, 120° angles) + annotations: + coordination_number: '3' + TRIGONAL_PYRAMIDAL: + description: Trigonal pyramidal coordination geometry + annotations: + coordination_number: '3' + T_SHAPED: + description: T-shaped coordination geometry + annotations: + coordination_number: '3' + TETRAHEDRAL: + title: tetrahedral molecular geometry + description: Tetrahedral coordination geometry (4 ligands, 109.5° angles) + meaning: NCIT:C103215 + annotations: + coordination_number: '4' + SQUARE_PLANAR: + title: Square Planar 1 Molecular Geometry + description: Square planar coordination geometry (4 ligands in plane) + meaning: NCIT:C103211 + annotations: + coordination_number: '4' + TRIGONAL_BIPYRAMIDAL: + description: Trigonal bipyramidal coordination geometry (5 ligands) + annotations: + coordination_number: '5' + SQUARE_PYRAMIDAL: + description: Square pyramidal coordination geometry (5 ligands) + annotations: + coordination_number: '5' + PENTAGONAL_PLANAR: + description: Pentagonal planar coordination geometry (5 ligands in plane) + annotations: + coordination_number: '5' + OCTAHEDRAL: + title: Octahedral 12 Molecular Geometry + description: Octahedral coordination geometry (6 ligands) + meaning: NCIT:C103216 + annotations: + coordination_number: '6' + TRIGONAL_PRISMATIC: + description: Trigonal prismatic coordination geometry (6 ligands) + annotations: + coordination_number: '6' + PENTAGONAL_BIPYRAMIDAL: + description: Pentagonal bipyramidal coordination geometry (7 ligands) + annotations: + coordination_number: '7' + HEXAGONAL_BIPYRAMIDAL: + description: Hexagonal bipyramidal coordination geometry (8 ligands) + annotations: + coordination_number: '8' + SQUARE_ANTIPRISMATIC: + description: Square antiprismatic coordination geometry (8 ligands) + annotations: + coordination_number: '8' + DODECAHEDRAL: + description: Dodecahedral coordination geometry (8 ligands) + annotations: + coordination_number: '8' + CUBIC: + description: Cubic coordination geometry (8 ligands) + annotations: + coordination_number: '8' + BENT: + description: Bent or angular coordination geometry + annotations: + coordination_number: '2' + SEE_SAW: + description: See-saw coordination geometry (4 ligands) + annotations: + coordination_number: '4' + is_a: StructuralBiologySchemaEnum + annotations: + source_domain: bio + source_schema: structural_biology + MetalLigandType: + title: Metal Ligand Type + description: Types of metal-containing chemical components + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + METAL_CATION: + description: Metal cation (e.g., Ca2+, Mg2+, Zn2+, Fe3+) + annotations: + examples: Ca2+, Mg2+, Zn2+, Fe2+, Fe3+, Cu2+, Mn2+ + METAL_CONTAINING_LIGAND: + description: Metal-containing ligand or cofactor + annotations: + examples: heme, chlorophyll, cobalamin, Fe-S cluster + is_a: StructuralBiologySchemaEnum + annotations: + source_domain: bio + source_schema: structural_biology + ProteinModificationType: + title: Protein Modification Type + description: Types of protein modifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + METAL_COORDINATION: + title: iron-sulfur cluster containing modification + description: Metal coordination modification + meaning: MOD:00739 + annotations: + examples: zinc finger, iron-sulfur cluster binding + PHOSPHORYLATION: + title: phosphorylated residue + description: Phosphorylation modification + meaning: MOD:00696 + GLYCOSYLATION: + title: complex glycosylation + description: Glycosylation modification + meaning: MOD:00725 + ACETYLATION: + title: monoacetylated residue + description: Acetylation modification + meaning: MOD:00394 + METHYLATION: + title: monomethylated residue + description: Methylation modification + meaning: MOD:00599 + UBIQUITINATION: + title: ubiquitination signature tetrapeptidyl lysine + description: Ubiquitination modification + meaning: MOD:01240 + SUMOYLATION: + title: sumoylated lysine + description: SUMOylation modification + meaning: MOD:01149 + HYDROXYLATION: + title: hydroxylated residue + description: Hydroxylation modification + meaning: MOD:00677 + LIPIDATION: + description: Lipidation modification + PROTEOLYTIC_CLEAVAGE: + title: proteolysis + description: Proteolytic cleavage + meaning: GO:0006508 + CROSSLINKING: + title: crosslinked residues + description: Crosslinking modification + meaning: MOD:00033 + is_a: StructuralBiologySchemaEnum + annotations: + source_domain: bio + source_schema: structural_biology TaxonomySchemaEnum: description: Schema-level enum for taxonomy in bio is_a: BioDomainEnum @@ -7958,6 +12009,13 @@ enums: annotations: source_file: bio/taxonomy.yaml OrganismTaxonEnum: + title: Organism Taxon + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - NCBITaxon:1 @@ -7970,7 +12028,14 @@ enums: source_domain: bio source_schema: taxonomy CommonOrganismTaxaEnum: + title: Common Organism Taxa description: Common model organisms used in biological research, mapped to NCBI Taxonomy IDs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BACTERIA: description: Bacteria domain @@ -8323,7 +12388,14 @@ enums: source_domain: bio source_schema: taxonomy TaxonomicRank: + title: Taxonomic Rank description: Standard taxonomic ranks used in biological classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DOMAIN: description: Domain (highest rank) @@ -8371,7 +12443,14 @@ enums: source_domain: bio source_schema: taxonomy BiologicalKingdom: + title: Biological Kingdom description: Major kingdoms/domains of life + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BACTERIA: description: Bacteria domain @@ -8402,6 +12481,166 @@ enums: annotations: source_domain: bio source_schema: taxonomy + TransplantationSchemaEnum: + description: Schema-level enum for transplantation in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/transplantation.yaml + TransplantationTypeEnum: + title: Transplantation Types + description: Classification of transplants based on the genetic relationship between donor and recipient organisms. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + XENOGRAFT: + description: Transplantation of cells, tissues, or organs between animals of different species + meaning: NCIT:C12932 + aliases: + - xenotransplant + - heterograft + annotations: + donor_recipient: different species + example: human tumor in mouse + ALLOGRAFT: + description: Transplantation of cells, tissues, or organs between genetically different individuals of the same species + meaning: SNOMED:7970006 + aliases: + - allogeneic transplant + - homograft + annotations: + donor_recipient: same species, different individual + example: bone marrow transplant + AUTOGRAFT: + description: Transplantation of tissue from one body location to another within the same individual + meaning: NCIT:C40997 + aliases: + - autologous transplant + - autotransplant + annotations: + donor_recipient: same individual + example: skin graft, autologous stem cell transplant + ISOGRAFT: + description: Transplantation of cells, tissues, or organs between genetically identical individuals (e.g., identical + twins, inbred strains) + meaning: NCIT:C41000 + aliases: + - syngeneic transplant + - isogeneic transplant + annotations: + donor_recipient: genetically identical + example: transplant between identical twins + is_a: TransplantationSchemaEnum + annotations: + source_domain: bio + source_schema: transplantation + XenograftModelEnum: + title: Xenograft Model Types + description: Types of xenograft models used in cancer and disease research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PDX: + description: Patient-derived xenograft - tumor tissue directly from patient + meaning: NCIT:C122738 + aliases: + - patient-derived xenograft + annotations: + source: patient tumor + passage: primary or passaged + CDX: + description: Cell line-derived xenograft - from established cell lines + aliases: + - cell line-derived xenograft + annotations: + source: cell line + PDOX: + description: Patient-derived orthotopic xenograft + aliases: + - patient-derived orthotopic xenograft + annotations: + implantation: orthotopic site + HUMANIZED_MOUSE: + description: Mouse engrafted with human immune cells + meaning: NCIT:C122961 + aliases: + - humanized mouse model + annotations: + engraftment: human immune system + is_a: TransplantationSchemaEnum + annotations: + source_domain: bio + source_schema: transplantation + ModelSystemTypeEnum: + title: Research Model System Types + description: Types of model systems used in biological research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CELL_LINE: + description: Immortalized or primary cell lines + meaning: NCIT:C16403 + PRIMARY_CELLS: + description: Primary cells directly from tissue + meaning: NCIT:C70598 + ORGANOID: + description: Three-dimensional organ-like cultures + meaning: NCIT:C172259 + SPHEROID: + description: Three-dimensional cell aggregates + meaning: NCIT:C176153 + TISSUE_EXPLANT: + description: Tissue explant culture + meaning: NCIT:C127861 + ANIMAL_MODEL: + description: In vivo animal model + meaning: NCIT:C71164 + TRANSGENIC_MODEL: + description: Genetically engineered transgenic animal + meaning: NCIT:C14348 + KNOCKOUT_MODEL: + description: Gene knockout animal model + meaning: NCIT:C14341 + KNOCKIN_MODEL: + description: Gene knock-in animal model + PDX_MODEL: + description: Patient-derived xenograft model + meaning: NCIT:C122738 + GEMM: + description: Genetically engineered mouse model + aliases: + - genetically engineered mouse model + ZEBRAFISH_MODEL: + description: Zebrafish disease model + DROSOPHILA_MODEL: + description: Drosophila (fruit fly) disease model + C_ELEGANS_MODEL: + description: C. elegans disease model + YEAST_MODEL: + description: Yeast genetic model + IPSC_DERIVED: + description: Induced pluripotent stem cell-derived model + meaning: EFO:0004905 + aliases: + - iPSC-derived + is_a: TransplantationSchemaEnum + annotations: + source_domain: bio + source_schema: transplantation TrophicLevelsSchemaEnum: description: Schema-level enum for trophic_levels in bio is_a: BioDomainEnum @@ -8409,7 +12648,14 @@ enums: annotations: source_file: bio/trophic_levels.yaml TrophicLevelEnum: + title: Trophic Level description: Trophic levels are the feeding position in a food chain + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AUTOTROPH: description: Organism capable of synthesizing its own food from inorganic substances @@ -8523,7 +12769,14 @@ enums: annotations: source_file: bio/uniprot_species.yaml UniProtSpeciesCode: + title: Uni Prot Species Code description: UniProt species mnemonic codes for reference proteomes with associated metadata + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SP_9ABAC: description: 'Lambdina fiscellaria nucleopolyhedrovirus - Proteome: UP000201190' @@ -8532,6 +12785,8 @@ enums: exact_mappings: - NCBITaxon:1642929 - uniprot.proteome:UP000201190 + annotations: + sources: existing SP_9ACAR: description: 'Tropilaelaps mercedesae - Proteome: UP000192247' meaning: NCBITaxon:418985 @@ -8539,6 +12794,8 @@ enums: exact_mappings: - NCBITaxon:418985 - uniprot.proteome:UP000192247 + annotations: + sources: existing SP_9ACTN: description: 'Candidatus Protofrankia datiscae - Proteome: UP000001549' meaning: NCBITaxon:2716812 @@ -8546,6 +12803,8 @@ enums: exact_mappings: - NCBITaxon:2716812 - uniprot.proteome:UP000001549 + annotations: + sources: existing SP_9ACTO: description: 'Actinomyces massiliensis F0489 - Proteome: UP000002941' meaning: NCBITaxon:1125718 @@ -8553,6 +12812,8 @@ enums: exact_mappings: - NCBITaxon:1125718 - uniprot.proteome:UP000002941 + annotations: + sources: existing SP_9ADEN: description: 'Human adenovirus 53 - Proteome: UP000463865' meaning: NCBITaxon:556926 @@ -8560,6 +12821,8 @@ enums: exact_mappings: - NCBITaxon:556926 - uniprot.proteome:UP000463865 + annotations: + sources: existing SP_9AGAM: description: 'Jaapia argillacea MUCL 33604 - Proteome: UP000027265' meaning: NCBITaxon:933084 @@ -8567,6 +12830,8 @@ enums: exact_mappings: - NCBITaxon:933084 - uniprot.proteome:UP000027265 + annotations: + sources: existing SP_9AGAR: description: 'Collybiopsis luxurians FD-317 M1 - Proteome: UP000053593' meaning: NCBITaxon:944289 @@ -8574,6 +12839,8 @@ enums: exact_mappings: - NCBITaxon:944289 - uniprot.proteome:UP000053593 + annotations: + sources: existing SP_9ALPC: description: 'Feline coronavirus - Proteome: UP000141821' meaning: NCBITaxon:12663 @@ -8581,6 +12848,8 @@ enums: exact_mappings: - NCBITaxon:12663 - uniprot.proteome:UP000141821 + annotations: + sources: existing SP_9ALPH: description: 'Testudinid alphaherpesvirus 3 - Proteome: UP000100290' meaning: NCBITaxon:2560801 @@ -8588,6 +12857,8 @@ enums: exact_mappings: - NCBITaxon:2560801 - uniprot.proteome:UP000100290 + annotations: + sources: existing SP_9ALTE: description: 'Paraglaciecola arctica BSs20135 - Proteome: UP000006327' meaning: NCBITaxon:493475 @@ -8595,6 +12866,8 @@ enums: exact_mappings: - NCBITaxon:493475 - uniprot.proteome:UP000006327 + annotations: + sources: existing SP_9ALVE: description: 'Perkinsus sp. BL_2016 - Proteome: UP000298064' meaning: NCBITaxon:2494336 @@ -8602,6 +12875,8 @@ enums: exact_mappings: - NCBITaxon:2494336 - uniprot.proteome:UP000298064 + annotations: + sources: existing SP_9AMPH: description: 'Microcaecilia unicolor - Proteome: UP000515156' meaning: NCBITaxon:1415580 @@ -8609,6 +12884,8 @@ enums: exact_mappings: - NCBITaxon:1415580 - uniprot.proteome:UP000515156 + annotations: + sources: existing SP_9ANNE: description: 'Dimorphilus gyrociliatus - Proteome: UP000549394' meaning: NCBITaxon:2664684 @@ -8616,13 +12893,17 @@ enums: exact_mappings: - NCBITaxon:2664684 - uniprot.proteome:UP000549394 + annotations: + sources: existing SP_9ANUR: - description: 'Leptobrachium leishanense (Leishan spiny toad) - Proteome: UP000694569' + description: 'Leptobrachium leishanense - Proteome: UP000694569' meaning: NCBITaxon:445787 title: Leptobrachium leishanense exact_mappings: - NCBITaxon:445787 - uniprot.proteome:UP000694569 + annotations: + sources: existing SP_9APHY: description: 'Fibroporia radiculosa - Proteome: UP000006352' meaning: NCBITaxon:599839 @@ -8630,6 +12911,8 @@ enums: exact_mappings: - NCBITaxon:599839 - uniprot.proteome:UP000006352 + annotations: + sources: existing SP_9APIA: description: 'Heracleum sosnowskyi - Proteome: UP001237642' meaning: NCBITaxon:360622 @@ -8637,6 +12920,8 @@ enums: exact_mappings: - NCBITaxon:360622 - uniprot.proteome:UP001237642 + annotations: + sources: existing SP_9APIC: description: 'Babesia sp. Xinjiang - Proteome: UP000193856' meaning: NCBITaxon:462227 @@ -8644,6 +12929,8 @@ enums: exact_mappings: - NCBITaxon:462227 - uniprot.proteome:UP000193856 + annotations: + sources: existing SP_9AQUI: description: 'Sulfurihydrogenibium yellowstonense SS-5 - Proteome: UP000005540' meaning: NCBITaxon:432331 @@ -8651,6 +12938,8 @@ enums: exact_mappings: - NCBITaxon:432331 - uniprot.proteome:UP000005540 + annotations: + sources: existing SP_9ARAC: description: 'Trichonephila inaurata madagascariensis - Proteome: UP000886998' meaning: NCBITaxon:2747483 @@ -8658,6 +12947,8 @@ enums: exact_mappings: - NCBITaxon:2747483 - uniprot.proteome:UP000886998 + annotations: + sources: existing SP_9ARCH: description: 'Candidatus Nitrosarchaeum limnium BG20 - Proteome: UP000014065' meaning: NCBITaxon:859192 @@ -8665,6 +12956,8 @@ enums: exact_mappings: - NCBITaxon:859192 - uniprot.proteome:UP000014065 + annotations: + sources: existing SP_9ASCO: description: 'Kuraishia capsulata CBS 1993 - Proteome: UP000019384' meaning: NCBITaxon:1382522 @@ -8672,6 +12965,8 @@ enums: exact_mappings: - NCBITaxon:1382522 - uniprot.proteome:UP000019384 + annotations: + sources: existing SP_9ASPA: description: 'Dendrobium catenatum - Proteome: UP000233837' meaning: NCBITaxon:906689 @@ -8679,6 +12974,8 @@ enums: exact_mappings: - NCBITaxon:906689 - uniprot.proteome:UP000233837 + annotations: + sources: existing SP_9ASTE: description: 'Cuscuta australis - Proteome: UP000249390' meaning: NCBITaxon:267555 @@ -8686,6 +12983,8 @@ enums: exact_mappings: - NCBITaxon:267555 - uniprot.proteome:UP000249390 + annotations: + sources: existing SP_9ASTR: description: 'Mikania micrantha - Proteome: UP000326396' meaning: NCBITaxon:192012 @@ -8693,13 +12992,17 @@ enums: exact_mappings: - NCBITaxon:192012 - uniprot.proteome:UP000326396 + annotations: + sources: existing SP_9AVES: - description: 'Anser brachyrhynchus (Pink-footed goose) - Proteome: UP000694426' + description: 'Anser brachyrhynchus - Proteome: UP000694426' meaning: NCBITaxon:132585 title: Anser brachyrhynchus exact_mappings: - NCBITaxon:132585 - uniprot.proteome:UP000694426 + annotations: + sources: existing SP_9BACE: description: 'Bacteroides caccae CL03T12C61 - Proteome: UP000002965' meaning: NCBITaxon:997873 @@ -8707,6 +13010,8 @@ enums: exact_mappings: - NCBITaxon:997873 - uniprot.proteome:UP000002965 + annotations: + sources: existing SP_9BACI: description: 'Fictibacillus macauensis ZFHKF-1 - Proteome: UP000004080' meaning: NCBITaxon:1196324 @@ -8714,6 +13019,8 @@ enums: exact_mappings: - NCBITaxon:1196324 - uniprot.proteome:UP000004080 + annotations: + sources: existing SP_9BACL: description: 'Paenibacillus sp. HGF7 - Proteome: UP000003445' meaning: NCBITaxon:944559 @@ -8721,6 +13028,8 @@ enums: exact_mappings: - NCBITaxon:944559 - uniprot.proteome:UP000003445 + annotations: + sources: existing SP_9BACT: description: 'Parabacteroides johnsonii CL02T12C29 - Proteome: UP000001218' meaning: NCBITaxon:999419 @@ -8728,6 +13037,8 @@ enums: exact_mappings: - NCBITaxon:999419 - uniprot.proteome:UP000001218 + annotations: + sources: existing SP_9BACU: description: 'Samia ricini nucleopolyhedrovirus - Proteome: UP001226138' meaning: NCBITaxon:1920700 @@ -8735,6 +13046,8 @@ enums: exact_mappings: - NCBITaxon:1920700 - uniprot.proteome:UP001226138 + annotations: + sources: existing SP_9BASI: description: 'Malassezia pachydermatis - Proteome: UP000037751' meaning: NCBITaxon:77020 @@ -8742,6 +13055,8 @@ enums: exact_mappings: - NCBITaxon:77020 - uniprot.proteome:UP000037751 + annotations: + sources: existing SP_9BBAC: description: 'Plutella xylostella granulovirus - Proteome: UP000201310' meaning: NCBITaxon:98383 @@ -8749,6 +13064,8 @@ enums: exact_mappings: - NCBITaxon:98383 - uniprot.proteome:UP000201310 + annotations: + sources: existing SP_9BETA: description: 'Saimiriine betaherpesvirus 4 - Proteome: UP000097892' meaning: NCBITaxon:1535247 @@ -8756,6 +13073,8 @@ enums: exact_mappings: - NCBITaxon:1535247 - uniprot.proteome:UP000097892 + annotations: + sources: existing SP_9BETC: description: 'Coronavirus BtRt-BetaCoV/GX2018 - Proteome: UP001228689' meaning: NCBITaxon:2591238 @@ -8763,6 +13082,8 @@ enums: exact_mappings: - NCBITaxon:2591238 - uniprot.proteome:UP001228689 + annotations: + sources: existing SP_9BIFI: description: 'Scardovia wiggsiae F0424 - Proteome: UP000006415' meaning: NCBITaxon:857290 @@ -8770,6 +13091,8 @@ enums: exact_mappings: - NCBITaxon:857290 - uniprot.proteome:UP000006415 + annotations: + sources: existing SP_9BILA: description: 'Ancylostoma ceylanicum - Proteome: UP000024635' meaning: NCBITaxon:53326 @@ -8777,6 +13100,8 @@ enums: exact_mappings: - NCBITaxon:53326 - uniprot.proteome:UP000024635 + annotations: + sources: existing SP_9BIVA: description: 'Potamilus streckersoni - Proteome: UP001195483' meaning: NCBITaxon:2493646 @@ -8784,6 +13109,8 @@ enums: exact_mappings: - NCBITaxon:2493646 - uniprot.proteome:UP001195483 + annotations: + sources: existing SP_9BORD: description: 'Bordetella sp. N - Proteome: UP000064621' meaning: NCBITaxon:1746199 @@ -8791,6 +13118,8 @@ enums: exact_mappings: - NCBITaxon:1746199 - uniprot.proteome:UP000064621 + annotations: + sources: existing SP_9BRAD: description: 'Afipia broomeae ATCC 49717 - Proteome: UP000001096' meaning: NCBITaxon:883078 @@ -8798,6 +13127,8 @@ enums: exact_mappings: - NCBITaxon:883078 - uniprot.proteome:UP000001096 + annotations: + sources: existing SP_9BRAS: description: 'Capsella rubella - Proteome: UP000029121' meaning: NCBITaxon:81985 @@ -8805,6 +13136,8 @@ enums: exact_mappings: - NCBITaxon:81985 - uniprot.proteome:UP000029121 + annotations: + sources: existing SP_9BROM: description: 'Prune dwarf virus - Proteome: UP000202132' meaning: NCBITaxon:33760 @@ -8812,6 +13145,8 @@ enums: exact_mappings: - NCBITaxon:33760 - uniprot.proteome:UP000202132 + annotations: + sources: existing SP_9BURK: description: 'Candidatus Paraburkholderia kirkii UZHbot1 - Proteome: UP000003511' meaning: NCBITaxon:1055526 @@ -8819,6 +13154,8 @@ enums: exact_mappings: - NCBITaxon:1055526 - uniprot.proteome:UP000003511 + annotations: + sources: existing SP_9CARY: description: 'Carnegiea gigantea - Proteome: UP001153076' meaning: NCBITaxon:171969 @@ -8826,6 +13163,8 @@ enums: exact_mappings: - NCBITaxon:171969 - uniprot.proteome:UP001153076 + annotations: + sources: existing SP_9CAUD: description: 'Salmonella phage Vi06 - Proteome: UP000000335' meaning: NCBITaxon:866889 @@ -8833,6 +13172,8 @@ enums: exact_mappings: - NCBITaxon:866889 - uniprot.proteome:UP000000335 + annotations: + sources: existing SP_9CAUL: description: 'Brevundimonas abyssalis TAR-001 - Proteome: UP000016569' meaning: NCBITaxon:1391729 @@ -8840,6 +13181,8 @@ enums: exact_mappings: - NCBITaxon:1391729 - uniprot.proteome:UP000016569 + annotations: + sources: existing SP_9CBAC: description: 'Neodiprion sertifer nucleopolyhedrovirus - Proteome: UP000243697' meaning: NCBITaxon:111874 @@ -8847,6 +13190,8 @@ enums: exact_mappings: - NCBITaxon:111874 - uniprot.proteome:UP000243697 + annotations: + sources: existing SP_9CELL: description: 'Actinotalea ferrariae CF5-4 - Proteome: UP000019753' meaning: NCBITaxon:948458 @@ -8854,34 +13199,44 @@ enums: exact_mappings: - NCBITaxon:948458 - uniprot.proteome:UP000019753 + annotations: + sources: existing SP_9CERV: - description: 'Cervus hanglu yarkandensis (Yarkand deer) - Proteome: UP000631465' + description: 'Cervus hanglu yarkandensis - Proteome: UP000631465' meaning: NCBITaxon:84702 title: Cervus hanglu yarkandensis exact_mappings: - NCBITaxon:84702 - uniprot.proteome:UP000631465 + annotations: + sources: existing SP_9CETA: - description: 'Catagonus wagneri (Chacoan peccary) - Proteome: UP000694540' + description: 'Catagonus wagneri - Proteome: UP000694540' meaning: NCBITaxon:51154 title: Catagonus wagneri exact_mappings: - NCBITaxon:51154 - uniprot.proteome:UP000694540 + annotations: + sources: existing SP_9CHAR: - description: 'Rostratula benghalensis (greater painted-snipe) - Proteome: UP000545435' + description: 'Rostratula benghalensis - Proteome: UP000545435' meaning: NCBITaxon:118793 title: Rostratula benghalensis exact_mappings: - NCBITaxon:118793 - uniprot.proteome:UP000545435 + annotations: + sources: existing SP_9CHIR: - description: 'Phyllostomus discolor (pale spear-nosed bat) - Proteome: UP000504628' + description: 'Phyllostomus discolor - Proteome: UP000504628' meaning: NCBITaxon:89673 title: Phyllostomus discolor exact_mappings: - NCBITaxon:89673 - uniprot.proteome:UP000504628 + annotations: + sources: existing SP_9CHLA: description: 'Chlamydiales bacterium SCGC AG-110-P3 - Proteome: UP000196763' meaning: NCBITaxon:1871323 @@ -8889,6 +13244,8 @@ enums: exact_mappings: - NCBITaxon:1871323 - uniprot.proteome:UP000196763 + annotations: + sources: existing SP_9CHLB: description: 'Chlorobium ferrooxidans DSM 13031 - Proteome: UP000004162' meaning: NCBITaxon:377431 @@ -8896,6 +13253,8 @@ enums: exact_mappings: - NCBITaxon:377431 - uniprot.proteome:UP000004162 + annotations: + sources: existing SP_9CHLO: description: 'Helicosporidium sp. ATCC 50920 - Proteome: UP000026042' meaning: NCBITaxon:1291522 @@ -8903,6 +13262,8 @@ enums: exact_mappings: - NCBITaxon:1291522 - uniprot.proteome:UP000026042 + annotations: + sources: existing SP_9CHLR: description: 'Ardenticatena maritima - Proteome: UP000037784' meaning: NCBITaxon:872965 @@ -8910,6 +13271,8 @@ enums: exact_mappings: - NCBITaxon:872965 - uniprot.proteome:UP000037784 + annotations: + sources: existing SP_9CHRO: description: 'Gloeocapsa sp. PCC 7428 - Proteome: UP000010476' meaning: NCBITaxon:1173026 @@ -8917,13 +13280,17 @@ enums: exact_mappings: - NCBITaxon:1173026 - uniprot.proteome:UP000010476 + annotations: + sources: existing SP_9CICH: - description: 'Maylandia zebra (zebra mbuna) - Proteome: UP000265160' + description: 'Maylandia zebra - Proteome: UP000265160' meaning: NCBITaxon:106582 title: Maylandia zebra exact_mappings: - NCBITaxon:106582 - uniprot.proteome:UP000265160 + annotations: + sources: existing SP_9CILI: description: 'Stentor coeruleus - Proteome: UP000187209' meaning: NCBITaxon:5963 @@ -8931,6 +13298,8 @@ enums: exact_mappings: - NCBITaxon:5963 - uniprot.proteome:UP000187209 + annotations: + sources: existing SP_9CIRC: description: 'Raven circovirus - Proteome: UP000097131' meaning: NCBITaxon:345250 @@ -8938,6 +13307,8 @@ enums: exact_mappings: - NCBITaxon:345250 - uniprot.proteome:UP000097131 + annotations: + sources: existing SP_9CLOS: description: 'Grapevine leafroll-associated virus 10 - Proteome: UP000203128' meaning: NCBITaxon:367121 @@ -8945,6 +13316,8 @@ enums: exact_mappings: - NCBITaxon:367121 - uniprot.proteome:UP000203128 + annotations: + sources: existing SP_9CLOT: description: 'Candidatus Arthromitus sp. SFB-rat-Yit - Proteome: UP000001273' meaning: NCBITaxon:1041504 @@ -8952,6 +13325,8 @@ enums: exact_mappings: - NCBITaxon:1041504 - uniprot.proteome:UP000001273 + annotations: + sources: existing SP_9CNID: description: 'Clytia hemisphaerica - Proteome: UP000594262' meaning: NCBITaxon:252671 @@ -8959,20 +13334,26 @@ enums: exact_mappings: - NCBITaxon:252671 - uniprot.proteome:UP000594262 + annotations: + sources: existing SP_9COLU: - description: 'Pampusana beccarii (Western bronze ground-dove) - Proteome: UP000541332' + description: 'Pampusana beccarii - Proteome: UP000541332' meaning: NCBITaxon:2953425 title: Pampusana beccarii exact_mappings: - NCBITaxon:2953425 - uniprot.proteome:UP000541332 + annotations: + sources: existing SP_9CORV: - description: 'Cnemophilus loriae (Loria''s bird-of-paradise) - Proteome: UP000517678' + description: 'Cnemophilus loriae - Proteome: UP000517678' meaning: NCBITaxon:254448 title: Cnemophilus loriae exact_mappings: - NCBITaxon:254448 - uniprot.proteome:UP000517678 + annotations: + sources: existing SP_9CORY: description: 'Corynebacterium genitalium ATCC 33030 - Proteome: UP000004208' meaning: NCBITaxon:585529 @@ -8980,6 +13361,8 @@ enums: exact_mappings: - NCBITaxon:585529 - uniprot.proteome:UP000004208 + annotations: + sources: existing SP_9COXI: description: 'Coxiella endosymbiont of Amblyomma americanum - Proteome: UP000059222' meaning: NCBITaxon:325775 @@ -8987,6 +13370,8 @@ enums: exact_mappings: - NCBITaxon:325775 - uniprot.proteome:UP000059222 + annotations: + sources: existing SP_9CREN: description: 'Metallosphaera yellowstonensis MK1 - Proteome: UP000003980' meaning: NCBITaxon:671065 @@ -8994,6 +13379,8 @@ enums: exact_mappings: - NCBITaxon:671065 - uniprot.proteome:UP000003980 + annotations: + sources: existing SP_9CRUS: description: 'Daphnia magna - Proteome: UP000076858' meaning: NCBITaxon:35525 @@ -9001,13 +13388,17 @@ enums: exact_mappings: - NCBITaxon:35525 - uniprot.proteome:UP000076858 + annotations: + sources: existing SP_9CUCU: - description: 'Ceutorhynchus assimilis (cabbage seed weevil) - Proteome: UP001152799' + description: 'Ceutorhynchus assimilis - Proteome: UP001152799' meaning: NCBITaxon:467358 title: Ceutorhynchus assimilis exact_mappings: - NCBITaxon:467358 - uniprot.proteome:UP001152799 + annotations: + sources: existing SP_9CYAN: description: 'Leptolyngbyaceae cyanobacterium JSC-12 - Proteome: UP000001332' meaning: NCBITaxon:864702 @@ -9015,6 +13406,8 @@ enums: exact_mappings: - NCBITaxon:864702 - uniprot.proteome:UP000001332 + annotations: + sources: existing SP_9DEIN: description: 'Meiothermus sp. QL-1 - Proteome: UP000255346' meaning: NCBITaxon:2058095 @@ -9022,6 +13415,8 @@ enums: exact_mappings: - NCBITaxon:2058095 - uniprot.proteome:UP000255346 + annotations: + sources: existing SP_9DEIO: description: 'Deinococcus sp. RL - Proteome: UP000027898' meaning: NCBITaxon:1489678 @@ -9029,6 +13424,8 @@ enums: exact_mappings: - NCBITaxon:1489678 - uniprot.proteome:UP000027898 + annotations: + sources: existing SP_9DELA: description: 'Human T-cell leukemia virus type I - Proteome: UP000108043' meaning: NCBITaxon:11908 @@ -9036,6 +13433,8 @@ enums: exact_mappings: - NCBITaxon:11908 - uniprot.proteome:UP000108043 + annotations: + sources: existing SP_9DELT: description: 'Lujinxingia litoralis - Proteome: UP000249169' meaning: NCBITaxon:2211119 @@ -9043,13 +13442,17 @@ enums: exact_mappings: - NCBITaxon:2211119 - uniprot.proteome:UP000249169 + annotations: + sources: existing SP_9DEND: - description: 'Xiphorhynchus elegans (elegant woodcreeper) - Proteome: UP000551443' + description: 'Xiphorhynchus elegans - Proteome: UP000551443' meaning: NCBITaxon:269412 title: Xiphorhynchus elegans exact_mappings: - NCBITaxon:269412 - uniprot.proteome:UP000551443 + annotations: + sources: existing SP_9DINO: description: 'Symbiodinium necroappetens - Proteome: UP000601435' meaning: NCBITaxon:1628268 @@ -9057,6 +13460,8 @@ enums: exact_mappings: - NCBITaxon:1628268 - uniprot.proteome:UP000601435 + annotations: + sources: existing SP_9DIPT: description: 'Clunio marinus - Proteome: UP000183832' meaning: NCBITaxon:568069 @@ -9064,6 +13469,8 @@ enums: exact_mappings: - NCBITaxon:568069 - uniprot.proteome:UP000183832 + annotations: + sources: existing SP_9EIME: description: 'Eimeria praecox - Proteome: UP000018201' meaning: NCBITaxon:51316 @@ -9071,6 +13478,8 @@ enums: exact_mappings: - NCBITaxon:51316 - uniprot.proteome:UP000018201 + annotations: + sources: existing SP_9EMBE: description: 'Emberiza fucata - Proteome: UP000580681' meaning: NCBITaxon:337179 @@ -9078,6 +13487,8 @@ enums: exact_mappings: - NCBITaxon:337179 - uniprot.proteome:UP000580681 + annotations: + sources: existing SP_9ENTE: description: 'Enterococcus asini ATCC 700915 - Proteome: UP000013777' meaning: NCBITaxon:1158606 @@ -9085,6 +13496,8 @@ enums: exact_mappings: - NCBITaxon:1158606 - uniprot.proteome:UP000013777 + annotations: + sources: existing SP_9ENTR: description: 'secondary endosymbiont of Heteropsylla cubana - Proteome: UP000003937' meaning: NCBITaxon:134287 @@ -9092,6 +13505,8 @@ enums: exact_mappings: - NCBITaxon:134287 - uniprot.proteome:UP000003937 + annotations: + sources: existing SP_9ERIC: description: 'Rhododendron williamsianum - Proteome: UP000428333' meaning: NCBITaxon:262921 @@ -9099,6 +13514,8 @@ enums: exact_mappings: - NCBITaxon:262921 - uniprot.proteome:UP000428333 + annotations: + sources: existing SP_9EUCA: description: 'Petrolisthes manimaculis - Proteome: UP001292094' meaning: NCBITaxon:1843537 @@ -9106,6 +13523,8 @@ enums: exact_mappings: - NCBITaxon:1843537 - uniprot.proteome:UP001292094 + annotations: + sources: existing SP_9EUGL: description: 'Perkinsela sp. CCAP 1560/4 - Proteome: UP000036983' meaning: NCBITaxon:1314962 @@ -9113,6 +13532,8 @@ enums: exact_mappings: - NCBITaxon:1314962 - uniprot.proteome:UP000036983 + annotations: + sources: existing SP_9EUKA: description: 'Chrysochromulina tobinii - Proteome: UP000037460' meaning: NCBITaxon:1460289 @@ -9120,6 +13541,8 @@ enums: exact_mappings: - NCBITaxon:1460289 - uniprot.proteome:UP000037460 + annotations: + sources: existing SP_9EUPU: description: 'Candidula unifasciata - Proteome: UP000678393' meaning: NCBITaxon:100452 @@ -9127,6 +13550,8 @@ enums: exact_mappings: - NCBITaxon:100452 - uniprot.proteome:UP000678393 + annotations: + sources: existing SP_9EURO: description: 'Cladophialophora psammophila CBS 110553 - Proteome: UP000019471' meaning: NCBITaxon:1182543 @@ -9134,6 +13559,8 @@ enums: exact_mappings: - NCBITaxon:1182543 - uniprot.proteome:UP000019471 + annotations: + sources: existing SP_9EURY: description: 'Methanoplanus limicola DSM 2279 - Proteome: UP000005741' meaning: NCBITaxon:937775 @@ -9141,6 +13568,8 @@ enums: exact_mappings: - NCBITaxon:937775 - uniprot.proteome:UP000005741 + annotations: + sources: existing SP_9FABA: description: 'Senna tora - Proteome: UP000634136' meaning: NCBITaxon:362788 @@ -9148,6 +13577,8 @@ enums: exact_mappings: - NCBITaxon:362788 - uniprot.proteome:UP000634136 + annotations: + sources: existing SP_9FIRM: description: 'Ruminococcaceae bacterium D16 - Proteome: UP000002801' meaning: NCBITaxon:552398 @@ -9155,6 +13586,8 @@ enums: exact_mappings: - NCBITaxon:552398 - uniprot.proteome:UP000002801 + annotations: + sources: existing SP_9FLAO: description: 'Capnocytophaga sp. oral taxon 338 str. F0234 - Proteome: UP000003023' meaning: NCBITaxon:888059 @@ -9162,6 +13595,8 @@ enums: exact_mappings: - NCBITaxon:888059 - uniprot.proteome:UP000003023 + annotations: + sources: existing SP_9FLAV: description: 'Tunisian sheep-like pestivirus - Proteome: UP001157330' meaning: NCBITaxon:3071305 @@ -9169,6 +13604,8 @@ enums: exact_mappings: - NCBITaxon:3071305 - uniprot.proteome:UP001157330 + annotations: + sources: existing SP_9FLOR: description: 'Gracilariopsis chorda - Proteome: UP000247409' meaning: NCBITaxon:448386 @@ -9176,6 +13613,8 @@ enums: exact_mappings: - NCBITaxon:448386 - uniprot.proteome:UP000247409 + annotations: + sources: existing SP_9FRIN: description: 'Urocynchramus pylzowi - Proteome: UP000524542' meaning: NCBITaxon:571890 @@ -9183,6 +13622,8 @@ enums: exact_mappings: - NCBITaxon:571890 - uniprot.proteome:UP000524542 + annotations: + sources: existing SP_9FUNG: description: 'Lichtheimia corymbifera JMRC:FSU:9682 - Proteome: UP000027586' meaning: NCBITaxon:1263082 @@ -9190,6 +13631,8 @@ enums: exact_mappings: - NCBITaxon:1263082 - uniprot.proteome:UP000027586 + annotations: + sources: existing SP_9FURN: description: 'Furnarius figulus - Proteome: UP000529852' meaning: NCBITaxon:463165 @@ -9197,6 +13640,8 @@ enums: exact_mappings: - NCBITaxon:463165 - uniprot.proteome:UP000529852 + annotations: + sources: existing SP_9FUSO: description: 'Fusobacterium gonidiaformans 3-1-5R - Proteome: UP000002975' meaning: NCBITaxon:469605 @@ -9204,13 +13649,17 @@ enums: exact_mappings: - NCBITaxon:469605 - uniprot.proteome:UP000002975 + annotations: + sources: existing SP_9GALL: - description: 'Odontophorus gujanensis (marbled wood quail) - Proteome: UP000522663' + description: 'Odontophorus gujanensis - Proteome: UP000522663' meaning: NCBITaxon:886794 title: Odontophorus gujanensis exact_mappings: - NCBITaxon:886794 - uniprot.proteome:UP000522663 + annotations: + sources: existing SP_9GAMA: description: 'Bovine gammaherpesvirus 6 - Proteome: UP000121539' meaning: NCBITaxon:1504288 @@ -9218,6 +13667,8 @@ enums: exact_mappings: - NCBITaxon:1504288 - uniprot.proteome:UP000121539 + annotations: + sources: existing SP_9GAMC: description: 'Anser fabalis coronavirus NCN2 - Proteome: UP001251675' meaning: NCBITaxon:2860474 @@ -9225,22 +13676,28 @@ enums: exact_mappings: - NCBITaxon:2860474 - uniprot.proteome:UP001251675 + annotations: + sources: existing SP_9GAMM: - description: 'Buchnera aphidicola (Cinara tujafilina) - Proteome: UP000006811' + description: 'Buchnera aphidicola (Buchnera aphidicola (Cinara tujafilina)) - Proteome: UP000006811' meaning: NCBITaxon:261317 title: Buchnera aphidicola - aliases: - - Buchnera aphidicola (Cinara tujafilina) exact_mappings: - NCBITaxon:261317 - uniprot.proteome:UP000006811 + aliases: + - Buchnera aphidicola (Cinara tujafilina) + annotations: + sources: existing SP_9GAST: - description: 'Elysia crispata (lettuce slug) - Proteome: UP001283361' + description: 'Elysia crispata - Proteome: UP001283361' meaning: NCBITaxon:231223 title: Elysia crispata exact_mappings: - NCBITaxon:231223 - uniprot.proteome:UP001283361 + annotations: + sources: existing SP_9GEMI: description: 'East African cassava mosaic Zanzibar virus - Proteome: UP000201107' meaning: NCBITaxon:223275 @@ -9248,6 +13705,8 @@ enums: exact_mappings: - NCBITaxon:223275 - uniprot.proteome:UP000201107 + annotations: + sources: existing SP_9GLOM: description: 'Paraglomus occultum - Proteome: UP000789572' meaning: NCBITaxon:144539 @@ -9255,20 +13714,26 @@ enums: exact_mappings: - NCBITaxon:144539 - uniprot.proteome:UP000789572 + annotations: + sources: existing SP_9GOBI: - description: 'Neogobius melanostomus (round goby) - Proteome: UP000694523' + description: 'Neogobius melanostomus - Proteome: UP000694523' meaning: NCBITaxon:47308 title: Neogobius melanostomus exact_mappings: - NCBITaxon:47308 - uniprot.proteome:UP000694523 + annotations: + sources: existing SP_9GRUI: - description: 'Atlantisia rogersi (Inaccessible Island rail) - Proteome: UP000518911' + description: 'Atlantisia rogersi - Proteome: UP000518911' meaning: NCBITaxon:2478892 title: Atlantisia rogersi exact_mappings: - NCBITaxon:2478892 - uniprot.proteome:UP000518911 + annotations: + sources: existing SP_9HELI: description: 'Helicobacter bilis ATCC 43879 - Proteome: UP000005085' meaning: NCBITaxon:613026 @@ -9276,6 +13741,8 @@ enums: exact_mappings: - NCBITaxon:613026 - uniprot.proteome:UP000005085 + annotations: + sources: existing SP_9HELO: description: 'Rhynchosporium graminicola - Proteome: UP000178129' meaning: NCBITaxon:2792576 @@ -9283,6 +13750,8 @@ enums: exact_mappings: - NCBITaxon:2792576 - uniprot.proteome:UP000178129 + annotations: + sources: existing SP_9HEMI: description: 'Cinara cedri - Proteome: UP000325440' meaning: NCBITaxon:506608 @@ -9290,6 +13759,8 @@ enums: exact_mappings: - NCBITaxon:506608 - uniprot.proteome:UP000325440 + annotations: + sources: existing SP_9HEPA: description: 'Duck hepatitis B virus - Proteome: UP000137229' meaning: NCBITaxon:12639 @@ -9297,6 +13768,8 @@ enums: exact_mappings: - NCBITaxon:12639 - uniprot.proteome:UP000137229 + annotations: + sources: existing SP_9HEXA: description: 'Allacma fusca - Proteome: UP000708208' meaning: NCBITaxon:39272 @@ -9304,6 +13777,8 @@ enums: exact_mappings: - NCBITaxon:39272 - uniprot.proteome:UP000708208 + annotations: + sources: existing SP_9HYME: description: 'Melipona quadrifasciata - Proteome: UP000053105' meaning: NCBITaxon:166423 @@ -9311,6 +13786,8 @@ enums: exact_mappings: - NCBITaxon:166423 - uniprot.proteome:UP000053105 + annotations: + sources: existing SP_9HYPH: description: 'Mesorhizobium amorphae CCNWGS0123 - Proteome: UP000002949' meaning: NCBITaxon:1082933 @@ -9318,6 +13795,8 @@ enums: exact_mappings: - NCBITaxon:1082933 - uniprot.proteome:UP000002949 + annotations: + sources: existing SP_9HYPO: description: '[Torrubiella] hemipterigena - Proteome: UP000039046' meaning: NCBITaxon:1531966 @@ -9325,15 +13804,20 @@ enums: exact_mappings: - NCBITaxon:1531966 - uniprot.proteome:UP000039046 + annotations: + sources: existing SP_9INFA: - description: 'Influenza A virus (A/California/VRDL364/2009 (mixed) - Proteome: UP000109975' + description: 'Influenza A virus (A/California/VRDL364/2009 (Influenza A virus (A/California/VRDL364/2009(mixed))) + - Proteome: UP000109975' meaning: NCBITaxon:1049605 title: Influenza A virus (A/California/VRDL364/2009 - aliases: - - Influenza A virus (A/California/VRDL364/2009(mixed)) exact_mappings: - NCBITaxon:1049605 - uniprot.proteome:UP000109975 + aliases: + - Influenza A virus (A/California/VRDL364/2009(mixed)) + annotations: + sources: existing SP_9INSE: description: 'Cloeon dipterum - Proteome: UP000494165' meaning: NCBITaxon:197152 @@ -9341,29 +13825,138 @@ enums: exact_mappings: - NCBITaxon:197152 - uniprot.proteome:UP000494165 + annotations: + sources: existing SP_9LABR: - description: 'Labrus bergylta (ballan wrasse) - Proteome: UP000261660' + description: 'Labrus bergylta - Proteome: UP000261660' meaning: NCBITaxon:56723 title: Labrus bergylta exact_mappings: - NCBITaxon:56723 - uniprot.proteome:UP000261660 + annotations: + sources: existing + SP_ACIB2: + description: 'Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 + / NCIMB 12457 / NCTC 12156 / 81) (A. baumannii ATCC 19606) - Proteome: UP000498640' + meaning: NCBITaxon:575584 + title: Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / + NCIMB 12457 / NCTC 12156 / 81) + exact_mappings: + - NCBITaxon:575584 + - uniprot.proteome:UP000498640 + aliases: + - A. baumannii ATCC 19606 + annotations: + sources: GO + SP_ANOCA: + description: 'Anolis carolinensis (Green anole (American chameleon)) - Proteome: UP000001646' + meaning: NCBITaxon:28377 + title: Anolis carolinensis + exact_mappings: + - NCBITaxon:28377 + - uniprot.proteome:UP000001646 + aliases: + - Green anole (American chameleon) + annotations: + sources: GO + SP_ANOGA: + description: 'Anopheles gambiae (African malaria mosquito) - Proteome: UP000007062' + meaning: NCBITaxon:7165 + title: Anopheles gambiae + exact_mappings: + - NCBITaxon:7165 + - uniprot.proteome:UP000007062 + aliases: + - African malaria mosquito + annotations: + sources: GO + SP_AQUAE: + description: 'Aquifex aeolicus (aquaficae bacteria) - Proteome: UP000000798' + meaning: NCBITaxon:224324 + title: Aquifex aeolicus + exact_mappings: + - NCBITaxon:224324 + - uniprot.proteome:UP000000798 + aliases: + - aquaficae bacteria + annotations: + sources: GO SP_ARATH: - description: 'Arabidopsis thaliana (Thale cress) - Proteome: UP000006548' + description: 'Arabidopsis thaliana (Mouse-ear cress) - Proteome: UP000006548' meaning: NCBITaxon:3702 title: Arabidopsis thaliana exact_mappings: - NCBITaxon:3702 - uniprot.proteome:UP000006548 aliases: - - Thale cress + - Mouse-ear cress + annotations: + sources: common, GO + SP_ASPFU: + description: 'Neosartorya fumigata (ascomycote fungus) - Proteome: UP000002530' + meaning: NCBITaxon:330879 + title: Neosartorya fumigata + exact_mappings: + - NCBITaxon:330879 + - uniprot.proteome:UP000002530 + aliases: + - ascomycote fungus + annotations: + sources: GO + SP_BACAN: + description: 'Bacillus anthracis - Proteome: UP000000594' + meaning: NCBITaxon:1392 + title: Bacillus anthracis + exact_mappings: + - NCBITaxon:1392 + - uniprot.proteome:UP000000594 + annotations: + sources: GO + SP_BACCR: + description: 'Bacillus cereus (bacillus cereus) - Proteome: UP000001417' + meaning: NCBITaxon:226900 + title: Bacillus cereus + exact_mappings: + - NCBITaxon:226900 + - uniprot.proteome:UP000001417 + aliases: + - bacillus cereus + annotations: + sources: GO SP_BACSU: - description: 'Bacillus subtilis subsp. subtilis str. 168 - Proteome: UP000001570' + description: 'Bacillus subtilis subsp. subtilis str. 168 (b subtilis) - Proteome: UP000001570' meaning: NCBITaxon:224308 title: Bacillus subtilis subsp. subtilis str. 168 exact_mappings: - NCBITaxon:224308 - uniprot.proteome:UP000001570 + aliases: + - b subtilis + annotations: + sources: common, GO + SP_BACTN: + description: 'Bacteroides thetaiotaomicron (bacteroidetes bacteria) - Proteome: UP000001414' + meaning: NCBITaxon:226186 + title: Bacteroides thetaiotaomicron + exact_mappings: + - NCBITaxon:226186 + - uniprot.proteome:UP000001414 + aliases: + - bacteroidetes bacteria + annotations: + sources: GO + SP_BATDJ: + description: 'Batrachochytrium dendrobatidis (Frog chytrid fungus) - Proteome: UP000007241' + meaning: NCBITaxon:684364 + title: Batrachochytrium dendrobatidis + exact_mappings: + - NCBITaxon:684364 + - uniprot.proteome:UP000007241 + aliases: + - Frog chytrid fungus + annotations: + sources: GO SP_BOVIN: description: 'Bos taurus (Cattle) - Proteome: UP000009136' meaning: NCBITaxon:9913 @@ -9373,13 +13966,124 @@ enums: - uniprot.proteome:UP000009136 aliases: - Cattle + annotations: + sources: common, GO + SP_BRACM: + description: 'Brassica campestris (Field mustard) - Proteome: UP000011750' + meaning: NCBITaxon:3711 + title: Brassica campestris + exact_mappings: + - NCBITaxon:3711 + - uniprot.proteome:UP000011750 + aliases: + - Field mustard + annotations: + sources: GO + SP_BRADI: + description: 'Brachypodium distachyon (Purple false brome) - Proteome: UP000008810' + meaning: NCBITaxon:15368 + title: Brachypodium distachyon + exact_mappings: + - NCBITaxon:15368 + - uniprot.proteome:UP000008810 + aliases: + - Purple false brome + annotations: + sources: GO + SP_BRADU: + description: 'Bradyrhizobium diazoefficiens (alphaproteobacteria) - Proteome: UP000002526' + meaning: NCBITaxon:224911 + title: Bradyrhizobium diazoefficiens + exact_mappings: + - NCBITaxon:224911 + - uniprot.proteome:UP000002526 + aliases: + - alphaproteobacteria + annotations: + sources: GO + SP_BRAFL: + description: 'Branchiostoma floridae (Florida lancelet (Amphioxus)) - Proteome: UP000001554' + meaning: NCBITaxon:7739 + title: Branchiostoma floridae + exact_mappings: + - NCBITaxon:7739 + - uniprot.proteome:UP000001554 + aliases: + - Florida lancelet (Amphioxus) + annotations: + sources: GO + SP_CAEBR: + description: 'Caenorhabditis briggsae (nematode worm) - Proteome: UP000008549' + meaning: NCBITaxon:6238 + title: Caenorhabditis briggsae + exact_mappings: + - NCBITaxon:6238 + - uniprot.proteome:UP000008549 + aliases: + - nematode worm + annotations: + sources: GO SP_CAEEL: - description: 'Caenorhabditis elegans - Proteome: UP000001940' + description: 'Caenorhabditis elegans (nematode worm) - Proteome: UP000001940' meaning: NCBITaxon:6239 title: Caenorhabditis elegans exact_mappings: - NCBITaxon:6239 - uniprot.proteome:UP000001940 + aliases: + - nematode worm + annotations: + sources: common, GO + SP_CAMJE: + description: 'Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) - Proteome: UP000000799' + meaning: NCBITaxon:192222 + title: Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) + exact_mappings: + - NCBITaxon:192222 + - uniprot.proteome:UP000000799 + annotations: + sources: GO + SP_CANAL: + description: 'Candida albicans (Yeast) - Proteome: UP000000559' + meaning: NCBITaxon:237561 + title: Candida albicans + exact_mappings: + - NCBITaxon:237561 + - uniprot.proteome:UP000000559 + aliases: + - Yeast + annotations: + sources: GO + SP_CANCO: + description: 'Candida orthopsilosis (strain 90-125) (Co 90-125) - Proteome: UP000005018' + meaning: NCBITaxon:1136231 + title: Candida orthopsilosis (strain 90-125) (Co 90-125) + exact_mappings: + - NCBITaxon:1136231 + - uniprot.proteome:UP000005018 + annotations: + sources: GO + SP_CANDC: + description: 'Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) - Proteome: + UP000002605' + meaning: NCBITaxon:573826 + title: Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) + exact_mappings: + - NCBITaxon:573826 + - uniprot.proteome:UP000002605 + annotations: + sources: GO + SP_CANGB: + description: 'Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) (Nakaseomyces + glabratus) - Proteome: UP000002428' + meaning: NCBITaxon:284593 + title: Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) (Nakaseomyces + glabratus) + exact_mappings: + - NCBITaxon:284593 + - uniprot.proteome:UP000002428 + annotations: + sources: GO SP_CANLF: description: 'Canis lupus familiaris (Dog) - Proteome: UP000805418' meaning: NCBITaxon:9615 @@ -9389,6 +14093,26 @@ enums: - uniprot.proteome:UP000805418 aliases: - Dog + annotations: + sources: common, GO + SP_CANPA: + description: 'Candida parapsilosis (strain CDC 317 / ATCC MYA-4646) - Proteome: UP000005221' + meaning: NCBITaxon:578454 + title: Candida parapsilosis (strain CDC 317 / ATCC MYA-4646) + exact_mappings: + - NCBITaxon:578454 + - uniprot.proteome:UP000005221 + annotations: + sources: GO + SP_CANTI: + description: 'Candida tropicalis (strain ATCC MYA-3404 / T1) - Proteome: UP000002037' + meaning: NCBITaxon:294747 + title: Candida tropicalis (strain ATCC MYA-3404 / T1) + exact_mappings: + - NCBITaxon:294747 + - uniprot.proteome:UP000002037 + annotations: + sources: GO SP_CHICK: description: 'Gallus gallus (Chicken) - Proteome: UP000000539' meaning: NCBITaxon:9031 @@ -9398,6 +14122,104 @@ enums: - uniprot.proteome:UP000000539 aliases: - Chicken + annotations: + sources: common, GO + SP_CHLAA: + description: 'Chloroflexus aurantiacus (chloroflexi bacteria) - Proteome: UP000002008' + meaning: NCBITaxon:324602 + title: Chloroflexus aurantiacus + exact_mappings: + - NCBITaxon:324602 + - uniprot.proteome:UP000002008 + aliases: + - chloroflexi bacteria + annotations: + sources: GO + SP_CHLRE: + description: 'Chlamydomonas reinhardtii (green algae) - Proteome: UP000006906' + meaning: NCBITaxon:3055 + title: Chlamydomonas reinhardtii + exact_mappings: + - NCBITaxon:3055 + - uniprot.proteome:UP000006906 + aliases: + - green algae + annotations: + sources: GO + SP_CHLTR: + description: 'Chlamydia trachomatis (chlamydia) - Proteome: UP000000431' + meaning: NCBITaxon:272561 + title: Chlamydia trachomatis + exact_mappings: + - NCBITaxon:272561 + - uniprot.proteome:UP000000431 + aliases: + - chlamydia + annotations: + sources: GO + SP_CIOIN: + description: 'Ciona intestinalis (Transparent sea squirt) - Proteome: UP000008144' + meaning: NCBITaxon:7719 + title: Ciona intestinalis + exact_mappings: + - NCBITaxon:7719 + - uniprot.proteome:UP000008144 + aliases: + - Transparent sea squirt + annotations: + sources: GO + SP_CITK8: + description: 'Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) - Proteome: UP000008148' + meaning: NCBITaxon:290338 + title: Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) + exact_mappings: + - NCBITaxon:290338 + - uniprot.proteome:UP000008148 + annotations: + sources: GO + SP_CLALU: + description: 'Clavispora lusitaniae (strain ATCC 42720) - Proteome: UP000007703' + meaning: NCBITaxon:306902 + title: Clavispora lusitaniae (strain ATCC 42720) + exact_mappings: + - NCBITaxon:306902 + - uniprot.proteome:UP000007703 + annotations: + sources: GO + SP_CLOBH: + description: 'Clostridium botulinum (firmicutes bacteria) - Proteome: UP000001986' + meaning: NCBITaxon:441771 + title: Clostridium botulinum + exact_mappings: + - NCBITaxon:441771 + - uniprot.proteome:UP000001986 + aliases: + - firmicutes bacteria + annotations: + sources: GO + SP_COXBU: + description: 'Coxiella burnetii (gammaproteobacteria) - Proteome: UP000002671' + meaning: NCBITaxon:227377 + title: Coxiella burnetii + exact_mappings: + - NCBITaxon:227377 + - uniprot.proteome:UP000002671 + aliases: + - gammaproteobacteria + annotations: + sources: GO + SP_CRYD1: + description: 'Cryptococcus neoformans var. neoformans serotype D (Filobasidiella neoformans) (C. neoformans) - Proteome: + UP000002149' + meaning: NCBITaxon:214684 + title: Cryptococcus neoformans var. neoformans serotype D (Filobasidiella neoformans) + exact_mappings: + - NCBITaxon:214684 + - uniprot.proteome:UP000002149 + aliases: + - C. neoformans + annotations: + sources: GO SP_DANRE: description: 'Danio rerio (Zebrafish) - Proteome: UP000000437' meaning: NCBITaxon:7955 @@ -9407,6 +14229,74 @@ enums: - uniprot.proteome:UP000000437 aliases: - Zebrafish + annotations: + sources: common, GO + SP_DAPPU: + description: 'Daphnia pulex (Water flea) - Proteome: UP000000305' + meaning: NCBITaxon:6669 + title: Daphnia pulex + exact_mappings: + - NCBITaxon:6669 + - uniprot.proteome:UP000000305 + aliases: + - Water flea + annotations: + sources: GO + SP_DEBHA: + description: 'Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) (Torulaspora + hansenii) - Proteome: UP000000599' + meaning: NCBITaxon:284592 + title: Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) (Torulaspora + hansenii) + exact_mappings: + - NCBITaxon:284592 + - uniprot.proteome:UP000000599 + annotations: + sources: GO + SP_DEIRA: + description: 'Deinococcus radiodurans (deinococcus bacteria) - Proteome: UP000002524' + meaning: NCBITaxon:243230 + title: Deinococcus radiodurans + exact_mappings: + - NCBITaxon:243230 + - uniprot.proteome:UP000002524 + aliases: + - deinococcus bacteria + annotations: + sources: GO + SP_DICDI: + description: 'Dictyostelium discoideum (Social amoeba) - Proteome: UP000002195' + meaning: NCBITaxon:44689 + title: Dictyostelium discoideum + exact_mappings: + - NCBITaxon:44689 + - uniprot.proteome:UP000002195 + aliases: + - Social amoeba + annotations: + sources: GO + SP_DICPU: + description: 'Dictyostelium purpureum (Slime mold) - Proteome: UP000001064' + meaning: NCBITaxon:5786 + title: Dictyostelium purpureum + exact_mappings: + - NCBITaxon:5786 + - uniprot.proteome:UP000001064 + aliases: + - Slime mold + annotations: + sources: GO + SP_DICTD: + description: 'Dictyoglomus turgidum (dictyoglomi bacteria) - Proteome: UP000007719' + meaning: NCBITaxon:515635 + title: Dictyoglomus turgidum + exact_mappings: + - NCBITaxon:515635 + - uniprot.proteome:UP000007719 + aliases: + - dictyoglomi bacteria + annotations: + sources: GO SP_DROME: description: 'Drosophila melanogaster (Fruit fly) - Proteome: UP000000803' meaning: NCBITaxon:7227 @@ -9416,22 +14306,154 @@ enums: - uniprot.proteome:UP000000803 aliases: - Fruit fly + annotations: + sources: common, GO + SP_E. coli ECO57: + description: 'Escherichia coli O157:H7 - Proteome: UP000000558' + meaning: NCBITaxon:83334 + title: Escherichia coli O157:H7 + exact_mappings: + - NCBITaxon:83334 + - uniprot.proteome:UP000000558 + annotations: + sources: GO SP_ECOLI: - description: 'Escherichia coli K-12 - Proteome: UP000000625' + description: 'Escherichia coli K-12 (E. coli) - Proteome: UP000000625' meaning: NCBITaxon:83333 title: Escherichia coli K-12 exact_mappings: - NCBITaxon:83333 - uniprot.proteome:UP000000625 + aliases: + - E. coli + annotations: + sources: common, GO + SP_EMENI: + description: 'Emericella nidulans (ascomycote fungus) - Proteome: UP000000560' + meaning: NCBITaxon:227321 + title: Emericella nidulans + exact_mappings: + - NCBITaxon:227321 + - uniprot.proteome:UP000000560 + aliases: + - ascomycote fungus + annotations: + sources: GO + SP_ENTCA: + description: 'Enterococcus casseliflavus EC20 - Proteome: UP000012675' + meaning: NCBITaxon:565655 + title: Enterococcus casseliflavus EC20 + exact_mappings: + - NCBITaxon:565655 + - uniprot.proteome:UP000012675 + annotations: + sources: GO + SP_ENTFA: + description: 'Enterococcus faecalis (strain ATCC 700802 / V583) - Proteome: UP000001415' + meaning: NCBITaxon:226185 + title: Enterococcus faecalis (strain ATCC 700802 / V583) + exact_mappings: + - NCBITaxon:226185 + - uniprot.proteome:UP000001415 + annotations: + sources: GO + SP_ENTGA: + description: 'Enterococcus gallinarum - Proteome: UP000254807' + meaning: NCBITaxon:1353 + title: Enterococcus gallinarum + exact_mappings: + - NCBITaxon:1353 + - uniprot.proteome:UP000254807 + annotations: + sources: GO + SP_ENTH1: + description: 'Entamoeba histolytica (amoeba) - Proteome: UP000001926' + meaning: NCBITaxon:294381 + title: Entamoeba histolytica + exact_mappings: + - NCBITaxon:294381 + - uniprot.proteome:UP000001926 + aliases: + - amoeba + annotations: + sources: GO + SP_EREGS: + description: 'Eremothecium gossypii (Yeast) - Proteome: UP000000591' + meaning: NCBITaxon:284811 + title: Eremothecium gossypii + exact_mappings: + - NCBITaxon:284811 + - uniprot.proteome:UP000000591 + aliases: + - Yeast + annotations: + sources: GO SP_FELCA: description: 'Felis catus (Cat) - Proteome: UP000011712' meaning: NCBITaxon:9685 title: Felis catus exact_mappings: - - NCBITaxon:9685 - - uniprot.proteome:UP000011712 + - NCBITaxon:9685 + - uniprot.proteome:UP000011712 + aliases: + - Cat + annotations: + sources: common, GO + SP_FMDVO: + description: 'Foot-and-mouth disease virus serotype O (FMDV) (FMDV) - Proteome: UP000008765' + meaning: NCBITaxon:12118 + title: Foot-and-mouth disease virus serotype O (FMDV) + exact_mappings: + - NCBITaxon:12118 + - uniprot.proteome:UP000008765 + aliases: + - FMDV + annotations: + sources: GO + SP_FUSNN: + description: 'Fusobacterium nucleatum (strain ATCC 25586) (F. nucleatum ATCC 25586) - Proteome: UP000241660' + meaning: NCBITaxon:190304 + title: Fusobacterium nucleatum (strain ATCC 25586) + exact_mappings: + - NCBITaxon:190304 + - uniprot.proteome:UP000241660 + aliases: + - F. nucleatum ATCC 25586 + annotations: + sources: GO + SP_GEOSL: + description: 'Geobacter sulfurreducens (deltaproteobacteria) - Proteome: UP000000577' + meaning: NCBITaxon:243231 + title: Geobacter sulfurreducens + exact_mappings: + - NCBITaxon:243231 + - uniprot.proteome:UP000000577 + aliases: + - deltaproteobacteria + annotations: + sources: GO + SP_GIAIC: + description: 'Giardia intestinalis (giardia) - Proteome: UP000001548' + meaning: NCBITaxon:184922 + title: Giardia intestinalis + exact_mappings: + - NCBITaxon:184922 + - uniprot.proteome:UP000001548 aliases: - - Cat + - giardia + annotations: + sources: GO + SP_GLOVI: + description: 'Gloeobacter violaceus (cyanobacteria) - Proteome: UP000000557' + meaning: NCBITaxon:251221 + title: Gloeobacter violaceus + exact_mappings: + - NCBITaxon:251221 + - uniprot.proteome:UP000000557 + aliases: + - cyanobacteria + annotations: + sources: GO SP_GORGO: description: 'Gorilla gorilla gorilla (Western lowland gorilla) - Proteome: UP000001519' meaning: NCBITaxon:9593 @@ -9441,7 +14463,140 @@ enums: - uniprot.proteome:UP000001519 aliases: - Western lowland gorilla - - Gorilla gorilla + annotations: + sources: common, GO + SP_GOSHI: + description: 'Gossypium hirsutum (Upland cotton) - Proteome: UP000189702' + meaning: NCBITaxon:3635 + title: Gossypium hirsutum + exact_mappings: + - NCBITaxon:3635 + - uniprot.proteome:UP000189702 + aliases: + - Upland cotton + annotations: + sources: GO + SP_HAEIN: + description: 'Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (H. influenzae strain ATCC 51907) + - Proteome: UP000000579' + meaning: NCBITaxon:71421 + title: Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) + exact_mappings: + - NCBITaxon:71421 + - uniprot.proteome:UP000000579 + aliases: + - H. influenzae strain ATCC 51907 + annotations: + sources: GO + SP_HALH5: + description: 'Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (Bacillus + halodurans) - Proteome: UP000001258' + meaning: NCBITaxon:272558 + title: Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (Bacillus halodurans) + exact_mappings: + - NCBITaxon:272558 + - uniprot.proteome:UP000001258 + annotations: + sources: GO + SP_HALSA: + description: 'Halobacterium salinarum (euryarchaea) - Proteome: UP000000554' + meaning: NCBITaxon:64091 + title: Halobacterium salinarum + exact_mappings: + - NCBITaxon:64091 + - uniprot.proteome:UP000000554 + aliases: + - euryarchaea + annotations: + sources: GO + SP_HBVCJ: + description: 'Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-) (HBV-C) - Proteome: UP000008591' + meaning: NCBITaxon:928302 + title: Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-) + exact_mappings: + - NCBITaxon:928302 + - uniprot.proteome:UP000008591 + aliases: + - HBV-C + annotations: + sources: GO + SP_HCMVA: + description: 'Human cytomegalovirus (strain AD169) (Human herpesvirus 5 (HHV-5)) - Proteome: UP000008992' + meaning: NCBITaxon:10360 + title: Human cytomegalovirus (strain AD169) + exact_mappings: + - NCBITaxon:10360 + - uniprot.proteome:UP000008992 + aliases: + - Human herpesvirus 5 (HHV-5) + annotations: + sources: GO + SP_HCMVM: + description: 'Human cytomegalovirus (Human herpesvirus 5) strain Merlin (HHV-5 Merlin) - Proteome: UP000000938' + meaning: NCBITaxon:295027 + title: Human cytomegalovirus (Human herpesvirus 5) strain Merlin + exact_mappings: + - NCBITaxon:295027 + - uniprot.proteome:UP000000938 + aliases: + - HHV-5 Merlin + annotations: + sources: GO + SP_HCV77: + description: 'Hepatitis C virus genotype 1a (isolate H77) (HCV) - Proteome: UP000000518' + meaning: NCBITaxon:63746 + title: Hepatitis C virus genotype 1a (isolate H77) + exact_mappings: + - NCBITaxon:63746 + - uniprot.proteome:UP000000518 + aliases: + - HCV + annotations: + sources: GO + SP_HELAN: + description: 'Helianthus annuus (Common sunflower) - Proteome: UP000215914' + meaning: NCBITaxon:4232 + title: Helianthus annuus + exact_mappings: + - NCBITaxon:4232 + - uniprot.proteome:UP000215914 + aliases: + - Common sunflower + annotations: + sources: GO + SP_HELPY: + description: 'Helicobacter pylori (Campylobacter pylori) strain ATCC 700392 / 26695 (H. pylori) - Proteome: UP000000429' + meaning: NCBITaxon:85962 + title: Helicobacter pylori (Campylobacter pylori) strain ATCC 700392 / 26695 + exact_mappings: + - NCBITaxon:85962 + - uniprot.proteome:UP000000429 + aliases: + - H. pylori + annotations: + sources: GO + SP_HELRO: + description: 'Helobdella robusta (Californian leech) - Proteome: UP000015101' + meaning: NCBITaxon:6412 + title: Helobdella robusta + exact_mappings: + - NCBITaxon:6412 + - uniprot.proteome:UP000015101 + aliases: + - Californian leech + annotations: + sources: GO + SP_HHV11: + description: 'Human herpesvirus 1 (strain 17) (Human herpes simplex virus 1 (HHV-1)) - Proteome: UP000009294' + meaning: NCBITaxon:10299 + title: Human herpesvirus 1 (strain 17) + exact_mappings: + - NCBITaxon:10299 + - uniprot.proteome:UP000009294 + aliases: + - Human herpes simplex virus 1 (HHV-1) + annotations: + sources: GO SP_HORSE: description: 'Equus caballus (Horse) - Proteome: UP000002281' meaning: NCBITaxon:9796 @@ -9451,6 +14606,28 @@ enums: - uniprot.proteome:UP000002281 aliases: - Horse + annotations: + sources: common, GO + SP_HORVV: + description: 'Hordeum vulgare subsp. vulgare (Domesticated barley) - Proteome: UP000011116' + meaning: NCBITaxon:112509 + title: Hordeum vulgare subsp. vulgare + exact_mappings: + - NCBITaxon:112509 + - uniprot.proteome:UP000011116 + aliases: + - Domesticated barley + annotations: + sources: GO + SP_HPV16: + description: 'Human papillomavirus type 16 - Proteome: UP000009251' + meaning: NCBITaxon:333760 + title: Human papillomavirus type 16 + exact_mappings: + - NCBITaxon:333760 + - uniprot.proteome:UP000009251 + annotations: + sources: GO SP_HUMAN: description: 'Homo sapiens (Human) - Proteome: UP000005640' meaning: NCBITaxon:9606 @@ -9460,6 +14637,143 @@ enums: - uniprot.proteome:UP000005640 aliases: - Human + annotations: + sources: common, GO + SP_HV1AN: + description: 'Human immunodeficiency virus type 1 group O (isolate ANT70) - Proteome: UP000007689' + meaning: NCBITaxon:327105 + title: Human immunodeficiency virus type 1 group O (isolate ANT70) + exact_mappings: + - NCBITaxon:327105 + - uniprot.proteome:UP000007689 + annotations: + sources: GO + SP_IXOSC: + description: 'Ixodes scapularis (Deer tick) - Proteome: UP000001555' + meaning: NCBITaxon:6945 + title: Ixodes scapularis + exact_mappings: + - NCBITaxon:6945 + - uniprot.proteome:UP000001555 + aliases: + - Deer tick + annotations: + sources: GO + SP_JUGRE: + description: 'Juglans regia (English walnut) - Proteome: UP000235220' + meaning: NCBITaxon:51240 + title: Juglans regia + exact_mappings: + - NCBITaxon:51240 + - uniprot.proteome:UP000235220 + aliases: + - English walnut + annotations: + sources: GO + SP_KLENI: + description: 'Klebsormidium nitens (Green alga) - Proteome: UP000054558' + meaning: NCBITaxon:105231 + title: Klebsormidium nitens + exact_mappings: + - NCBITaxon:105231 + - uniprot.proteome:UP000054558 + aliases: + - Green alga + annotations: + sources: GO + SP_KLEPH: + description: 'Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) - Proteome: UP000007841' + meaning: NCBITaxon:1125630 + title: Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) + exact_mappings: + - NCBITaxon:1125630 + - uniprot.proteome:UP000007841 + annotations: + sources: GO + SP_KLEPO: + description: 'Klebsiella pneumoniae subsp. ozaenae (subspecies) - Proteome: UP000255382' + meaning: NCBITaxon:574 + title: Klebsiella pneumoniae subsp. ozaenae (subspecies) + exact_mappings: + - NCBITaxon:574 + - uniprot.proteome:UP000255382 + annotations: + sources: GO + SP_KORCO: + description: 'Korarchaeum cryptofilum (candidatus archaea) - Proteome: UP000001686' + meaning: NCBITaxon:374847 + title: Korarchaeum cryptofilum + exact_mappings: + - NCBITaxon:374847 + - uniprot.proteome:UP000001686 + aliases: + - candidatus archaea + annotations: + sources: GO + SP_LACSA: + description: 'Lactuca sativa (Garden lettuce) - Proteome: UP000235145' + meaning: NCBITaxon:4236 + title: Lactuca sativa + exact_mappings: + - NCBITaxon:4236 + - uniprot.proteome:UP000235145 + aliases: + - Garden lettuce + annotations: + sources: GO + SP_LEIMA: + description: 'Leishmania major strain Friedlin (leishmania) - Proteome: UP000000542' + meaning: NCBITaxon:347515 + title: Leishmania major strain Friedlin + exact_mappings: + - NCBITaxon:347515 + - uniprot.proteome:UP000000542 + aliases: + - leishmania + annotations: + sources: GO + SP_LEPIN: + description: 'Leptospira interrogans (spirochaetes bacteria) - Proteome: UP000001408' + meaning: NCBITaxon:189518 + title: Leptospira interrogans + exact_mappings: + - NCBITaxon:189518 + - uniprot.proteome:UP000001408 + aliases: + - spirochaetes bacteria + annotations: + sources: GO + SP_LEPOC: + description: 'Lepisosteus oculatus (Spotted gar) - Proteome: UP000018468' + meaning: NCBITaxon:7918 + title: Lepisosteus oculatus + exact_mappings: + - NCBITaxon:7918 + - uniprot.proteome:UP000018468 + aliases: + - Spotted gar + annotations: + sources: GO + SP_LISMO: + description: 'Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) - Proteome: UP000000817' + meaning: NCBITaxon:169963 + title: Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) + exact_mappings: + - NCBITaxon:169963 + - uniprot.proteome:UP000000817 + annotations: + sources: GO + SP_LODEL: + description: 'Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (Saccharomyces + elongisporus) - Proteome: UP000001996' + meaning: NCBITaxon:379508 + title: Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (Saccharomyces + elongisporus) + exact_mappings: + - NCBITaxon:379508 + - uniprot.proteome:UP000001996 + annotations: + sources: GO SP_MACMU: description: 'Macaca mulatta (Rhesus macaque) - Proteome: UP000006718' meaning: NCBITaxon:9544 @@ -9469,6 +14783,8 @@ enums: - uniprot.proteome:UP000006718 aliases: - Rhesus macaque + annotations: + sources: common, GO SP_MAIZE: description: 'Zea mays (Maize) - Proteome: UP000007305' meaning: NCBITaxon:4577 @@ -9478,6 +14794,97 @@ enums: - uniprot.proteome:UP000007305 aliases: - Maize + annotations: + sources: common, GO + SP_MANES: + description: 'Manihot esculenta (Cassava) - Proteome: UP000091857' + meaning: NCBITaxon:3983 + title: Manihot esculenta + exact_mappings: + - NCBITaxon:3983 + - uniprot.proteome:UP000091857 + aliases: + - Cassava + annotations: + sources: GO + SP_MARPO: + description: 'Marchantia polymorpha (Common liverwort) - Proteome: UP000244005' + meaning: NCBITaxon:3197 + title: Marchantia polymorpha + exact_mappings: + - NCBITaxon:3197 + - uniprot.proteome:UP000244005 + aliases: + - Common liverwort + annotations: + sources: GO + SP_MEASC: + description: 'Measles virus (Subacute sclerose panencephalitis virus) strain Ichinose-B95a (MeV strain Ichinose-B95a) + - Proteome: UP000008699' + meaning: NCBITaxon:645098 + title: Measles virus (Subacute sclerose panencephalitis virus) strain Ichinose-B95a + exact_mappings: + - NCBITaxon:645098 + - uniprot.proteome:UP000008699 + aliases: + - MeV strain Ichinose-B95a + annotations: + sources: GO + SP_MEDTR: + description: 'Medicago truncatula (Barrel medic) - Proteome: UP000002051' + meaning: NCBITaxon:3880 + title: Medicago truncatula + exact_mappings: + - NCBITaxon:3880 + - uniprot.proteome:UP000002051 + aliases: + - Barrel medic + annotations: + sources: GO + SP_METAC: + description: 'Methanosarcina acetivorans (euryarchaea) - Proteome: UP000002487' + meaning: NCBITaxon:188937 + title: Methanosarcina acetivorans + exact_mappings: + - NCBITaxon:188937 + - uniprot.proteome:UP000002487 + aliases: + - euryarchaea + annotations: + sources: GO + SP_METJA: + description: 'Methanocaldococcus jannaschii (methanococci archaea) - Proteome: UP000000805' + meaning: NCBITaxon:243232 + title: Methanocaldococcus jannaschii + exact_mappings: + - NCBITaxon:243232 + - uniprot.proteome:UP000000805 + aliases: + - methanococci archaea + annotations: + sources: GO + SP_MONBE: + description: 'Monosiga brevicollis (sponge) - Proteome: UP000001357' + meaning: NCBITaxon:81824 + title: Monosiga brevicollis + exact_mappings: + - NCBITaxon:81824 + - uniprot.proteome:UP000001357 + aliases: + - sponge + annotations: + sources: GO + SP_MONDO: + description: 'Monodelphis domestica (Gray short-tailed opossum) - Proteome: UP000002280' + meaning: NCBITaxon:13616 + title: Monodelphis domestica + exact_mappings: + - NCBITaxon:13616 + - uniprot.proteome:UP000002280 + aliases: + - Gray short-tailed opossum + annotations: + sources: GO SP_MOUSE: description: 'Mus musculus (Mouse) - Proteome: UP000000589' meaning: NCBITaxon:10090 @@ -9487,6 +14894,145 @@ enums: - uniprot.proteome:UP000000589 aliases: - Mouse + annotations: + sources: common, GO + SP_MYCGE: + description: 'Mycoplasma genitalium (mollicutes bacteria) - Proteome: UP000000807' + meaning: NCBITaxon:243273 + title: Mycoplasma genitalium + exact_mappings: + - NCBITaxon:243273 + - uniprot.proteome:UP000000807 + aliases: + - mollicutes bacteria + annotations: + sources: GO + SP_MYCMD: + description: 'Mycosarcoma maydis (Ustilago maydis) (Corn smut fungus) - Proteome: UP000000561' + meaning: NCBITaxon:5270 + title: Mycosarcoma maydis (Ustilago maydis) + exact_mappings: + - NCBITaxon:5270 + - uniprot.proteome:UP000000561 + aliases: + - Corn smut fungus + annotations: + sources: GO + SP_MYCPN: + description: 'Mycoplasma pneumoniae strain ATCC 29342 / M129 / Subtype 1 - Proteome: UP000000808' + meaning: NCBITaxon:272634 + title: Mycoplasma pneumoniae strain ATCC 29342 / M129 / Subtype 1 + exact_mappings: + - NCBITaxon:272634 + - uniprot.proteome:UP000000808 + annotations: + sources: GO + SP_MYCTA: + description: 'Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) - Proteome: UP000001988' + meaning: NCBITaxon:419947 + title: Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) + exact_mappings: + - NCBITaxon:419947 + - uniprot.proteome:UP000001988 + annotations: + sources: GO + SP_MYCTU: + description: 'Mycobacterium tuberculosis H37Rv (actinobacteria) - Proteome: UP000001584' + meaning: NCBITaxon:83332 + title: Mycobacterium tuberculosis H37Rv + exact_mappings: + - NCBITaxon:83332 + - uniprot.proteome:UP000001584 + aliases: + - actinobacteria + annotations: + sources: GO + SP_NEIMB: + description: 'Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) (betaproteobacteria) - Proteome: UP000000425' + meaning: NCBITaxon:122586 + title: Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) + exact_mappings: + - NCBITaxon:122586 + - uniprot.proteome:UP000000425 + aliases: + - betaproteobacteria + annotations: + sources: GO + SP_NEIME: + description: 'Neisseria meningitidis MC58 - Proteome: UP000000425' + meaning: NCBITaxon:122586 + title: Neisseria meningitidis MC58 + exact_mappings: + - NCBITaxon:122586 + - uniprot.proteome:UP000000425 + annotations: + sources: existing + SP_NELNU: + description: 'Nelumbo nucifera (Sacred lotus) - Proteome: UP000189703' + meaning: NCBITaxon:4432 + title: Nelumbo nucifera + exact_mappings: + - NCBITaxon:4432 + - uniprot.proteome:UP000189703 + aliases: + - Sacred lotus + annotations: + sources: GO + SP_NEMVE: + description: 'Nematostella vectensis (Starlet sea anemone) - Proteome: UP000001593' + meaning: NCBITaxon:45351 + title: Nematostella vectensis + exact_mappings: + - NCBITaxon:45351 + - uniprot.proteome:UP000001593 + aliases: + - Starlet sea anemone + annotations: + sources: GO + SP_NEUCR: + description: 'Neurospora crassa (ascomycote fungus) - Proteome: UP000001805' + meaning: NCBITaxon:367110 + title: Neurospora crassa + exact_mappings: + - NCBITaxon:367110 + - uniprot.proteome:UP000001805 + aliases: + - ascomycote fungus + annotations: + sources: GO + SP_NITMS: + description: 'Nitrosopumilus maritimus (thaumarchaea) - Proteome: UP000000792' + meaning: NCBITaxon:436308 + title: Nitrosopumilus maritimus + exact_mappings: + - NCBITaxon:436308 + - uniprot.proteome:UP000000792 + aliases: + - thaumarchaea + annotations: + sources: GO + SP_ORNAN: + description: 'Ornithorhynchus anatinus (Duckbill platypus) - Proteome: UP000002279' + meaning: NCBITaxon:9258 + title: Ornithorhynchus anatinus + exact_mappings: + - NCBITaxon:9258 + - uniprot.proteome:UP000002279 + aliases: + - Duckbill platypus + annotations: + sources: GO + SP_ORYLA: + description: 'Oryzias latipes (Japanese rice fish) - Proteome: UP000001038' + meaning: NCBITaxon:8090 + title: Oryzias latipes + exact_mappings: + - NCBITaxon:8090 + - uniprot.proteome:UP000001038 + aliases: + - Japanese rice fish + annotations: + sources: GO SP_ORYSJ: description: 'Oryza sativa subsp. japonica (Rice) - Proteome: UP000059680' meaning: NCBITaxon:39947 @@ -9496,7 +15042,8 @@ enums: - uniprot.proteome:UP000059680 aliases: - Rice - - Oryza sativa Japonica Group + annotations: + sources: common, GO SP_PANTR: description: 'Pan troglodytes (Chimpanzee) - Proteome: UP000002277' meaning: NCBITaxon:9598 @@ -9506,6 +15053,74 @@ enums: - uniprot.proteome:UP000002277 aliases: - Chimpanzee + annotations: + sources: common, GO + SP_PARTE: + description: 'Paramecium tetraurelia (alveolate) - Proteome: UP000000600' + meaning: NCBITaxon:5888 + title: Paramecium tetraurelia + exact_mappings: + - NCBITaxon:5888 + - uniprot.proteome:UP000000600 + aliases: + - alveolate + annotations: + sources: GO + SP_PEA: + description: 'Pisum sativum (Garden pea) - Proteome: UP001058974' + meaning: NCBITaxon:3888 + title: Pisum sativum + exact_mappings: + - NCBITaxon:3888 + - uniprot.proteome:UP001058974 + aliases: + - Garden pea + annotations: + sources: common + SP_PHANO: + description: 'Phaeosphaeria nodorum (Glume blotch fungus) - Proteome: UP000663193' + meaning: NCBITaxon:321614 + title: Phaeosphaeria nodorum + exact_mappings: + - NCBITaxon:321614 + - uniprot.proteome:UP000663193 + aliases: + - Glume blotch fungus + annotations: + sources: GO + SP_PHYPA: + description: 'Physcomitrella patens (Spreading-leaved earth moss) - Proteome: UP000006727' + meaning: NCBITaxon:3218 + title: Physcomitrella patens + exact_mappings: + - NCBITaxon:3218 + - uniprot.proteome:UP000006727 + aliases: + - Spreading-leaved earth moss + annotations: + sources: GO + SP_PHYRM: + description: 'Phytophthora ramorum (Sudden oak death agent) - Proteome: UP000005238' + meaning: NCBITaxon:164328 + title: Phytophthora ramorum + exact_mappings: + - NCBITaxon:164328 + - uniprot.proteome:UP000005238 + aliases: + - Sudden oak death agent + annotations: + sources: GO + SP_PICGU: + description: 'Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) + (Candida guilliermondii) - Proteome: UP000001997' + meaning: NCBITaxon:294746 + title: Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (Candida + guilliermondii) + exact_mappings: + - NCBITaxon:294746 + - uniprot.proteome:UP000001997 + annotations: + sources: GO SP_PIG: description: 'Sus scrofa (Pig) - Proteome: UP000008227' meaning: NCBITaxon:9823 @@ -9515,6 +15130,85 @@ enums: - uniprot.proteome:UP000008227 aliases: - Pig + annotations: + sources: common, GO + SP_PLAF7: + description: 'Plasmodium falciparum 3D7 (Malaria parasite) - Proteome: UP000001450' + meaning: NCBITaxon:36329 + title: Plasmodium falciparum 3D7 + exact_mappings: + - NCBITaxon:36329 + - uniprot.proteome:UP000001450 + aliases: + - Malaria parasite + annotations: + sources: GO + SP_POPTR: + description: 'Populus trichocarpa (Western balsam poplar) - Proteome: UP000006729' + meaning: NCBITaxon:3694 + title: Populus trichocarpa + exact_mappings: + - NCBITaxon:3694 + - uniprot.proteome:UP000006729 + aliases: + - Western balsam poplar + annotations: + sources: GO + SP_PRIPA: + description: 'Pristionchus pacificus (Parasitic nematode) - Proteome: UP000005239' + meaning: NCBITaxon:54126 + title: Pristionchus pacificus + exact_mappings: + - NCBITaxon:54126 + - uniprot.proteome:UP000005239 + aliases: + - Parasitic nematode + annotations: + sources: GO + SP_PRUPE: + description: 'Prunus persica (Peach) - Proteome: UP000006882' + meaning: NCBITaxon:3760 + title: Prunus persica + exact_mappings: + - NCBITaxon:3760 + - uniprot.proteome:UP000006882 + aliases: + - Peach + annotations: + sources: GO + SP_PSEAE: + description: 'Pseudomonas aeruginosa PAO1 (gammaproteobacteria) - Proteome: UP000002438' + meaning: NCBITaxon:208964 + title: Pseudomonas aeruginosa PAO1 + exact_mappings: + - NCBITaxon:208964 + - uniprot.proteome:UP000002438 + aliases: + - gammaproteobacteria + annotations: + sources: GO + SP_PUCGT: + description: 'Puccinia graminis (Black stem rust fungus) - Proteome: UP000008783' + meaning: NCBITaxon:418459 + title: Puccinia graminis + exact_mappings: + - NCBITaxon:418459 + - uniprot.proteome:UP000008783 + aliases: + - Black stem rust fungus + annotations: + sources: GO + SP_PYRAE: + description: 'Pyrobaculum aerophilum (crenarchaea) - Proteome: UP000002439' + meaning: NCBITaxon:178306 + title: Pyrobaculum aerophilum + exact_mappings: + - NCBITaxon:178306 + - uniprot.proteome:UP000002439 + aliases: + - crenarchaea + annotations: + sources: GO SP_RABIT: description: 'Oryctolagus cuniculus (Rabbit) - Proteome: UP000001811' meaning: NCBITaxon:9986 @@ -9524,15 +15218,63 @@ enums: - uniprot.proteome:UP000001811 aliases: - Rabbit + annotations: + sources: common SP_RAT: description: 'Rattus norvegicus (Rat) - Proteome: UP000002494' meaning: NCBITaxon:10116 title: Rattus norvegicus exact_mappings: - - NCBITaxon:10116 - - uniprot.proteome:UP000002494 + - NCBITaxon:10116 + - uniprot.proteome:UP000002494 + aliases: + - Rat + annotations: + sources: common, GO + SP_RHOBA: + description: 'Rhodopirellula baltica (planctomycetes bacteria) - Proteome: UP000001025' + meaning: NCBITaxon:243090 + title: Rhodopirellula baltica + exact_mappings: + - NCBITaxon:243090 + - uniprot.proteome:UP000001025 + aliases: + - planctomycetes bacteria + annotations: + sources: GO + SP_SACS2: + description: 'Sulfolobus solfataricus (crenarchaea) - Proteome: UP000001974' + meaning: NCBITaxon:273057 + title: Sulfolobus solfataricus + exact_mappings: + - NCBITaxon:273057 + - uniprot.proteome:UP000001974 + aliases: + - crenarchaea + annotations: + sources: GO + SP_SALTY: + description: 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (S. typhimurium LT2) - Proteome: UP000001014' + meaning: NCBITaxon:99287 + title: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) + exact_mappings: + - NCBITaxon:99287 + - uniprot.proteome:UP000001014 aliases: - - Rat + - S. typhimurium LT2 + annotations: + sources: GO + SP_SCHJY: + description: 'Schizosaccharomyces japonicus (Fission yeast) - Proteome: UP000001744' + meaning: NCBITaxon:402676 + title: Schizosaccharomyces japonicus + exact_mappings: + - NCBITaxon:402676 + - uniprot.proteome:UP000001744 + aliases: + - Fission yeast + annotations: + sources: GO SP_SCHPO: description: 'Schizosaccharomyces pombe 972h- (Fission yeast) - Proteome: UP000002485' meaning: NCBITaxon:284812 @@ -9542,6 +15284,19 @@ enums: - uniprot.proteome:UP000002485 aliases: - Fission yeast + annotations: + sources: common, GO + SP_SCLS1: + description: 'Sclerotinia sclerotiorum (White mold) - Proteome: UP000001312' + meaning: NCBITaxon:665079 + title: Sclerotinia sclerotiorum + exact_mappings: + - NCBITaxon:665079 + - uniprot.proteome:UP000001312 + aliases: + - White mold + annotations: + sources: GO SP_SHEEP: description: 'Ovis aries (Sheep) - Proteome: UP000002356' meaning: NCBITaxon:9940 @@ -9551,94 +15306,50 @@ enums: - uniprot.proteome:UP000002356 aliases: - Sheep - SP_XENLA: - description: 'Xenopus laevis (African clawed frog) - Proteome: UP000186698' - meaning: NCBITaxon:8355 - title: Xenopus laevis - exact_mappings: - - NCBITaxon:8355 - - uniprot.proteome:UP000186698 - aliases: - - African clawed frog - SP_XENTR: - description: 'Xenopus tropicalis (Western clawed frog) - Proteome: UP000008143' - meaning: NCBITaxon:8364 - title: Xenopus tropicalis - exact_mappings: - - NCBITaxon:8364 - - uniprot.proteome:UP000008143 - aliases: - - Western clawed frog - SP_YEAST: - description: 'Saccharomyces cerevisiae S288C (Baker''s yeast) - Proteome: UP000002311' - meaning: NCBITaxon:559292 - title: Saccharomyces cerevisiae S288C - exact_mappings: - - NCBITaxon:559292 - - uniprot.proteome:UP000002311 - aliases: - - Baker's yeast - SP_DICDI: - description: 'Dictyostelium discoideum (Slime mold) - Proteome: UP000002195' - meaning: NCBITaxon:44689 - title: Dictyostelium discoideum + annotations: + sources: common + SP_SHEON: + description: 'Shewanella oneidensis (shewanella) - Proteome: UP000008186' + meaning: NCBITaxon:211586 + title: Shewanella oneidensis exact_mappings: - - NCBITaxon:44689 - - uniprot.proteome:UP000002195 + - NCBITaxon:211586 + - uniprot.proteome:UP000008186 aliases: - - Slime mold - SP_HELPY: - description: 'Helicobacter pylori 26695 - Proteome: UP000000429' - meaning: NCBITaxon:85962 - title: Helicobacter pylori 26695 - exact_mappings: - - NCBITaxon:85962 - - uniprot.proteome:UP000000429 - SP_LEIMA: - description: Leishmania major strain Friedlin - meaning: NCBITaxon:347515 - title: Leishmania major strain Friedlin + - shewanella + annotations: + sources: GO + SP_SHIFL: + description: 'Shigella flexneri - Proteome: UP000001006' + meaning: NCBITaxon:623 + title: Shigella flexneri exact_mappings: - - NCBITaxon:347515 - SP_MEDTR: - description: 'Medicago truncatula (Barrel medic) - Proteome: UP000002051' - meaning: NCBITaxon:3880 - title: Medicago truncatula + - NCBITaxon:623 + - uniprot.proteome:UP000001006 + annotations: + sources: GO + SP_SOLLC: + description: 'Solanum lycopersicum (Tomato) - Proteome: UP000004994' + meaning: NCBITaxon:4081 + title: Solanum lycopersicum exact_mappings: - - NCBITaxon:3880 - - uniprot.proteome:UP000002051 + - NCBITaxon:4081 + - uniprot.proteome:UP000004994 aliases: - - Barrel medic - SP_MYCTU: - description: 'Mycobacterium tuberculosis H37Rv - Proteome: UP000001584' - meaning: NCBITaxon:83332 - title: Mycobacterium tuberculosis H37Rv - exact_mappings: - - NCBITaxon:83332 - - uniprot.proteome:UP000001584 - SP_NEIME: - description: 'Neisseria meningitidis MC58 - Proteome: UP000000425' - meaning: NCBITaxon:122586 - title: Neisseria meningitidis MC58 - exact_mappings: - - NCBITaxon:122586 - - uniprot.proteome:UP000000425 - SP_PLAF7: - description: 'Plasmodium falciparum 3D7 (Malaria parasite) - Proteome: UP000001450' - meaning: NCBITaxon:36329 - title: Plasmodium falciparum 3D7 + - Tomato + annotations: + sources: GO + SP_SORBI: + description: 'Sorghum bicolor (Sorghum) - Proteome: UP000000768' + meaning: NCBITaxon:4558 + title: Sorghum bicolor exact_mappings: - - NCBITaxon:36329 - - uniprot.proteome:UP000001450 + - NCBITaxon:4558 + - uniprot.proteome:UP000000768 aliases: - - Malaria parasite - SP_PSEAE: - description: 'Pseudomonas aeruginosa PAO1 - Proteome: UP000002438' - meaning: NCBITaxon:208964 - title: Pseudomonas aeruginosa PAO1 - exact_mappings: - - NCBITaxon:208964 - - uniprot.proteome:UP000002438 + - Sorghum + annotations: + sources: GO SP_SOYBN: description: 'Glycine max (Soybean) - Proteome: UP000008827' meaning: NCBITaxon:3847 @@ -9648,6 +15359,30 @@ enums: - uniprot.proteome:UP000008827 aliases: - Soybean + annotations: + sources: GO + SP_SPIOL: + description: 'Spinacia oleracea (Spinach) - Proteome: UP001155700' + meaning: NCBITaxon:3562 + title: Spinacia oleracea + exact_mappings: + - NCBITaxon:3562 + - uniprot.proteome:UP001155700 + aliases: + - Spinach + annotations: + sources: GO + SP_STAA8: + description: 'Staphylococcus aureus (strain NCTC 8325 / PS 47) (S. aureus NCTC 8325) - Proteome: UP000008816' + meaning: NCBITaxon:93061 + title: Staphylococcus aureus (strain NCTC 8325 / PS 47) + exact_mappings: + - NCBITaxon:93061 + - uniprot.proteome:UP000008816 + aliases: + - S. aureus NCTC 8325 + annotations: + sources: GO SP_STAAU: description: 'Staphylococcus aureus subsp. aureus NCTC 8325 - Proteome: UP000008816' meaning: NCBITaxon:93061 @@ -9655,13 +15390,154 @@ enums: exact_mappings: - NCBITaxon:93061 - uniprot.proteome:UP000008816 + annotations: + sources: existing + SP_STRCL: + description: 'Streptomyces clavuligerus - Proteome: UP000002357' + meaning: NCBITaxon:1901 + title: Streptomyces clavuligerus + exact_mappings: + - NCBITaxon:1901 + - uniprot.proteome:UP000002357 + annotations: + sources: GO + SP_STRCO: + description: 'Streptomyces coelicolor (actinobacteria) - Proteome: UP000001973' + meaning: NCBITaxon:100226 + title: Streptomyces coelicolor + exact_mappings: + - NCBITaxon:100226 + - uniprot.proteome:UP000001973 + aliases: + - actinobacteria + annotations: + sources: GO + SP_STRP1: + description: 'Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 / Serotype M1) - Proteome: UP000000750' + meaning: NCBITaxon:301447 + title: 'Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 / Serotype M1)' + exact_mappings: + - NCBITaxon:301447 + - uniprot.proteome:UP000000750 + annotations: + sources: GO + SP_STRP2: + description: 'Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) - Proteome: UP000001452' + meaning: NCBITaxon:373153 + title: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) + exact_mappings: + - NCBITaxon:373153 + - uniprot.proteome:UP000001452 + annotations: + sources: GO SP_STRPN: - description: 'Streptococcus pneumoniae R6 - Proteome: UP000000586' + description: 'Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) - Proteome: UP000000586' + meaning: NCBITaxon:171101 + title: Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) + exact_mappings: + - NCBITaxon:171101 + - uniprot.proteome:UP000000586 + annotations: + sources: GO + SP_STRPU: + description: 'Strongylocentrotus purpuratus (Purple sea urchin) - Proteome: UP000007110' + meaning: NCBITaxon:7668 + title: Strongylocentrotus purpuratus + exact_mappings: + - NCBITaxon:7668 + - uniprot.proteome:UP000007110 + aliases: + - Purple sea urchin + annotations: + sources: GO + SP_STRR6: + description: 'Streptococcus pneumoniae (strep) - Proteome: UP000000586' meaning: NCBITaxon:171101 - title: Streptococcus pneumoniae R6 + title: Streptococcus pneumoniae exact_mappings: - NCBITaxon:171101 - uniprot.proteome:UP000000586 + aliases: + - strep + annotations: + sources: GO + SP_SYNY3: + description: 'Synechocystis sp. (cyanobacteria) - Proteome: UP000001425' + meaning: NCBITaxon:1111708 + title: Synechocystis sp. + exact_mappings: + - NCBITaxon:1111708 + - uniprot.proteome:UP000001425 + aliases: + - cyanobacteria + annotations: + sources: GO + SP_THAPS: + description: 'Thalassiosira pseudonana (Marine diatom) - Proteome: UP000001449' + meaning: NCBITaxon:35128 + title: Thalassiosira pseudonana + exact_mappings: + - NCBITaxon:35128 + - uniprot.proteome:UP000001449 + aliases: + - Marine diatom + annotations: + sources: GO + SP_THECC: + description: 'Theobroma cacao (Cacao) - Proteome: UP000026915' + meaning: NCBITaxon:3641 + title: Theobroma cacao + exact_mappings: + - NCBITaxon:3641 + - uniprot.proteome:UP000026915 + aliases: + - Cacao + annotations: + sources: GO + SP_THEKO: + description: 'Thermococcus kodakaraensis (euryarchaea) - Proteome: UP000000536' + meaning: NCBITaxon:69014 + title: Thermococcus kodakaraensis + exact_mappings: + - NCBITaxon:69014 + - uniprot.proteome:UP000000536 + aliases: + - euryarchaea + annotations: + sources: GO + SP_THEMA: + description: 'Thermotoga maritima (thermotogae bacteria) - Proteome: UP000008183' + meaning: NCBITaxon:243274 + title: Thermotoga maritima + exact_mappings: + - NCBITaxon:243274 + - uniprot.proteome:UP000008183 + aliases: + - thermotogae bacteria + annotations: + sources: GO + SP_THEYD: + description: 'Thermodesulfovibrio yellowstonii (nitrospirae bacteria) - Proteome: UP000000718' + meaning: NCBITaxon:289376 + title: Thermodesulfovibrio yellowstonii + exact_mappings: + - NCBITaxon:289376 + - uniprot.proteome:UP000000718 + aliases: + - nitrospirae bacteria + annotations: + sources: GO + SP_TOBAC: + description: 'Nicotiana tabacum (Common tobacco) - Proteome: UP000084051' + meaning: NCBITaxon:4097 + title: Nicotiana tabacum + exact_mappings: + - NCBITaxon:4097 + - uniprot.proteome:UP000084051 + aliases: + - Common tobacco + annotations: + sources: common, GO SP_TOXGO: description: 'Toxoplasma gondii ME49 - Proteome: UP000001529' meaning: NCBITaxon:508771 @@ -9669,13 +15545,107 @@ enums: exact_mappings: - NCBITaxon:508771 - uniprot.proteome:UP000001529 + annotations: + sources: existing + SP_TRIAD: + description: 'Trichoplax adhaerens (placozoan) - Proteome: UP000009022' + meaning: NCBITaxon:10228 + title: Trichoplax adhaerens + exact_mappings: + - NCBITaxon:10228 + - uniprot.proteome:UP000009022 + aliases: + - placozoan + annotations: + sources: GO + SP_TRICA: + description: 'Tribolium castaneum (Red flour beetle) - Proteome: UP000007266' + meaning: NCBITaxon:7070 + title: Tribolium castaneum + exact_mappings: + - NCBITaxon:7070 + - uniprot.proteome:UP000007266 + aliases: + - Red flour beetle + annotations: + sources: GO + SP_TRIV3: + description: 'Trichomonas vaginalis (excavate) - Proteome: UP000001542' + meaning: NCBITaxon:412133 + title: Trichomonas vaginalis + exact_mappings: + - NCBITaxon:412133 + - uniprot.proteome:UP000001542 + aliases: + - excavate + annotations: + sources: GO SP_TRYB2: - description: 'Trypanosoma brucei brucei TREU927 - Proteome: UP000008524' + description: 'Trypanosoma brucei brucei TREU927 (excavate) - Proteome: UP000008524' meaning: NCBITaxon:185431 title: Trypanosoma brucei brucei TREU927 exact_mappings: - NCBITaxon:185431 - uniprot.proteome:UP000008524 + aliases: + - excavate + annotations: + sources: GO + SP_VACCW: + description: 'Vaccinia virus (strain Western Reserve) (VACV strain WR) - Proteome: UP000000344' + meaning: NCBITaxon:10254 + title: Vaccinia virus (strain Western Reserve) + exact_mappings: + - NCBITaxon:10254 + - uniprot.proteome:UP000000344 + aliases: + - VACV strain WR + annotations: + sources: GO + SP_VAR67: + description: 'Variola virus (Smallpox virus) (isolate Human/India/Ind3/1967) (VARV) - Proteome: UP000002060' + meaning: NCBITaxon:587200 + title: Variola virus (Smallpox virus) (isolate Human/India/Ind3/1967) + exact_mappings: + - NCBITaxon:587200 + - uniprot.proteome:UP000002060 + aliases: + - VARV + annotations: + sources: GO + SP_VIBCH: + description: 'Vibrio cholerae (cholera) - Proteome: UP000000584' + meaning: NCBITaxon:243277 + title: Vibrio cholerae + exact_mappings: + - NCBITaxon:243277 + - uniprot.proteome:UP000000584 + aliases: + - cholera + annotations: + sources: GO + SP_VITVI: + description: 'Vitis vinifera (Grape) - Proteome: UP000009183' + meaning: NCBITaxon:29760 + title: Vitis vinifera + exact_mappings: + - NCBITaxon:29760 + - uniprot.proteome:UP000009183 + aliases: + - Grape + annotations: + sources: GO + SP_VZVD: + description: 'Varicella-zoster virus (Human herpesvirus 3) strain Dumas (HHV-3 strain Dumas) - Proteome: UP000002602' + meaning: NCBITaxon:10338 + title: Varicella-zoster virus (Human herpesvirus 3) strain Dumas + exact_mappings: + - NCBITaxon:10338 + - uniprot.proteome:UP000002602 + aliases: + - HHV-3 strain Dumas + annotations: + sources: GO SP_WHEAT: description: 'Triticum aestivum (Wheat) - Proteome: UP000019116' meaning: NCBITaxon:4565 @@ -9684,8504 +15654,18836 @@ enums: - NCBITaxon:4565 - uniprot.proteome:UP000019116 aliases: - - Wheat - SP_PEA: - description: 'Pisum sativum (Garden pea) - Proteome: UP001058974' - meaning: NCBITaxon:3888 - title: Pisum sativum - exact_mappings: - - NCBITaxon:3888 - - uniprot.proteome:UP001058974 + - Wheat + annotations: + sources: GO + SP_XANCP: + description: 'Xanthomonas campestris (xanthomonas) - Proteome: UP000001010' + meaning: NCBITaxon:340 + title: Xanthomonas campestris pv. campestris + exact_mappings: + - NCBITaxon:340 + - uniprot.proteome:UP000001010 + aliases: + - xanthomonas + annotations: + sources: GO + SP_XENLA: + description: 'Xenopus laevis (African clawed frog) - Proteome: UP000186698' + meaning: NCBITaxon:8355 + title: Xenopus laevis + exact_mappings: + - NCBITaxon:8355 + - uniprot.proteome:UP000186698 + aliases: + - African clawed frog + annotations: + sources: common, GO + SP_XENTR: + description: 'Xenopus tropicalis (Western clawed frog) - Proteome: UP000008143' + meaning: NCBITaxon:8364 + title: Xenopus tropicalis + exact_mappings: + - NCBITaxon:8364 + - uniprot.proteome:UP000008143 + aliases: + - Western clawed frog + annotations: + sources: common, GO + SP_YARLI: + description: 'Yarrowia lipolytica (Yeast) - Proteome: UP000001300' + meaning: NCBITaxon:4952 + title: Yarrowia lipolytica + exact_mappings: + - NCBITaxon:4952 + - uniprot.proteome:UP000001300 + aliases: + - Yeast + annotations: + sources: GO + SP_YEAST: + description: 'Saccharomyces cerevisiae S288C (Baker''s yeast) - Proteome: UP000002311' + meaning: NCBITaxon:559292 + title: Saccharomyces cerevisiae S288C + exact_mappings: + - NCBITaxon:559292 + - uniprot.proteome:UP000002311 + aliases: + - Baker's yeast + annotations: + sources: common, GO + SP_YERPE: + description: 'Yersinia pestis (plague bacteria) - Proteome: UP000000815' + meaning: NCBITaxon:632 + title: Yersinia pestis + exact_mappings: + - NCBITaxon:632 + - uniprot.proteome:UP000000815 + aliases: + - plague bacteria + annotations: + sources: GO + SP_ZIKV: + description: 'Zika virus (ZIKV) - Proteome: UP000054557' + meaning: NCBITaxon:64320 + title: Zika virus + exact_mappings: + - NCBITaxon:64320 + - uniprot.proteome:UP000054557 + aliases: + - ZIKV + annotations: + sources: GO + is_a: UniprotSpeciesSchemaEnum + annotations: + source_domain: bio + source_schema: uniprot_species + ViralGenomeTypesSchemaEnum: + description: Schema-level enum for viral_genome_types in bio + is_a: BioDomainEnum + abstract: true + annotations: + source_file: bio/viral_genome_types.yaml + ViralGenomeTypeEnum: + title: Viral Genome Type + description: Types of viral genomes based on Baltimore classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + conforms_to: https://en.wikipedia.org/wiki/Baltimore_classification + permissible_values: + DNA: + description: Viral genome composed of DNA + meaning: CHEBI:16991 + title: deoxyribonucleic acid + DSDNA: + description: Double-stranded DNA viral genome + meaning: NCIT:C14348 + title: Double Stranded DNA Virus + is_a: DNA + aliases: + - Baltimore Group I + - Group I + SSDNA: + description: Single-stranded DNA viral genome + meaning: NCIT:C14350 + title: Single Stranded DNA Virus + is_a: DNA + aliases: + - Baltimore Group II + - Group II + RNA: + description: Viral genome composed of RNA + meaning: CHEBI:33697 + title: ribonucleic acid + DSRNA: + description: Double-stranded RNA viral genome + meaning: NCIT:C28518 + title: Double Stranded RNA Virus + is_a: RNA aliases: - - Garden pea - - Lathyrus oleraceus - SP_TOBAC: - description: 'Nicotiana tabacum (Common tobacco) - Proteome: UP000084051' - meaning: NCBITaxon:4097 - title: Nicotiana tabacum - exact_mappings: - - NCBITaxon:4097 - - uniprot.proteome:UP000084051 + - Baltimore Group III + - Group III + SSRNA: + description: Single-stranded RNA viral genome + meaning: NCIT:C95939 + title: Single-Stranded RNA + is_a: RNA + SSRNA_POSITIVE: + description: Positive-sense single-stranded RNA viral genome + meaning: NCIT:C14351 + title: Positive Sense ssRNA Virus + is_a: SSRNA aliases: - - Common tobacco - is_a: UniprotSpeciesSchemaEnum + - Baltimore Group IV + - Group IV + - (+)ssRNA + SSRNA_NEGATIVE: + description: Negative-sense single-stranded RNA viral genome + meaning: NCIT:C14346 + title: Negative Sense ssRNA Virus + is_a: SSRNA + aliases: + - Baltimore Group V + - Group V + - (-)ssRNA + SSRNA_RT: + description: Single-stranded RNA viruses that replicate through a DNA intermediate (retroviruses) + meaning: NCIT:C14347 + title: Deltaretrovirus + is_a: SSRNA + aliases: + - Baltimore Group VI + - Group VI + - Retroviruses + DSDNA_RT: + description: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate (pararetroviruses) + meaning: NCIT:C14349 + title: Other Virus Grouping + is_a: DSDNA + aliases: + - Baltimore Group VII + - Group VII + - Pararetroviruses + MIXED: + description: Mixed or hybrid viral genome type + meaning: NCIT:C128790 + title: Hybrid + UNCHARACTERIZED: + description: Viral genome type not yet characterized + meaning: NCIT:C17998 + title: Unknown + is_a: ViralGenomeTypesSchemaEnum + annotations: + source_domain: bio + source_schema: viral_genome_types + BioprocessingDomainEnum: + description: Domain-level enum for bioprocessing value sets + is_a: ValueSetEnum + abstract: true + BiomanufacturingSchemaEnum: + description: Schema-level enum for biomanufacturing in bioprocessing + is_a: BioprocessingDomainEnum + abstract: true + annotations: + source_file: bioprocessing/biomanufacturing.yaml + BiomanufacturingScaleType: + title: Biomanufacturing Scale Type + description: Scale classifications for biomanufacturing operations, from micro-scale screening through commercial production + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BENCH_SCALE: + description: Laboratory bench scale operations, typically less than 10 liters + annotations: + volume_range: <10 L + purpose: Initial development and screening + PILOT_SCALE: + description: Pilot plant scale operations for process development, typically 10-1000 liters + annotations: + volume_range: 10-1000 L + purpose: Process development and optimization + DEMONSTRATION_SCALE: + description: Demonstration scale operations for technology validation, typically 1000-10000 liters + annotations: + volume_range: 1000-10000 L + purpose: Technology demonstration and validation + COMMERCIAL_SCALE: + description: Full commercial production scale, typically greater than 10000 liters + annotations: + volume_range: '>10000 L' + purpose: Commercial manufacturing + MICRO_SCALE: + description: Micro-scale operations using microfluidic or microtiter plate formats, typically less than 1 mL + annotations: + volume_range: <1 mL + purpose: High-throughput screening and optimization + is_a: BiomanufacturingSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: biomanufacturing + BioproductCategoryType: + title: Bioproduct Category Type + description: Categories of products derived from biological manufacturing processes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BIOFUEL: + title: fuel + description: Biologically derived fuel including ethanol, biodiesel, and biogas + meaning: CHEBI:33292 + BIOCHEMICAL: + description: Chemical compounds produced through biological processes + related_mappings: + - CHEBI:52206 + annotations: + examples: organic acids, amino acids, platform chemicals + BIOPLASTIC: + description: Biodegradable or bio-based plastic materials such as PHA, PLA, and PBS + annotations: + examples: polyhydroxyalkanoates, polylactic acid + BIOSURFACTANT: + description: Surface-active compounds produced by microorganisms + related_mappings: + - CHEBI:35195 + annotations: + examples: rhamnolipids, sophorolipids, surfactin + BIOACTIVE_COMPOUND: + description: Biologically active compounds with therapeutic or functional properties + annotations: + examples: alkaloids, terpenoids, flavonoids + INDUSTRIAL_ENZYME: + title: Enzyme + description: Enzymes produced for industrial applications such as detergents, textiles, and food processing + meaning: NCIT:C16554 + BIOFERTILIZER: + title: biofertilizer + description: Biological preparations containing living microorganisms that enhance plant nutrient availability + meaning: AGRO:00020001 + BIOPESTICIDE: + description: Biological agents used for pest control in agriculture + broad_mappings: + - CHEBI:25944 + annotations: + examples: Bacillus thuringiensis, entomopathogenic fungi + BIOPHARMACEUTICAL: + title: Biological Agent + description: Pharmaceutical products derived from biological sources or manufactured using biotechnology + meaning: NCIT:C307 + annotations: + examples: recombinant proteins, monoclonal antibodies, vaccines + FOOD_INGREDIENT: + title: food ingredient + description: Biologically produced ingredients for food and beverage applications + meaning: FOODON:00004274 + is_a: BiomanufacturingSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: biomanufacturing + BioprocessOptimizationType: + title: Bioprocess Optimization Type + description: Strategies and approaches for optimizing biomanufacturing processes to improve yield, productivity, and product + quality + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MEDIA_OPTIMIZATION: + description: Optimization of growth media composition including carbon sources, nitrogen sources, and micronutrients + STRAIN_ENGINEERING: + description: Genetic modification and selection of production strains for improved performance + annotations: + approaches: metabolic engineering, directed evolution, adaptive laboratory evolution + PROCESS_INTENSIFICATION: + description: Engineering approaches to increase volumetric productivity and reduce process footprint + CONTINUOUS_PROCESSING: + description: Conversion from batch to continuous operation for improved efficiency and consistency + FED_BATCH_OPTIMIZATION: + description: Optimization of feeding strategies in fed-batch processes to maximize product yield + DOWNSTREAM_PURIFICATION: + description: Optimization of product recovery and purification processes + broad_mappings: + - OBI:0001505 + annotations: + approaches: chromatography, membrane separation, extraction + IN_LINE_ANALYTICS: + description: Implementation of real-time process analytical technology (PAT) for process monitoring and control + close_mappings: + - PROCO:0000227 + annotations: + technologies: Raman spectroscopy, NIR, online HPLC + DIGITAL_TWIN_MODELING: + description: Use of computational process models for simulation, prediction, and optimization + annotations: + approaches: mechanistic models, hybrid models, machine learning + is_a: BiomanufacturingSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: biomanufacturing + ScaleUpSchemaEnum: + description: Schema-level enum for scale_up in bioprocessing + is_a: BioprocessingDomainEnum + abstract: true + annotations: + source_file: bioprocessing/scale_up.yaml + ProcessScaleEnum: + title: Process Scale + description: Scale of bioprocessing operations from lab bench to commercial production + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BENCH_SCALE: + description: Laboratory bench scale (typically < 10 L) + annotations: + volume_range: 0.1-10 L + typical_volume: 1-5 L + purpose: Initial development and screening + PILOT_SCALE: + description: Pilot plant scale (10-1000 L) + annotations: + volume_range: 10-1000 L + typical_volume: 50-500 L + purpose: Process development and optimization + DEMONSTRATION_SCALE: + description: Demonstration scale (1000-10000 L) + annotations: + volume_range: 1000-10000 L + typical_volume: 2000-5000 L + purpose: Technology demonstration and validation + PRODUCTION_SCALE: + description: Commercial production scale (>10000 L) + related_mappings: + - NCIT:C112927 + annotations: + volume_range: '>10000 L' + typical_volume: 20000-200000 L + purpose: Commercial manufacturing + MICROFLUIDIC_SCALE: + description: Microfluidic scale (<1 mL) + related_mappings: + - mesh:D044085 + annotations: + volume_range: <1 mL + typical_volume: 1-1000 μL + purpose: High-throughput screening + is_a: ScaleUpSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: scale_up + BioreactorTypeEnum: + title: Bioreactor Type + description: Types of bioreactors used in fermentation and cell culture + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + STIRRED_TANK: + description: Stirred tank reactor (STR/CSTR) + related_mappings: + - OBI:0001046 + annotations: + mixing: Mechanical agitation + common_volumes: 1-200000 L + AIRLIFT: + description: Airlift bioreactor + related_mappings: + - ENVO:00002125 + - OBI:0001046 + annotations: + mixing: Gas sparging + advantages: Low shear, no mechanical parts + BUBBLE_COLUMN: + description: Bubble column bioreactor + related_mappings: + - OBI:0001046 + annotations: + mixing: Gas bubbling + advantages: Simple design, good mass transfer + PACKED_BED: + description: Packed bed bioreactor + annotations: + configuration: Fixed bed of immobilized cells/enzymes + flow: Continuous + FLUIDIZED_BED: + description: Fluidized bed bioreactor + annotations: + configuration: Suspended solid particles + mixing: Fluid flow + MEMBRANE: + title: membrane bioreactor + description: Membrane bioreactor + meaning: ENVO:03600010 + annotations: + feature: Integrated membrane separation + application: Cell retention, product separation + WAVE_BAG: + description: Wave/rocking bioreactor + annotations: + mixing: Rocking motion + advantages: Single-use, low shear + HOLLOW_FIBER: + description: Hollow fiber bioreactor + annotations: + configuration: Hollow fiber membranes + application: High-density cell culture + PHOTOBIOREACTOR: + description: Photobioreactor for photosynthetic organisms + annotations: + light_source: Required + organisms: Algae, cyanobacteria + is_a: ScaleUpSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: scale_up + FermentationModeEnum: + title: Fermentation Mode + description: Modes of fermentation operation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BATCH: + title: batch cell culture + description: Batch fermentation + meaning: MSIO:0000181 + annotations: + operation: All nutrients added at start + duration: Fixed time period + FED_BATCH: + description: Fed-batch fermentation + related_mappings: + - MSIO:0000165 + - MSIO:0000166 + annotations: + operation: Nutrients added during run + advantage: Control of growth rate + CONTINUOUS: + title: continuous fermentation cell culture + description: Continuous fermentation (chemostat) + meaning: MSIO:0000155 + annotations: + operation: Continuous feed and harvest + steady_state: true + PERFUSION: + description: Perfusion culture + annotations: + operation: Continuous media exchange with cell retention + application: High-density cell culture + REPEATED_BATCH: + description: Repeated batch fermentation + annotations: + operation: Sequential batches with partial harvest + advantage: Reduced downtime + SEMI_CONTINUOUS: + description: Semi-continuous operation + annotations: + operation: Periodic harvest and refill + advantage: Extended production + is_a: ScaleUpSchemaEnum annotations: - source_domain: bio - source_schema: uniprot_species - ViralGenomeTypesSchemaEnum: - description: Schema-level enum for viral_genome_types in bio - is_a: BioDomainEnum - abstract: true + source_domain: bioprocessing + source_schema: scale_up + OxygenationStrategyEnum: + title: Oxygenation Strategy + description: Oxygen supply strategies for fermentation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AEROBIC: + description: Aerobic with active aeration + related_mappings: + - ENVO:00002126 + annotations: + oxygen: Required + typical_DO: 20-80% saturation + ANAEROBIC: + description: Anaerobic (no oxygen) + related_mappings: + - ENVO:00002124 + annotations: + oxygen: Excluded + atmosphere: N2 or CO2 + MICROAEROBIC: + description: Microaerobic (limited oxygen) + annotations: + oxygen: Limited + typical_DO: <5% saturation + FACULTATIVE: + description: Facultative (with/without oxygen) + annotations: + oxygen: Optional + flexibility: Organism-dependent + is_a: ScaleUpSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: scale_up + AgitationTypeEnum: + title: Agitation Type + description: Types of agitation/mixing in bioreactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + RUSHTON_TURBINE: + description: Rushton turbine impeller + annotations: + type: Radial flow + power_number: 5-6 + PITCHED_BLADE: + description: Pitched blade turbine + annotations: + type: Axial flow + angle: 45 degrees + MARINE_PROPELLER: + description: Marine propeller + annotations: + type: Axial flow + low_shear: true + ANCHOR: + description: Anchor impeller + annotations: + type: Close clearance + viscous_fluids: true + HELICAL_RIBBON: + description: Helical ribbon impeller + annotations: + type: Close clearance + high_viscosity: true + MAGNETIC_BAR: + description: Magnetic stir bar + annotations: + scale: Laboratory + volume: <5 L + ORBITAL_SHAKING: + description: Orbital shaking + annotations: + type: Platform shaker + application: Shake flasks + NO_AGITATION: + description: No mechanical agitation + annotations: + mixing: Gas sparging or static + is_a: ScaleUpSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: scale_up + DownstreamProcessEnum: + title: Downstream Process + description: Downstream processing unit operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CENTRIFUGATION: + title: analytical centrifugation + description: Centrifugal separation + meaning: CHMO:0002010 + annotations: + principle: Density difference + types: Disk stack, tubular, decanter + FILTRATION: + description: Filtration (micro/ultra/nano) + meaning: CHMO:0001640 + annotations: + types: Dead-end, crossflow, depth + CHROMATOGRAPHY: + description: Chromatographic separation + meaning: CHMO:0001000 + annotations: + types: Ion exchange, affinity, size exclusion + EXTRACTION: + description: Liquid-liquid extraction + meaning: CHMO:0001577 + annotations: + principle: Partitioning between phases + PRECIPITATION: + description: Precipitation/crystallization + meaning: CHMO:0001688 + annotations: + agents: Salts, solvents, pH + EVAPORATION: + description: Evaporation/concentration + meaning: CHMO:0001574 + annotations: + types: Falling film, MVR, TVR + DISTILLATION: + description: Distillation + meaning: CHMO:0001534 + title: continuous distillation + annotations: + principle: Boiling point difference + DRYING: + description: Drying operations + meaning: CHMO:0001551 + title: direct drying + annotations: + types: Spray, freeze, vacuum + HOMOGENIZATION: + description: Cell disruption/homogenization + annotations: + methods: High pressure, bead mill + is_a: ScaleUpSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: scale_up + FeedstockTypeEnum: + title: Feedstock Type + description: Types of feedstocks for bioprocessing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GLUCOSE: + description: Glucose/dextrose + meaning: CHEBI:17234 + annotations: + source: Corn, sugarcane + carbon_source: true + SUCROSE: + description: Sucrose + meaning: CHEBI:17992 + annotations: + source: Sugarcane, sugar beet + carbon_source: true + GLYCEROL: + description: Glycerol + meaning: CHEBI:17754 + annotations: + source: Biodiesel byproduct + carbon_source: true + MOLASSES: + description: Molasses + meaning: CHEBI:83163 + annotations: + source: Sugar processing byproduct + complex_medium: true + CORN_STEEP_LIQUOR: + description: Corn steep liquor + annotations: + source: Corn wet milling + nitrogen_source: true + YEAST_EXTRACT: + description: Yeast extract + meaning: FOODON:03315426 + annotations: + source: Autolyzed yeast + complex_nutrient: true + LIGNOCELLULOSIC: + description: Lignocellulosic biomass + annotations: + source: Agricultural residues, wood + pretreatment: Required + METHANOL: + description: Methanol + meaning: CHEBI:17790 + annotations: + carbon_source: true + methylotrophic: true + WASTE_STREAM: + description: Industrial waste stream + annotations: + variable_composition: true + sustainability: Circular economy + is_a: ScaleUpSchemaEnum + annotations: + source_domain: bioprocessing + source_schema: scale_up + ProductTypeEnum: + title: Product Type + description: Types of products from bioprocessing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BIOFUEL: + title: fuel + description: Biofuel (ethanol, biodiesel, etc.) + meaning: CHEBI:33292 + annotations: + category: Energy + PROTEIN: + description: Recombinant protein + meaning: NCIT:C17021 + annotations: + category: Biopharmaceutical + ENZYME: + description: Industrial enzyme + meaning: NCIT:C16554 + annotations: + category: Biocatalyst + ORGANIC_ACID: + description: Organic acid (citric, lactic, etc.) + meaning: CHEBI:64709 + annotations: + category: Chemical + AMINO_ACID: + description: Amino acid + meaning: CHEBI:33709 + annotations: + category: Nutritional + ANTIBIOTIC: + description: Antibiotic + meaning: CHEBI:33281 + title: antimicrobial agent + annotations: + category: Pharmaceutical + VITAMIN: + description: Vitamin + meaning: CHEBI:33229 + title: vitamin (role) + annotations: + category: Nutritional + BIOPOLYMER: + description: Biopolymer (PHA, PLA, etc.) + meaning: CHEBI:33694 + title: biomacromolecule + annotations: + category: Material + BIOMASS: + description: Microbial biomass + meaning: ENVO:01000155 + title: organic material + annotations: + category: Feed/food + SECONDARY_METABOLITE: + description: Secondary metabolite + meaning: CHEBI:25212 + title: metabolite + annotations: + category: Specialty chemical + is_a: ScaleUpSchemaEnum annotations: - source_file: bio/viral_genome_types.yaml - ViralGenomeTypeEnum: - description: Types of viral genomes based on Baltimore classification - conforms_to: https://en.wikipedia.org/wiki/Baltimore_classification + source_domain: bioprocessing + source_schema: scale_up + SterilizationMethodEnum: + title: Sterilization Method + description: Methods for sterilization in bioprocessing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - DNA: - description: Viral genome composed of DNA - meaning: CHEBI:16991 - title: deoxyribonucleic acid - DSDNA: - description: Double-stranded DNA viral genome - meaning: NCIT:C14348 - title: Double Stranded DNA Virus - is_a: DNA - aliases: - - Baltimore Group I - - Group I - SSDNA: - description: Single-stranded DNA viral genome - meaning: NCIT:C14350 - title: Single Stranded DNA Virus - is_a: DNA - aliases: - - Baltimore Group II - - Group II - RNA: - description: Viral genome composed of RNA - meaning: CHEBI:33697 - title: ribonucleic acid - DSRNA: - description: Double-stranded RNA viral genome - meaning: NCIT:C28518 - title: Double Stranded RNA Virus - is_a: RNA - aliases: - - Baltimore Group III - - Group III - SSRNA: - description: Single-stranded RNA viral genome - meaning: NCIT:C95939 - title: Single-Stranded RNA - is_a: RNA - SSRNA_POSITIVE: - description: Positive-sense single-stranded RNA viral genome - meaning: NCIT:C14351 - title: Positive Sense ssRNA Virus - is_a: SSRNA - aliases: - - Baltimore Group IV - - Group IV - - (+)ssRNA - SSRNA_NEGATIVE: - description: Negative-sense single-stranded RNA viral genome - meaning: NCIT:C14346 - title: Negative Sense ssRNA Virus - is_a: SSRNA - aliases: - - Baltimore Group V - - Group V - - (-)ssRNA - SSRNA_RT: - description: Single-stranded RNA viruses that replicate through a DNA intermediate (retroviruses) - meaning: NCIT:C14347 - title: Deltaretrovirus - is_a: SSRNA - aliases: - - Baltimore Group VI - - Group VI - - Retroviruses - DSDNA_RT: - description: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate (pararetroviruses) - meaning: NCIT:C14349 - title: Other Virus Grouping - is_a: DSDNA - aliases: - - Baltimore Group VII - - Group VII - - Pararetroviruses - MIXED: - description: Mixed or hybrid viral genome type - meaning: NCIT:C128790 - title: Hybrid - UNCHARACTERIZED: - description: Viral genome type not yet characterized - meaning: NCIT:C17998 - title: Unknown - is_a: ViralGenomeTypesSchemaEnum + STEAM_IN_PLACE: + description: Steam in place (SIP) + annotations: + temperature: 121-134°C + time: 15-30 min + AUTOCLAVE: + title: autoclaving + description: Autoclave sterilization + meaning: CHMO:0002846 + annotations: + temperature: 121°C + pressure: 15 psi + FILTER_STERILIZATION: + description: Filter sterilization (0.2 μm) + annotations: + pore_size: 0.2 μm + heat_labile: true + GAMMA_IRRADIATION: + description: Gamma irradiation + annotations: + dose: 25-40 kGy + single_use: true + ETHYLENE_OXIDE: + description: Ethylene oxide sterilization + annotations: + temperature: 30-60°C + plastic_compatible: true + UV_STERILIZATION: + description: UV sterilization + annotations: + wavelength: 254 nm + surface_only: true + CHEMICAL_STERILIZATION: + description: Chemical sterilization + annotations: + agents: Bleach, alcohol, peroxide + contact_time: Variable + is_a: ScaleUpSchemaEnum annotations: - source_domain: bio - source_schema: viral_genome_types - BioprocessingDomainEnum: - description: Domain-level enum for bioprocessing value sets + source_domain: bioprocessing + source_schema: scale_up + BusinessDomainEnum: + description: Domain-level enum for business value sets is_a: ValueSetEnum abstract: true - ScaleUpSchemaEnum: - description: Schema-level enum for scale_up in bioprocessing - is_a: BioprocessingDomainEnum + HumanResourcesSchemaEnum: + description: Schema-level enum for human_resources in business + is_a: BusinessDomainEnum abstract: true annotations: - source_file: bioprocessing/scale_up.yaml - ProcessScaleEnum: - description: Scale of bioprocessing operations from lab bench to commercial production + source_file: business/human_resources.yaml + EmploymentTypeEnum: + title: Employment Type + description: Types of employment arrangements and contracts + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FULL_TIME: + title: Full-Time Employment + description: Regular full-time employment status + annotations: + hours: typically 40 hours per week + benefits: full benefits package + classification: exempt or non-exempt + stability: permanent position + commitment: full organizational commitment + PART_TIME: + title: Part-Time Employment + description: Regular part-time employment status + annotations: + hours: less than full-time hours + benefits: limited or prorated benefits + flexibility: flexible scheduling + classification: typically non-exempt + commitment: ongoing but reduced hours + CONTRACT: + title: Contract Employment + description: Fixed-term contractual employment + annotations: + duration: defined contract period + relationship: contractual relationship + benefits: limited benefits + termination: defined end date + purpose: specific project or duration + TEMPORARY: + title: Temporary Employment + description: Short-term temporary employment + annotations: + duration: short-term assignment + agency: often through staffing agency + benefits: minimal benefits + purpose: seasonal or project work + flexibility: high flexibility + FREELANCE: + title: Freelance/Independent Contractor + description: Independent contractor or freelance work + annotations: + relationship: independent contractor + benefits: no traditional benefits + control: high work autonomy + taxes: responsible for own taxes + projects: project-based work + INTERN: + title: Internship + description: Student or entry-level internship program + annotations: + purpose: learning and experience + duration: limited duration + compensation: may be paid or unpaid + education: educational component + supervision: mentorship and guidance + SEASONAL: + title: Seasonal Employment + description: Employment tied to seasonal business needs + annotations: + pattern: recurring seasonal pattern + duration: specific seasons + industry: retail, agriculture, tourism + return: potential for seasonal return + benefits: limited benefits + CONSULTANT: + title: Consultant + description: Professional consulting services + annotations: + expertise: specialized expertise + relationship: advisory relationship + independence: independent professional + project: project or retainer basis + value: strategic value-add + VOLUNTEER: + title: Volunteer + description: Unpaid volunteer service + annotations: + compensation: unpaid service + motivation: altruistic motivation + commitment: voluntary commitment + purpose: mission-driven work + recognition: non-monetary recognition + is_a: HumanResourcesSchemaEnum + annotations: + source_domain: business + source_schema: human_resources + JobLevelEnum: + title: Job Level + description: Organizational job levels and career progression + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BENCH_SCALE: - description: Laboratory bench scale (typically < 10 L) + ENTRY_LEVEL: + title: Entry Level + description: Beginning career level positions annotations: - volume_range: 0.1-10 L - typical_volume: 1-5 L - purpose: Initial development and screening - PILOT_SCALE: - description: Pilot plant scale (10-1000 L) + experience: 0-2 years experience + responsibilities: basic operational tasks + supervision: high supervision required + development: learning and development focus + career_stage: career beginning + JUNIOR: + title: Junior Level + description: Junior professional level annotations: - volume_range: 10-1000 L - typical_volume: 50-500 L - purpose: Process development and optimization - DEMONSTRATION_SCALE: - description: Demonstration scale (1000-10000 L) + experience: 2-4 years experience + responsibilities: routine professional tasks + independence: some independence + mentorship: receiving mentorship + skill_building: skill development phase + MID_LEVEL: + title: Mid-Level + description: Experienced professional level annotations: - volume_range: 1000-10000 L - typical_volume: 2000-5000 L - purpose: Technology demonstration and validation - PRODUCTION_SCALE: - description: Commercial production scale (>10000 L) - related_mappings: - - NCIT:C112927 + experience: 4-8 years experience + responsibilities: complex project work + independence: high independence + mentorship: providing and receiving mentorship + expertise: developing expertise + SENIOR: + title: Senior Level + description: Senior professional level annotations: - volume_range: '>10000 L' - typical_volume: 20000-200000 L - purpose: Commercial manufacturing - MICROFLUIDIC_SCALE: - description: Microfluidic scale (<1 mL) - related_mappings: - - mesh:D044085 + experience: 8+ years experience + responsibilities: strategic project leadership + expertise: subject matter expertise + mentorship: mentoring others + influence: organizational influence + LEAD: + title: Team Lead + description: Team leadership role annotations: - volume_range: <1 mL - typical_volume: 1-1000 μL - purpose: High-throughput screening - is_a: ScaleUpSchemaEnum + responsibility: team leadership + people_management: direct reports + coordination: team coordination + accountability: team results + development: team development + MANAGER: + title: Manager + description: Management level position + annotations: + scope: departmental management + people_management: multiple direct reports + budget: budget responsibility + strategy: tactical strategy + operations: operational management + DIRECTOR: + title: Director + description: Director level executive + annotations: + scope: multi-departmental oversight + strategy: strategic planning + leadership: organizational leadership + stakeholders: senior stakeholder management + results: business results accountability + VP: + title: Vice President + description: Vice President executive level + annotations: + scope: business unit or functional area + strategy: strategic leadership + board: board interaction + organization: organizational impact + succession: succession planning + C_LEVEL: + title: C-Level Executive + description: Chief executive level + annotations: + scope: enterprise-wide responsibility + governance: corporate governance + vision: organizational vision + stakeholders: external stakeholder management + fiduciary: fiduciary responsibility + is_a: HumanResourcesSchemaEnum annotations: - source_domain: bioprocessing - source_schema: scale_up - BioreactorTypeEnum: - description: Types of bioreactors used in fermentation and cell culture + source_domain: business + source_schema: human_resources + HRFunctionEnum: + title: HR Function + description: Human resources functional areas and specializations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - STIRRED_TANK: - description: Stirred tank reactor (STR/CSTR) - related_mappings: - - OBI:0001046 + TALENT_ACQUISITION: + title: Talent Acquisition + description: Recruitment and hiring functions annotations: - mixing: Mechanical agitation - common_volumes: 1-200000 L - AIRLIFT: - description: Airlift bioreactor - related_mappings: - - ENVO:00002125 - - OBI:0001046 + activities: sourcing, screening, interviewing, hiring + focus: attracting and selecting talent + metrics: time to hire, quality of hire + strategy: workforce planning + technology: ATS and recruitment tools + EMPLOYEE_RELATIONS: + title: Employee Relations + description: Managing employee relationships and workplace issues annotations: - mixing: Gas sparging - advantages: Low shear, no mechanical parts - BUBBLE_COLUMN: - description: Bubble column bioreactor - related_mappings: - - OBI:0001046 + activities: conflict resolution, grievance handling + focus: positive employee relations + communication: employee communication + culture: workplace culture + mediation: dispute resolution + COMPENSATION_BENEFITS: + title: Compensation and Benefits + description: Managing compensation and benefits programs annotations: - mixing: Gas bubbling - advantages: Simple design, good mass transfer - PACKED_BED: - description: Packed bed bioreactor + activities: salary administration, benefits design + analysis: market analysis and benchmarking + compliance: regulatory compliance + cost: cost management + competitiveness: market competitiveness + PERFORMANCE_MANAGEMENT: + title: Performance Management + description: Employee performance evaluation and improvement annotations: - configuration: Fixed bed of immobilized cells/enzymes - flow: Continuous - FLUIDIZED_BED: - description: Fluidized bed bioreactor + activities: performance reviews, goal setting + development: performance improvement + measurement: performance metrics + feedback: continuous feedback + coaching: performance coaching + LEARNING_DEVELOPMENT: + title: Learning and Development + description: Employee training and development programs + annotations: + activities: training design, skill development + career: career development + leadership: leadership development + compliance: compliance training + technology: learning management systems + HR_ANALYTICS: + title: HR Analytics + description: HR data analysis and workforce metrics + annotations: + activities: data analysis, metrics reporting + insights: workforce insights + predictive: predictive analytics + dashboard: HR dashboards + decision_support: data-driven decisions + ORGANIZATIONAL_DEVELOPMENT: + title: Organizational Development + description: Organizational design and change management + annotations: + activities: change management, culture transformation + design: organizational design + effectiveness: organizational effectiveness + culture: culture development + transformation: business transformation + HR_COMPLIANCE: + title: HR Compliance + description: Employment law compliance and risk management + annotations: + activities: policy development, compliance monitoring + legal: employment law compliance + risk: HR risk management + auditing: compliance auditing + documentation: record keeping + HRIS_TECHNOLOGY: + title: HRIS and Technology + description: HR information systems and technology + annotations: + activities: system administration, data management + systems: HRIS implementation + automation: process automation + integration: system integration + security: data security + is_a: HumanResourcesSchemaEnum + annotations: + source_domain: business + source_schema: human_resources + CompensationTypeEnum: + title: Compensation Type + description: Types of employee compensation structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BASE_SALARY: + title: Base Salary + description: Fixed annual salary compensation + annotations: + structure: fixed annual amount + payment: regular pay periods + exemption: often exempt from overtime + predictability: predictable income + market: market benchmarked + HOURLY_WAGE: + title: Hourly Wage + description: Compensation paid per hour worked + annotations: + structure: rate per hour + overtime: overtime eligible + tracking: time tracking required + variability: variable based on hours + classification: non-exempt employees + COMMISSION: + title: Commission + description: Performance-based sales commission + annotations: + structure: percentage of sales + performance: performance-based + variability: highly variable + motivation: sales motivation + risk: income risk + BONUS: + title: Performance Bonus + description: Additional compensation for performance annotations: - configuration: Suspended solid particles - mixing: Fluid flow - MEMBRANE: - title: membrane bioreactor - description: Membrane bioreactor - meaning: ENVO:03600010 + timing: annual or periodic + criteria: performance criteria + discretionary: may be discretionary + recognition: performance recognition + retention: retention tool + STOCK_OPTIONS: + title: Stock Options + description: Equity compensation through stock options annotations: - feature: Integrated membrane separation - application: Cell retention, product separation - WAVE_BAG: - description: Wave/rocking bioreactor + equity: equity participation + vesting: vesting schedule + retention: long-term retention + upside: company growth upside + risk: market risk + PROFIT_SHARING: + title: Profit Sharing + description: Sharing of company profits with employees annotations: - mixing: Rocking motion - advantages: Single-use, low shear - HOLLOW_FIBER: - description: Hollow fiber bioreactor + structure: percentage of profits + performance: company performance based + culture: ownership culture + variability: variable based on profits + alignment: interest alignment + PIECE_RATE: + title: Piece Rate + description: Compensation based on units produced annotations: - configuration: Hollow fiber membranes - application: High-density cell culture - PHOTOBIOREACTOR: - description: Photobioreactor for photosynthetic organisms + structure: rate per unit produced + productivity: productivity-based + manufacturing: common in manufacturing + measurement: output measurement + efficiency: efficiency incentive + STIPEND: + title: Stipend + description: Fixed regular allowance or payment annotations: - light_source: Required - organisms: Algae, cyanobacteria - is_a: ScaleUpSchemaEnum + purpose: specific purpose payment + amount: modest fixed amount + regularity: regular payment + supplemental: supplemental income + categories: interns, volunteers, board members + is_a: HumanResourcesSchemaEnum annotations: - source_domain: bioprocessing - source_schema: scale_up - FermentationModeEnum: - description: Modes of fermentation operation + source_domain: business + source_schema: human_resources + PerformanceRatingEnum: + title: Performance Rating + description: Employee performance evaluation ratings + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BATCH: - title: batch cell culture - description: Batch fermentation - meaning: MSIO:0000181 - annotations: - operation: All nutrients added at start - duration: Fixed time period - FED_BATCH: - description: Fed-batch fermentation - related_mappings: - - MSIO:0000165 - - MSIO:0000166 + EXCEEDS_EXPECTATIONS: + title: Exceeds Expectations + description: Performance significantly above expected standards annotations: - operation: Nutrients added during run - advantage: Control of growth rate - CONTINUOUS: - title: continuous fermentation cell culture - description: Continuous fermentation (chemostat) - meaning: MSIO:0000155 + level: top performance tier + impact: significant business impact + recognition: high recognition + development: stretch assignments + percentage: typically 10-20% of population + MEETS_EXPECTATIONS: + title: Meets Expectations + description: Performance meets all expected standards annotations: - operation: Continuous feed and harvest - steady_state: true - PERFUSION: - description: Perfusion culture + level: satisfactory performance + standards: meets all job requirements + competency: demonstrates required competencies + consistency: consistent performance + percentage: typically 60-70% of population + PARTIALLY_MEETS: + title: Partially Meets Expectations + description: Performance meets some but not all standards annotations: - operation: Continuous media exchange with cell retention - application: High-density cell culture - REPEATED_BATCH: - description: Repeated batch fermentation + level: below standard performance + improvement: improvement needed + support: additional support required + development: focused development plan + percentage: typically 10-15% of population + DOES_NOT_MEET: + title: Does Not Meet Expectations + description: Performance below acceptable standards annotations: - operation: Sequential batches with partial harvest - advantage: Reduced downtime - SEMI_CONTINUOUS: - description: Semi-continuous operation + level: unsatisfactory performance + action: performance improvement plan + timeline: improvement timeline + consequences: potential consequences + percentage: typically 5-10% of population + OUTSTANDING: + title: Outstanding + description: Exceptional performance far exceeding standards annotations: - operation: Periodic harvest and refill - advantage: Extended production - is_a: ScaleUpSchemaEnum + level: exceptional performance + impact: transformational impact + leadership: demonstrates leadership + innovation: innovation and excellence + rarity: rare rating + is_a: HumanResourcesSchemaEnum annotations: - source_domain: bioprocessing - source_schema: scale_up - OxygenationStrategyEnum: - description: Oxygen supply strategies for fermentation + source_domain: business + source_schema: human_resources + RecruitmentSourceEnum: + title: Recruitment Source + description: Sources for candidate recruitment and sourcing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - AEROBIC: - description: Aerobic with active aeration - related_mappings: - - ENVO:00002126 + INTERNAL_REFERRAL: + title: Internal Employee Referral + description: Candidates referred by current employees annotations: - oxygen: Required - typical_DO: 20-80% saturation - ANAEROBIC: - description: Anaerobic (no oxygen) - related_mappings: - - ENVO:00002124 + source: employee networks + quality: typically high quality + cost: low cost per hire + cultural_fit: good cultural fit + retention: higher retention rates + JOB_BOARDS: + title: Online Job Boards + description: Candidates from online job posting sites annotations: - oxygen: Excluded - atmosphere: N2 or CO2 - MICROAEROBIC: - description: Microaerobic (limited oxygen) + reach: broad candidate reach + cost: moderate cost + volume: high application volume + screening: requires screening + examples: Indeed, LinkedIn, Monster + COMPANY_WEBSITE: + title: Company Career Website + description: Candidates applying through company website annotations: - oxygen: Limited - typical_DO: <5% saturation - FACULTATIVE: - description: Facultative (with/without oxygen) + interest: high company interest + brand: employer brand driven + quality: targeted candidates + direct: direct application + cost: low incremental cost + SOCIAL_MEDIA: + title: Social Media Recruiting + description: Candidates sourced through social media platforms annotations: - oxygen: Optional - flexibility: Organism-dependent - is_a: ScaleUpSchemaEnum + platforms: LinkedIn, Facebook, Twitter + active: active sourcing + networking: professional networking + targeting: targeted approach + engagement: relationship building + RECRUITMENT_AGENCIES: + title: External Recruitment Agencies + description: Candidates sourced through recruitment firms + annotations: + expertise: specialized expertise + cost: higher cost + speed: faster time to hire + screening: pre-screened candidates + specialization: industry specialization + CAMPUS_RECRUITING: + title: Campus and University Recruiting + description: Recruitment from educational institutions + annotations: + target: students and new graduates + programs: internship and graduate programs + relationships: university relationships + pipeline: talent pipeline + early_career: early career focus + PROFESSIONAL_NETWORKS: + title: Professional Networks + description: Recruitment through professional associations + annotations: + industry: industry-specific networks + expertise: specialized expertise + relationships: professional relationships + credibility: professional credibility + targeted: targeted recruitment + HEADHUNTERS: + title: Executive Search/Headhunters + description: Executive-level recruitment specialists + annotations: + level: senior and executive roles + expertise: specialized search expertise + network: extensive professional networks + confidential: confidential searches + cost: premium cost + is_a: HumanResourcesSchemaEnum annotations: - source_domain: bioprocessing - source_schema: scale_up - AgitationTypeEnum: - description: Types of agitation/mixing in bioreactors + source_domain: business + source_schema: human_resources + TrainingTypeEnum: + title: Training Type + description: Types of employee training and development programs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - RUSHTON_TURBINE: - description: Rushton turbine impeller + ONBOARDING: + title: New Employee Onboarding + description: Orientation and integration training for new hires annotations: - type: Radial flow - power_number: 5-6 - PITCHED_BLADE: - description: Pitched blade turbine + timing: first days/weeks of employment + purpose: integration and orientation + content: company culture, policies, role basics + delivery: structured program + outcome: successful integration + TECHNICAL_SKILLS: + title: Technical Skills Training + description: Job-specific technical competency development annotations: - type: Axial flow - angle: 45 degrees - MARINE_PROPELLER: - description: Marine propeller + focus: technical competencies + relevance: job-specific skills + methods: hands-on training + certification: may include certification + updating: continuous skill updates + LEADERSHIP_DEVELOPMENT: + title: Leadership Development + description: Management and leadership capability building annotations: - type: Axial flow - low_shear: true - ANCHOR: - description: Anchor impeller + target: managers and high-potential employees + skills: leadership and management skills + development: long-term development + mentorship: coaching and mentorship + succession: succession planning + COMPLIANCE_TRAINING: + title: Compliance Training + description: Required training for regulatory compliance annotations: - type: Close clearance - viscous_fluids: true - HELICAL_RIBBON: - description: Helical ribbon impeller + requirement: mandatory training + regulation: regulatory compliance + documentation: completion tracking + frequency: periodic updates + risk: risk mitigation + SOFT_SKILLS: + title: Soft Skills Development + description: Communication and interpersonal skills training annotations: - type: Close clearance - high_viscosity: true - MAGNETIC_BAR: - description: Magnetic stir bar + skills: communication, teamwork, problem-solving + application: broadly applicable + development: personal development + effectiveness: workplace effectiveness + collaboration: collaboration skills + SAFETY_TRAINING: + title: Safety Training + description: Workplace safety and health training annotations: - scale: Laboratory - volume: <5 L - ORBITAL_SHAKING: - description: Orbital shaking + focus: safety procedures and practices + compliance: OSHA compliance + prevention: accident prevention + emergency: emergency procedures + culture: safety culture + DIVERSITY_INCLUSION: + title: Diversity and Inclusion Training + description: Training on diversity, equity, and inclusion annotations: - type: Platform shaker - application: Shake flasks - NO_AGITATION: - description: No mechanical agitation + awareness: cultural awareness + bias: unconscious bias training + inclusion: inclusive practices + culture: inclusive culture + behavior: behavior change + CROSS_TRAINING: + title: Cross-Training + description: Training in multiple roles or departments annotations: - mixing: Gas sparging or static - is_a: ScaleUpSchemaEnum + flexibility: workforce flexibility + coverage: backup coverage + development: career development + understanding: broader understanding + collaboration: improved collaboration + is_a: HumanResourcesSchemaEnum annotations: - source_domain: bioprocessing - source_schema: scale_up - DownstreamProcessEnum: - description: Downstream processing unit operations + source_domain: business + source_schema: human_resources + EmployeeStatusEnum: + title: Employee Status + description: Current employment status classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - CENTRIFUGATION: - title: analytical centrifugation - description: Centrifugal separation - meaning: CHMO:0002010 + ACTIVE: + title: Active Employment + description: Currently employed and working annotations: - principle: Density difference - types: Disk stack, tubular, decanter - FILTRATION: - description: Filtration (micro/ultra/nano) - meaning: CHMO:0001640 + status: actively working + benefits: receiving full benefits + responsibilities: fulfilling job responsibilities + engagement: expected engagement + performance: subject to performance management + ON_LEAVE: + title: On Leave + description: Temporarily away from work on approved leave annotations: - types: Dead-end, crossflow, depth - CHROMATOGRAPHY: - description: Chromatographic separation - meaning: CHMO:0001000 + temporary: temporary absence + approval: approved leave + return: expected return date + benefits: may retain benefits + types: medical, family, personal leave + PROBATIONARY: + title: Probationary Period + description: New employee in probationary period annotations: - types: Ion exchange, affinity, size exclusion - EXTRACTION: - description: Liquid-liquid extraction - meaning: CHMO:0001577 + duration: defined probationary period + evaluation: ongoing evaluation + benefits: limited or delayed benefits + termination: easier termination + assessment: performance assessment + SUSPENDED: + title: Suspended + description: Temporarily suspended from work annotations: - principle: Partitioning between phases - PRECIPITATION: - description: Precipitation/crystallization - meaning: CHMO:0001688 + disciplinary: disciplinary action + investigation: pending investigation + pay: with or without pay + temporary: temporary status + review: pending review + TERMINATED: + title: Terminated + description: Employment has been terminated annotations: - agents: Salts, solvents, pH - EVAPORATION: - description: Evaporation/concentration - meaning: CHMO:0001574 + end: employment ended + voluntary: voluntary or involuntary + benefits: benefits cessation + final: final status + documentation: termination documentation + RETIRED: + title: Retired + description: Retired from employment annotations: - types: Falling film, MVR, TVR - DISTILLATION: - description: Distillation - meaning: CHMO:0001534 - title: continuous distillation + voluntary: voluntary departure + age: retirement age + benefits: retirement benefits + service: completed service + transition: career transition + is_a: HumanResourcesSchemaEnum + annotations: + source_domain: business + source_schema: human_resources + WorkArrangementEnum: + title: Work Arrangement + description: Work location and arrangement types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ON_SITE: + title: On-Site Work + description: Work performed at company facilities annotations: - principle: Boiling point difference - DRYING: - description: Drying operations - meaning: CHMO:0001551 - title: direct drying + location: company premises + collaboration: in-person collaboration + supervision: direct supervision + equipment: company-provided equipment + culture: office culture participation + REMOTE: + title: Remote Work + description: Work performed away from company facilities annotations: - types: Spray, freeze, vacuum - HOMOGENIZATION: - description: Cell disruption/homogenization + location: home or remote location + technology: technology-enabled work + flexibility: location flexibility + independence: high independence + communication: virtual communication + HYBRID: + title: Hybrid Work + description: Combination of on-site and remote work annotations: - methods: High pressure, bead mill - is_a: ScaleUpSchemaEnum + flexibility: location flexibility + balance: office and remote balance + collaboration: mixed collaboration modes + scheduling: flexible scheduling + adaptation: adaptive work style + FIELD_WORK: + title: Field Work + description: Work performed at client or field locations + annotations: + location: customer or field locations + travel: travel requirements + independence: field independence + client: client interaction + mobility: mobile work style + TELECOMMUTE: + title: Telecommuting + description: Regular remote work arrangement + annotations: + arrangement: formal remote arrangement + technology: telecommunication technology + productivity: productivity focus + work_life: work-life integration + communication: virtual team communication + is_a: HumanResourcesSchemaEnum annotations: - source_domain: bioprocessing - source_schema: scale_up - FeedstockTypeEnum: - description: Types of feedstocks for bioprocessing + source_domain: business + source_schema: human_resources + BenefitsCategoryEnum: + title: Benefits Category + description: Categories of employee benefits and compensation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - GLUCOSE: - description: Glucose/dextrose - meaning: CHEBI:17234 - annotations: - source: Corn, sugarcane - carbon_source: true - SUCROSE: - description: Sucrose - meaning: CHEBI:17992 + HEALTH_INSURANCE: + title: Health Insurance + description: Medical, dental, and vision insurance coverage annotations: - source: Sugarcane, sugar beet - carbon_source: true - GLYCEROL: - description: Glycerol - meaning: CHEBI:17754 + coverage: medical coverage + family: family coverage options + cost_sharing: employer contribution + networks: provider networks + essential: essential benefit + RETIREMENT_BENEFITS: + title: Retirement Benefits + description: Retirement savings and pension plans annotations: - source: Biodiesel byproduct - carbon_source: true - MOLASSES: - description: Molasses - meaning: CHEBI:83163 + savings: 401(k) or retirement savings + matching: employer matching + vesting: vesting schedules + planning: retirement planning + long_term: long-term benefit + PAID_TIME_OFF: + title: Paid Time Off + description: Vacation, sick leave, and personal time annotations: - source: Sugar processing byproduct - complex_medium: true - CORN_STEEP_LIQUOR: - description: Corn steep liquor + vacation: vacation time + sick: sick leave + personal: personal days + accrual: accrual systems + work_life: work-life balance + LIFE_INSURANCE: + title: Life Insurance + description: Life and disability insurance coverage annotations: - source: Corn wet milling - nitrogen_source: true - YEAST_EXTRACT: - description: Yeast extract - meaning: FOODON:03315426 + protection: financial protection + beneficiaries: beneficiary designation + disability: disability coverage + group: group coverage + peace_of_mind: financial security + FLEXIBLE_BENEFITS: + title: Flexible Benefits + description: Flexible spending and benefit choice options annotations: - source: Autolyzed yeast - complex_nutrient: true - LIGNOCELLULOSIC: - description: Lignocellulosic biomass + choice: benefit choice + spending: flexible spending accounts + customization: personalized benefits + tax_advantage: tax advantages + lifestyle: lifestyle accommodation + WELLNESS_PROGRAMS: + title: Wellness Programs + description: Employee health and wellness initiatives annotations: - source: Agricultural residues, wood - pretreatment: Required - METHANOL: - description: Methanol - meaning: CHEBI:17790 + health: health promotion + fitness: fitness programs + mental_health: mental health support + prevention: preventive care + culture: wellness culture + PROFESSIONAL_DEVELOPMENT: + title: Professional Development + description: Training, education, and career development benefits annotations: - carbon_source: true - methylotrophic: true - WASTE_STREAM: - description: Industrial waste stream + education: continuing education + training: professional training + career: career development + skill: skill enhancement + growth: professional growth + WORK_LIFE_BALANCE: + title: Work-Life Balance Benefits + description: Benefits supporting work-life integration annotations: - variable_composition: true - sustainability: Circular economy - is_a: ScaleUpSchemaEnum + flexibility: work flexibility + family: family support + childcare: childcare assistance + elder_care: elder care support + balance: life balance + is_a: HumanResourcesSchemaEnum annotations: - source_domain: bioprocessing - source_schema: scale_up - ProductTypeEnum: - description: Types of products from bioprocessing + source_domain: business + source_schema: human_resources + IndustryClassificationsSchemaEnum: + description: Schema-level enum for industry_classifications in business + is_a: BusinessDomainEnum + abstract: true + annotations: + source_file: business/industry_classifications.yaml + NAICSSectorEnum: + title: NAICS Sector + description: NAICS two-digit sector codes (North American Industry Classification System) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BIOFUEL: - title: fuel - description: Biofuel (ethanol, biodiesel, etc.) - meaning: CHEBI:33292 - annotations: - category: Energy - PROTEIN: - description: Recombinant protein - meaning: NCIT:C17021 + SECTOR_11: + title: Agriculture, Forestry, Fishing and Hunting + description: Establishments engaged in agriculture, forestry, fishing, and hunting annotations: - category: Biopharmaceutical - ENZYME: - description: Industrial enzyme - meaning: NCIT:C16554 + naics_code: '11' + activities: crop production, animal production, forestry, fishing + economic_base: natural resource extraction and production + SECTOR_21: + title: Mining, Quarrying, and Oil and Gas Extraction + description: Establishments engaged in extracting natural resources annotations: - category: Biocatalyst - ORGANIC_ACID: - description: Organic acid (citric, lactic, etc.) - meaning: CHEBI:64709 + naics_code: '21' + activities: oil and gas extraction, mining, support activities + economic_base: natural resource extraction + SECTOR_22: + title: Utilities + description: Establishments engaged in providing utilities annotations: - category: Chemical - AMINO_ACID: - description: Amino acid - meaning: CHEBI:33709 + naics_code: '22' + activities: electric power, natural gas, water, sewage, waste management + regulation: heavily regulated + SECTOR_23: + title: Construction + description: Establishments engaged in construction activities annotations: - category: Nutritional - ANTIBIOTIC: - description: Antibiotic - meaning: CHEBI:33281 - title: antimicrobial agent + naics_code: '23' + activities: building construction, heavy construction, specialty trade contractors + cyclical: highly cyclical industry + SECTOR_31_33: + title: Manufacturing + description: Establishments engaged in manufacturing goods annotations: - category: Pharmaceutical - VITAMIN: - description: Vitamin - meaning: CHEBI:33229 - title: vitamin (role) + naics_code: 31-33 + activities: food, chemicals, machinery, transportation equipment + value_added: transforms materials into finished goods + SECTOR_42: + title: Wholesale Trade + description: Establishments engaged in wholesale distribution annotations: - category: Nutritional - BIOPOLYMER: - description: Biopolymer (PHA, PLA, etc.) - meaning: CHEBI:33694 - title: biomacromolecule + naics_code: '42' + activities: merchant wholesalers, agents and brokers + function: intermediary between manufacturers and retailers + SECTOR_44_45: + title: Retail Trade + description: Establishments engaged in retail sales to consumers annotations: - category: Material - BIOMASS: - description: Microbial biomass - meaning: ENVO:01000155 - title: organic material + naics_code: 44-45 + activities: motor vehicle dealers, food stores, general merchandise + customer: sells to final consumers + SECTOR_48_49: + title: Transportation and Warehousing + description: Establishments providing transportation and warehousing services annotations: - category: Feed/food - SECONDARY_METABOLITE: - description: Secondary metabolite - meaning: CHEBI:25212 - title: metabolite + naics_code: 48-49 + activities: air, rail, water, truck transportation, warehousing + infrastructure: transportation infrastructure dependent + SECTOR_51: + title: Information + description: Establishments in information industries annotations: - category: Specialty chemical - is_a: ScaleUpSchemaEnum - annotations: - source_domain: bioprocessing - source_schema: scale_up - SterilizationMethodEnum: - description: Methods for sterilization in bioprocessing - permissible_values: - STEAM_IN_PLACE: - description: Steam in place (SIP) + naics_code: '51' + activities: publishing, broadcasting, telecommunications, data processing + technology: information technology and content + SECTOR_52: + title: Finance and Insurance + description: Establishments providing financial services annotations: - temperature: 121-134°C - time: 15-30 min - AUTOCLAVE: - title: autoclaving - description: Autoclave sterilization - meaning: CHMO:0002846 + naics_code: '52' + activities: banking, securities, insurance, funds and trusts + regulation: highly regulated financial sector + SECTOR_53: + title: Real Estate and Rental and Leasing + description: Establishments engaged in real estate and rental activities annotations: - temperature: 121°C - pressure: 15 psi - FILTER_STERILIZATION: - description: Filter sterilization (0.2 μm) + naics_code: '53' + activities: real estate, rental and leasing services + asset_type: real and personal property + SECTOR_54: + title: Professional, Scientific, and Technical Services + description: Establishments providing professional services annotations: - pore_size: 0.2 μm - heat_labile: true - GAMMA_IRRADIATION: - description: Gamma irradiation + naics_code: '54' + activities: legal, accounting, engineering, consulting, research + knowledge_based: knowledge and skill intensive + SECTOR_55: + title: Management of Companies and Enterprises + description: Establishments serving as holding companies or managing enterprises annotations: - dose: 25-40 kGy - single_use: true - ETHYLENE_OXIDE: - description: Ethylene oxide sterilization + naics_code: '55' + activities: holding companies, corporate management + function: corporate ownership and management + SECTOR_56: + title: Administrative and Support and Waste Management + description: Establishments providing administrative and support services annotations: - temperature: 30-60°C - plastic_compatible: true - UV_STERILIZATION: - description: UV sterilization + naics_code: '56' + activities: administrative services, waste management, remediation + support_function: business support services + SECTOR_61: + title: Educational Services + description: Establishments providing educational instruction annotations: - wavelength: 254 nm - surface_only: true - CHEMICAL_STERILIZATION: - description: Chemical sterilization + naics_code: '61' + activities: schools, colleges, training programs + public_private: public and private education + SECTOR_62: + title: Health Care and Social Assistance + description: Establishments providing health care and social assistance annotations: - agents: Bleach, alcohol, peroxide - contact_time: Variable - is_a: ScaleUpSchemaEnum - annotations: - source_domain: bioprocessing - source_schema: scale_up - BusinessDomainEnum: - description: Domain-level enum for business value sets - is_a: ValueSetEnum - abstract: true - HumanResourcesSchemaEnum: - description: Schema-level enum for human_resources in business - is_a: BusinessDomainEnum - abstract: true - annotations: - source_file: business/human_resources.yaml - EmploymentTypeEnum: - description: Types of employment arrangements and contracts - permissible_values: - FULL_TIME: - title: Full-Time Employment - description: Regular full-time employment status + naics_code: '62' + activities: hospitals, medical practices, social assistance + essential_services: essential public services + SECTOR_71: + title: Arts, Entertainment, and Recreation + description: Establishments in arts, entertainment, and recreation annotations: - hours: typically 40 hours per week - benefits: full benefits package - classification: exempt or non-exempt - stability: permanent position - commitment: full organizational commitment - PART_TIME: - title: Part-Time Employment - description: Regular part-time employment status + naics_code: '71' + activities: performing arts, spectator sports, museums, recreation + discretionary: discretionary consumer spending + SECTOR_72: + title: Accommodation and Food Services + description: Establishments providing accommodation and food services annotations: - hours: less than full-time hours - benefits: limited or prorated benefits - flexibility: flexible scheduling - classification: typically non-exempt - commitment: ongoing but reduced hours - CONTRACT: - title: Contract Employment - description: Fixed-term contractual employment + naics_code: '72' + activities: hotels, restaurants, food services + consumer_services: consumer hospitality services + SECTOR_81: + title: Other Services (except Public Administration) + description: Establishments providing other services annotations: - duration: defined contract period - relationship: contractual relationship - benefits: limited benefits - termination: defined end date - purpose: specific project or duration - TEMPORARY: - title: Temporary Employment - description: Short-term temporary employment + naics_code: '81' + activities: repair, personal care, religious organizations + diverse: diverse service activities + SECTOR_92: + title: Public Administration + description: Government establishments annotations: - duration: short-term assignment - agency: often through staffing agency - benefits: minimal benefits - purpose: seasonal or project work - flexibility: high flexibility - FREELANCE: - title: Freelance/Independent Contractor - description: Independent contractor or freelance work + naics_code: '92' + activities: executive, legislative, judicial, public safety + sector: government sector + is_a: IndustryClassificationsSchemaEnum + annotations: + source_domain: business + source_schema: industry_classifications + EconomicSectorEnum: + title: Economic Sector + description: Broad economic sector classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PRIMARY_SECTOR: + title: Primary Sector + description: Economic activities extracting natural resources annotations: - relationship: independent contractor - benefits: no traditional benefits - control: high work autonomy - taxes: responsible for own taxes - projects: project-based work - INTERN: - title: Internship - description: Student or entry-level internship program + activities: agriculture, mining, forestry, fishing + output: raw materials and natural resources + employment: typically lower employment share in developed economies + development_stage: dominant in early economic development + SECONDARY_SECTOR: + title: Secondary Sector + description: Economic activities manufacturing and processing goods annotations: - purpose: learning and experience - duration: limited duration - compensation: may be paid or unpaid - education: educational component - supervision: mentorship and guidance - SEASONAL: - title: Seasonal Employment - description: Employment tied to seasonal business needs + activities: manufacturing, construction, utilities + output: processed and manufactured goods + value_added: transforms raw materials into finished products + employment: historically significant in industrial economies + TERTIARY_SECTOR: + title: Tertiary Sector + description: Economic activities providing services annotations: - pattern: recurring seasonal pattern - duration: specific seasons - industry: retail, agriculture, tourism - return: potential for seasonal return - benefits: limited benefits - CONSULTANT: - title: Consultant - description: Professional consulting services + activities: retail, hospitality, transportation, finance, healthcare + output: services to consumers and businesses + growth: largest and fastest growing sector in developed economies + employment: dominant employment sector + QUATERNARY_SECTOR: + title: Quaternary Sector + description: Knowledge-based economic activities annotations: - expertise: specialized expertise - relationship: advisory relationship - independence: independent professional - project: project or retainer basis - value: strategic value-add - VOLUNTEER: - title: Volunteer - description: Unpaid volunteer service + activities: research, education, information technology, consulting + output: knowledge, information, and intellectual services + characteristics: high skill and education requirements + growth: rapidly growing in knowledge economies + QUINARY_SECTOR: + title: Quinary Sector + description: High-level decision-making and policy services annotations: - compensation: unpaid service - motivation: altruistic motivation - commitment: voluntary commitment - purpose: mission-driven work - recognition: non-monetary recognition - is_a: HumanResourcesSchemaEnum + activities: top-level government, healthcare, education, culture + output: highest level services and decision-making + characteristics: elite services and leadership roles + scope: limited to highest level activities + is_a: IndustryClassificationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - JobLevelEnum: - description: Organizational job levels and career progression + source_schema: industry_classifications + BusinessActivityTypeEnum: + title: Business Activity Type + description: Types of primary business activities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ENTRY_LEVEL: - title: Entry Level - description: Beginning career level positions + PRODUCTION: + title: Production/Manufacturing + description: Creating or manufacturing physical goods annotations: - experience: 0-2 years experience - responsibilities: basic operational tasks - supervision: high supervision required - development: learning and development focus - career_stage: career beginning - JUNIOR: - title: Junior Level - description: Junior professional level + output: physical products and goods + process: transformation of materials + assets: physical assets and equipment intensive + examples: factories, farms, mines + DISTRIBUTION: + title: Distribution/Trade + description: Moving goods from producers to consumers annotations: - experience: 2-4 years experience - responsibilities: routine professional tasks - independence: some independence - mentorship: receiving mentorship - skill_building: skill development phase - MID_LEVEL: - title: Mid-Level - description: Experienced professional level + function: intermediary between producers and consumers + value_added: place and time utility + examples: wholesalers, retailers, logistics companies + efficiency: improves market efficiency + SERVICES: + title: Service Provision + description: Providing intangible services to customers annotations: - experience: 4-8 years experience - responsibilities: complex project work - independence: high independence - mentorship: providing and receiving mentorship - expertise: developing expertise - SENIOR: - title: Senior Level - description: Senior professional level + output: intangible services + characteristics: labor intensive, customized + examples: consulting, healthcare, hospitality + customer_interaction: high customer interaction + TECHNOLOGY: + title: Technology/Innovation + description: Developing and applying technology solutions + annotations: + focus: technology development and application + innovation: research and development intensive + examples: software companies, biotech, engineering + intellectual_property: high intellectual property content + FINANCE: + title: Financial Services + description: Providing financial and investment services annotations: - experience: 8+ years experience - responsibilities: strategic project leadership - expertise: subject matter expertise - mentorship: mentoring others - influence: organizational influence - LEAD: - title: Team Lead - description: Team leadership role + function: financial intermediation and services + regulation: highly regulated + examples: banks, insurance, investment firms + capital: capital intensive + INFORMATION: + title: Information/Media + description: Creating, processing, and distributing information annotations: - responsibility: team leadership - people_management: direct reports - coordination: team coordination - accountability: team results - development: team development - MANAGER: - title: Manager - description: Management level position + output: information and content + channels: various distribution channels + examples: media companies, publishers, data processors + technology_dependent: technology platform dependent + EDUCATION: + title: Education/Training + description: Providing educational and training services annotations: - scope: departmental management - people_management: multiple direct reports - budget: budget responsibility - strategy: tactical strategy - operations: operational management - DIRECTOR: - title: Director - description: Director level executive + function: knowledge and skill development + public_private: public and private providers + examples: schools, universities, training companies + social_impact: high social impact + HEALTHCARE: + title: Healthcare/Medical + description: Providing health and medical services annotations: - scope: multi-departmental oversight - strategy: strategic planning - leadership: organizational leadership - stakeholders: senior stakeholder management - results: business results accountability - VP: - title: Vice President - description: Vice President executive level + function: health and medical care + regulation: highly regulated + examples: hospitals, clinics, pharmaceutical companies + essential: essential service + ENTERTAINMENT: + title: Entertainment/Recreation + description: Providing entertainment and recreational services annotations: - scope: business unit or functional area - strategy: strategic leadership - board: board interaction - organization: organizational impact - succession: succession planning - C_LEVEL: - title: C-Level Executive - description: Chief executive level + output: entertainment and leisure experiences + discretionary: discretionary consumer spending + examples: media, sports, tourism, gaming + experience_based: experience and emotion based + PROFESSIONAL_SERVICES: + title: Professional Services + description: Providing specialized professional expertise annotations: - scope: enterprise-wide responsibility - governance: corporate governance - vision: organizational vision - stakeholders: external stakeholder management - fiduciary: fiduciary responsibility - is_a: HumanResourcesSchemaEnum + characteristics: high skill and knowledge requirements + customization: highly customized services + examples: law firms, consulting, accounting + expertise: specialized professional expertise + is_a: IndustryClassificationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - HRFunctionEnum: - description: Human resources functional areas and specializations + source_schema: industry_classifications + IndustryMaturityEnum: + title: Industry Maturity + description: Industry lifecycle and maturity stages + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - TALENT_ACQUISITION: - title: Talent Acquisition - description: Recruitment and hiring functions + EMERGING: + title: Emerging Industry + description: New industry in early development stage annotations: - activities: sourcing, screening, interviewing, hiring - focus: attracting and selecting talent - metrics: time to hire, quality of hire - strategy: workforce planning - technology: ATS and recruitment tools - EMPLOYEE_RELATIONS: - title: Employee Relations - description: Managing employee relationships and workplace issues + characteristics: high uncertainty, rapid change + growth: high growth potential + technology: new or evolving technology + competition: few competitors, unclear standards + investment: high investment requirements + GROWTH: + title: Growth Industry + description: Industry experiencing rapid expansion annotations: - activities: conflict resolution, grievance handling - focus: positive employee relations - communication: employee communication - culture: workplace culture - mediation: dispute resolution - COMPENSATION_BENEFITS: - title: Compensation and Benefits - description: Managing compensation and benefits programs + characteristics: rapid market expansion + competition: increasing competition + standardization: emerging standards + investment: significant investment opportunities + profitability: improving profitability + MATURE: + title: Mature Industry + description: Established industry with stable growth annotations: - activities: salary administration, benefits design - analysis: market analysis and benchmarking - compliance: regulatory compliance - cost: cost management - competitiveness: market competitiveness - PERFORMANCE_MANAGEMENT: - title: Performance Management - description: Employee performance evaluation and improvement + characteristics: stable market conditions + growth: slower, steady growth + competition: established competitive structure + efficiency: focus on operational efficiency + consolidation: potential for consolidation + DECLINING: + title: Declining Industry + description: Industry experiencing contraction annotations: - activities: performance reviews, goal setting - development: performance improvement - measurement: performance metrics - feedback: continuous feedback - coaching: performance coaching - LEARNING_DEVELOPMENT: - title: Learning and Development - description: Employee training and development programs + characteristics: decreasing demand + competition: intensifying competition for shrinking market + cost_focus: focus on cost reduction + consolidation: significant consolidation + exit: companies exiting industry + TRANSFORMING: + title: Transforming Industry + description: Industry undergoing fundamental change annotations: - activities: training design, skill development - career: career development - leadership: leadership development - compliance: compliance training - technology: learning management systems - HR_ANALYTICS: - title: HR Analytics - description: HR data analysis and workforce metrics + characteristics: disruptive change and innovation + technology: technology-driven transformation + business_models: evolving business models + uncertainty: high uncertainty about future structure + opportunity: opportunities for innovation and disruption + is_a: IndustryClassificationsSchemaEnum + annotations: + source_domain: business + source_schema: industry_classifications + MarketStructureEnum: + title: Market Structure + description: Competitive structure of industry markets + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PERFECT_COMPETITION: + title: Perfect Competition + description: Many small firms with identical products annotations: - activities: data analysis, metrics reporting - insights: workforce insights - predictive: predictive analytics - dashboard: HR dashboards - decision_support: data-driven decisions - ORGANIZATIONAL_DEVELOPMENT: - title: Organizational Development - description: Organizational design and change management + competitors: many small competitors + products: homogeneous products + barriers: no barriers to entry + pricing: price takers + examples: agricultural commodities + MONOPOLISTIC_COMPETITION: + title: Monopolistic Competition + description: Many firms with differentiated products annotations: - activities: change management, culture transformation - design: organizational design - effectiveness: organizational effectiveness - culture: culture development - transformation: business transformation - HR_COMPLIANCE: - title: HR Compliance - description: Employment law compliance and risk management + competitors: many competitors + products: differentiated products + barriers: low barriers to entry + pricing: some pricing power + examples: restaurants, retail clothing + OLIGOPOLY: + title: Oligopoly + description: Few large firms dominating the market annotations: - activities: policy development, compliance monitoring - legal: employment law compliance - risk: HR risk management - auditing: compliance auditing - documentation: record keeping - HRIS_TECHNOLOGY: - title: HRIS and Technology - description: HR information systems and technology + competitors: few large competitors + concentration: high market concentration + barriers: significant barriers to entry + interdependence: strategic interdependence + examples: automobiles, telecommunications + MONOPOLY: + title: Monopoly + description: Single firm controlling the market annotations: - activities: system administration, data management - systems: HRIS implementation - automation: process automation - integration: system integration - security: data security - is_a: HumanResourcesSchemaEnum + competitors: single market leader + barriers: very high barriers to entry + pricing: price maker + regulation: often regulated + examples: utilities, patented products + DUOPOLY: + title: Duopoly + description: Two firms dominating the market + annotations: + competitors: two dominant competitors + competition: head-to-head competition + barriers: high barriers to entry + strategy: strategic competition + examples: aircraft manufacturing, some software markets + is_a: IndustryClassificationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - CompensationTypeEnum: - description: Types of employee compensation structures + source_schema: industry_classifications + IndustryRegulationLevelEnum: + title: Industry Regulation Level + description: Level of government regulation in different industries + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BASE_SALARY: - title: Base Salary - description: Fixed annual salary compensation - annotations: - structure: fixed annual amount - payment: regular pay periods - exemption: often exempt from overtime - predictability: predictable income - market: market benchmarked - HOURLY_WAGE: - title: Hourly Wage - description: Compensation paid per hour worked - annotations: - structure: rate per hour - overtime: overtime eligible - tracking: time tracking required - variability: variable based on hours - classification: non-exempt employees - COMMISSION: - title: Commission - description: Performance-based sales commission - annotations: - structure: percentage of sales - performance: performance-based - variability: highly variable - motivation: sales motivation - risk: income risk - BONUS: - title: Performance Bonus - description: Additional compensation for performance + HIGHLY_REGULATED: + title: Highly Regulated + description: Industries subject to extensive government oversight annotations: - timing: annual or periodic - criteria: performance criteria - discretionary: may be discretionary - recognition: performance recognition - retention: retention tool - STOCK_OPTIONS: - title: Stock Options - description: Equity compensation through stock options + oversight: extensive government oversight + compliance: complex compliance requirements + barriers: regulatory barriers to entry + examples: banking, healthcare, utilities, pharmaceuticals + reason: public safety, market power, or systemic risk + MODERATELY_REGULATED: + title: Moderately Regulated + description: Industries with significant but focused regulation annotations: - equity: equity participation - vesting: vesting schedule - retention: long-term retention - upside: company growth upside - risk: market risk - PROFIT_SHARING: - title: Profit Sharing - description: Sharing of company profits with employees + oversight: focused regulatory oversight + compliance: specific compliance requirements + areas: targeted regulatory areas + examples: food service, transportation, insurance + balance: balance between oversight and flexibility + LIGHTLY_REGULATED: + title: Lightly Regulated + description: Industries with minimal regulatory oversight annotations: - structure: percentage of profits - performance: company performance based - culture: ownership culture - variability: variable based on profits - alignment: interest alignment - PIECE_RATE: - title: Piece Rate - description: Compensation based on units produced + oversight: minimal regulatory oversight + compliance: basic compliance requirements + flexibility: high operational flexibility + examples: technology, consulting, retail + approach: market-based approach + SELF_REGULATED: + title: Self-Regulated + description: Industries primarily regulated by industry organizations annotations: - structure: rate per unit produced - productivity: productivity-based - manufacturing: common in manufacturing - measurement: output measurement - efficiency: efficiency incentive - STIPEND: - title: Stipend - description: Fixed regular allowance or payment + oversight: industry self-regulation + standards: industry-developed standards + compliance: voluntary compliance + examples: professional services, trade associations + effectiveness: varies by industry + DEREGULATED: + title: Deregulated + description: Industries formerly regulated but now market-based annotations: - purpose: specific purpose payment - amount: modest fixed amount - regularity: regular payment - supplemental: supplemental income - categories: interns, volunteers, board members - is_a: HumanResourcesSchemaEnum + history: formerly regulated industries + competition: market-based competition + transition: transition from regulation to competition + examples: airlines, telecommunications, energy + benefits: increased competition and efficiency + is_a: IndustryClassificationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - PerformanceRatingEnum: - description: Employee performance evaluation ratings + source_schema: industry_classifications + ManagementOperationsSchemaEnum: + description: Schema-level enum for management_operations in business + is_a: BusinessDomainEnum + abstract: true + annotations: + source_file: business/management_operations.yaml + ManagementMethodologyEnum: + title: Management Methodology + description: Management approaches and methodologies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - EXCEEDS_EXPECTATIONS: - title: Exceeds Expectations - description: Performance significantly above expected standards + TRADITIONAL_MANAGEMENT: + title: Traditional Management + description: Hierarchical command-and-control management approach annotations: - level: top performance tier - impact: significant business impact - recognition: high recognition - development: stretch assignments - percentage: typically 10-20% of population - MEETS_EXPECTATIONS: - title: Meets Expectations - description: Performance meets all expected standards + structure: hierarchical structure + authority: centralized authority + communication: top-down communication + control: direct supervision and control + AGILE_MANAGEMENT: + title: Agile Management + description: Flexible, iterative management approach annotations: - level: satisfactory performance - standards: meets all job requirements - competency: demonstrates required competencies - consistency: consistent performance - percentage: typically 60-70% of population - PARTIALLY_MEETS: - title: Partially Meets Expectations - description: Performance meets some but not all standards + flexibility: adaptive and flexible + iteration: iterative approach + collaboration: cross-functional collaboration + customer_focus: customer-centric + LEAN_MANAGEMENT: + title: Lean Management + description: Waste elimination and value optimization approach annotations: - level: below standard performance - improvement: improvement needed - support: additional support required - development: focused development plan - percentage: typically 10-15% of population - DOES_NOT_MEET: - title: Does Not Meet Expectations - description: Performance below acceptable standards + focus: waste elimination + value: value stream optimization + continuous_improvement: kaizen and continuous improvement + efficiency: operational efficiency + PARTICIPATIVE_MANAGEMENT: + title: Participative Management + description: Employee involvement in decision-making annotations: - level: unsatisfactory performance - action: performance improvement plan - timeline: improvement timeline - consequences: potential consequences - percentage: typically 5-10% of population - OUTSTANDING: - title: Outstanding - description: Exceptional performance far exceeding standards + involvement: employee participation + decision_making: shared decision-making + empowerment: employee empowerment + engagement: increased employee engagement + MATRIX_MANAGEMENT: + title: Matrix Management + description: Dual reporting relationships and shared authority annotations: - level: exceptional performance - impact: transformational impact - leadership: demonstrates leadership - innovation: innovation and excellence - rarity: rare rating - is_a: HumanResourcesSchemaEnum + structure: matrix reporting structure + authority: shared authority + flexibility: organizational flexibility + complexity: increased complexity + PROJECT_MANAGEMENT: + title: Project Management + description: Structured approach to managing projects + annotations: + methodology: project management methodology + lifecycle: project lifecycle management + deliverables: deliverable-focused + temporary: temporary organizational structure + RESULTS_ORIENTED_MANAGEMENT: + title: Results-Oriented Management + description: Focus on outcomes and performance results + annotations: + focus: results and outcomes + measurement: performance measurement + accountability: accountability for results + goals: goal-oriented approach + SERVANT_LEADERSHIP: + title: Servant Leadership + description: Leader serves and supports team members + annotations: + philosophy: service-oriented leadership + support: leader supports team + development: people development focus + empowerment: team empowerment + TRANSFORMATIONAL_MANAGEMENT: + title: Transformational Management + description: Change-oriented and inspirational management + annotations: + change: transformation and change focus + inspiration: inspirational leadership + vision: vision-driven + development: follower development + DEMOCRATIC_MANAGEMENT: + title: Democratic Management + description: Collaborative and consensus-building approach + annotations: + participation: democratic participation + consensus: consensus-building + equality: equal voice in decisions + transparency: transparent processes + is_a: ManagementOperationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - RecruitmentSourceEnum: - description: Sources for candidate recruitment and sourcing + source_schema: management_operations + StrategicFrameworkEnum: + title: Strategic Framework + description: Strategic planning and analysis frameworks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - INTERNAL_REFERRAL: - title: Internal Employee Referral - description: Candidates referred by current employees + SWOT_ANALYSIS: + title: SWOT Analysis + description: Strengths, Weaknesses, Opportunities, Threats analysis annotations: - source: employee networks - quality: typically high quality - cost: low cost per hire - cultural_fit: good cultural fit - retention: higher retention rates - JOB_BOARDS: - title: Online Job Boards - description: Candidates from online job posting sites + components: strengths, weaknesses, opportunities, threats + purpose: strategic positioning analysis + simplicity: simple and widely used + application: strategic planning and decision-making + PORTERS_FIVE_FORCES: + title: Porter's Five Forces + description: Industry competitiveness analysis framework annotations: - reach: broad candidate reach - cost: moderate cost - volume: high application volume - screening: requires screening - examples: Indeed, LinkedIn, Monster - COMPANY_WEBSITE: - title: Company Career Website - description: Candidates applying through company website + forces: competitive rivalry, supplier power, buyer power, substitutes, barriers + purpose: industry attractiveness analysis + competition: competitive strategy framework + application: industry analysis and strategy formulation + BALANCED_SCORECARD: + title: Balanced Scorecard + description: Performance measurement from multiple perspectives annotations: - interest: high company interest - brand: employer brand driven - quality: targeted candidates - direct: direct application - cost: low incremental cost - SOCIAL_MEDIA: - title: Social Media Recruiting - description: Candidates sourced through social media platforms + perspectives: financial, customer, internal process, learning + purpose: strategic performance measurement + balance: balanced view of performance + alignment: strategy alignment tool + BLUE_OCEAN_STRATEGY: + title: Blue Ocean Strategy + description: Creating uncontested market space strategy annotations: - platforms: LinkedIn, Facebook, Twitter - active: active sourcing - networking: professional networking - targeting: targeted approach - engagement: relationship building - RECRUITMENT_AGENCIES: - title: External Recruitment Agencies - description: Candidates sourced through recruitment firms + concept: value innovation and market creation + competition: competition avoidance + differentiation: differentiation and low cost + innovation: strategic innovation + ANSOFF_MATRIX: + title: Ansoff Matrix + description: Product and market growth strategy framework annotations: - expertise: specialized expertise - cost: higher cost - speed: faster time to hire - screening: pre-screened candidates - specialization: industry specialization - CAMPUS_RECRUITING: - title: Campus and University Recruiting - description: Recruitment from educational institutions + dimensions: products and markets + strategies: market penetration, development, diversification + growth: growth strategy framework + risk: risk assessment of growth options + BCG_MATRIX: + title: BCG Matrix + description: Portfolio analysis of business units annotations: - target: students and new graduates - programs: internship and graduate programs - relationships: university relationships - pipeline: talent pipeline - early_career: early career focus - PROFESSIONAL_NETWORKS: - title: Professional Networks - description: Recruitment through professional associations + dimensions: market growth and market share + categories: stars, cash cows, question marks, dogs + portfolio: business portfolio analysis + resource_allocation: resource allocation decisions + VALUE_CHAIN_ANALYSIS: + title: Value Chain Analysis + description: Analysis of value-creating activities annotations: - industry: industry-specific networks - expertise: specialized expertise - relationships: professional relationships - credibility: professional credibility - targeted: targeted recruitment - HEADHUNTERS: - title: Executive Search/Headhunters - description: Executive-level recruitment specialists + activities: primary and support activities + value: value creation analysis + advantage: competitive advantage source identification + optimization: value chain optimization + SCENARIO_PLANNING: + title: Scenario Planning + description: Multiple future scenario development and planning annotations: - level: senior and executive roles - expertise: specialized search expertise - network: extensive professional networks - confidential: confidential searches - cost: premium cost - is_a: HumanResourcesSchemaEnum + scenarios: multiple future scenarios + uncertainty: uncertainty management + planning: strategic contingency planning + flexibility: strategic flexibility + STRATEGIC_CANVAS: + title: Strategy Canvas + description: Visual representation of competitive factors + annotations: + visualization: visual strategy representation + factors: competitive factors analysis + comparison: competitor comparison + innovation: value innovation identification + CORE_COMPETENCY_ANALYSIS: + title: Core Competency Analysis + description: Identification and development of core competencies + annotations: + competencies: unique organizational capabilities + advantage: sustainable competitive advantage + focus: competency-based strategy + development: capability development + is_a: ManagementOperationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - TrainingTypeEnum: - description: Types of employee training and development programs + source_schema: management_operations + OperationalModelEnum: + title: Operational Model + description: Business operational models and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ONBOARDING: - title: New Employee Onboarding - description: Orientation and integration training for new hires + CENTRALIZED_OPERATIONS: + title: Centralized Operations + description: Centralized operational control and decision-making annotations: - timing: first days/weeks of employment - purpose: integration and orientation - content: company culture, policies, role basics - delivery: structured program - outcome: successful integration - TECHNICAL_SKILLS: - title: Technical Skills Training - description: Job-specific technical competency development + control: centralized control + efficiency: operational efficiency + standardization: standardized processes + coordination: central coordination + DECENTRALIZED_OPERATIONS: + title: Decentralized Operations + description: Distributed operational control and autonomy annotations: - focus: technical competencies - relevance: job-specific skills - methods: hands-on training - certification: may include certification - updating: continuous skill updates - LEADERSHIP_DEVELOPMENT: - title: Leadership Development - description: Management and leadership capability building + autonomy: local autonomy + responsiveness: market responsiveness + flexibility: operational flexibility + empowerment: local empowerment + HYBRID_OPERATIONS: + title: Hybrid Operations + description: Combination of centralized and decentralized elements annotations: - target: managers and high-potential employees - skills: leadership and management skills - development: long-term development - mentorship: coaching and mentorship - succession: succession planning - COMPLIANCE_TRAINING: - title: Compliance Training - description: Required training for regulatory compliance + combination: mixed centralized and decentralized + balance: balance between control and flexibility + optimization: situational optimization + complexity: increased complexity + OUTSOURCED_OPERATIONS: + title: Outsourced Operations + description: External service provider operational model annotations: - requirement: mandatory training - regulation: regulatory compliance - documentation: completion tracking - frequency: periodic updates - risk: risk mitigation - SOFT_SKILLS: - title: Soft Skills Development - description: Communication and interpersonal skills training + provider: external service providers + focus: core competency focus + cost: cost optimization + expertise: specialized expertise + SHARED_SERVICES: + title: Shared Services + description: Centralized services shared across business units annotations: - skills: communication, teamwork, problem-solving - application: broadly applicable - development: personal development - effectiveness: workplace effectiveness - collaboration: collaboration skills - SAFETY_TRAINING: - title: Safety Training - description: Workplace safety and health training + sharing: shared service delivery + efficiency: scale efficiency + standardization: service standardization + cost_effectiveness: cost-effective service delivery + NETWORK_OPERATIONS: + title: Network Operations + description: Collaborative network of partners and suppliers annotations: - focus: safety procedures and practices - compliance: OSHA compliance - prevention: accident prevention - emergency: emergency procedures - culture: safety culture - DIVERSITY_INCLUSION: - title: Diversity and Inclusion Training - description: Training on diversity, equity, and inclusion + network: partner and supplier network + collaboration: collaborative operations + flexibility: network flexibility + coordination: network coordination + PLATFORM_OPERATIONS: + title: Platform Operations + description: Platform-based business operational model annotations: - awareness: cultural awareness - bias: unconscious bias training - inclusion: inclusive practices - culture: inclusive culture - behavior: behavior change - CROSS_TRAINING: - title: Cross-Training - description: Training in multiple roles or departments + platform: platform-based operations + ecosystem: business ecosystem + scalability: scalable operations + network_effects: network effects + AGILE_OPERATIONS: + title: Agile Operations + description: Flexible and responsive operational approach + annotations: + agility: operational agility + responsiveness: market responsiveness + adaptation: rapid adaptation + iteration: iterative improvement + LEAN_OPERATIONS: + title: Lean Operations + description: Waste elimination and value-focused operations annotations: - flexibility: workforce flexibility - coverage: backup coverage - development: career development - understanding: broader understanding - collaboration: improved collaboration - is_a: HumanResourcesSchemaEnum + waste: waste elimination + value: value stream focus + efficiency: operational efficiency + continuous_improvement: continuous improvement + DIGITAL_OPERATIONS: + title: Digital Operations + description: Technology-enabled and digital-first operations + annotations: + technology: digital technology enabled + automation: process automation + data_driven: data-driven operations + scalability: digital scalability + is_a: ManagementOperationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - EmployeeStatusEnum: - description: Current employment status classifications + source_schema: management_operations + PerformanceMeasurementEnum: + title: Performance Measurement + description: Performance measurement systems and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ACTIVE: - title: Active Employment - description: Currently employed and working - annotations: - status: actively working - benefits: receiving full benefits - responsibilities: fulfilling job responsibilities - engagement: expected engagement - performance: subject to performance management - ON_LEAVE: - title: On Leave - description: Temporarily away from work on approved leave + KEY_PERFORMANCE_INDICATORS: + title: Key Performance Indicators (KPIs) + description: Specific metrics measuring critical performance areas annotations: - temporary: temporary absence - approval: approved leave - return: expected return date - benefits: may retain benefits - types: medical, family, personal leave - PROBATIONARY: - title: Probationary Period - description: New employee in probationary period + specificity: specific performance metrics + critical: critical success factors + measurement: quantitative measurement + tracking: performance tracking + OBJECTIVES_KEY_RESULTS: + title: Objectives and Key Results (OKRs) + description: Goal-setting framework with measurable outcomes annotations: - duration: defined probationary period - evaluation: ongoing evaluation - benefits: limited or delayed benefits - termination: easier termination - assessment: performance assessment - SUSPENDED: - title: Suspended - description: Temporarily suspended from work + objectives: qualitative objectives + results: quantitative key results + alignment: organizational alignment + transparency: transparent goal setting + BALANCED_SCORECARD_MEASUREMENT: + title: Balanced Scorecard Measurement + description: Multi-perspective performance measurement system annotations: - disciplinary: disciplinary action - investigation: pending investigation - pay: with or without pay - temporary: temporary status - review: pending review - TERMINATED: - title: Terminated - description: Employment has been terminated + perspectives: multiple performance perspectives + balance: balanced performance view + strategy: strategy-linked measurement + cause_effect: cause-and-effect relationships + RETURN_ON_INVESTMENT: + title: Return on Investment (ROI) + description: Financial return measurement relative to investment annotations: - end: employment ended - voluntary: voluntary or involuntary - benefits: benefits cessation - final: final status - documentation: termination documentation - RETIRED: - title: Retired - description: Retired from employment + financial: financial performance measure + investment: investment-based measurement + efficiency: capital efficiency + comparison: investment comparison + ECONOMIC_VALUE_ADDED: + title: Economic Value Added (EVA) + description: Value creation measurement after cost of capital annotations: - voluntary: voluntary departure - age: retirement age - benefits: retirement benefits - service: completed service - transition: career transition - is_a: HumanResourcesSchemaEnum - annotations: - source_domain: business - source_schema: human_resources - WorkArrangementEnum: - description: Work location and arrangement types - permissible_values: - ON_SITE: - title: On-Site Work - description: Work performed at company facilities + value: economic value creation + capital_cost: cost of capital consideration + shareholder: shareholder value focus + performance: true economic performance + CUSTOMER_SATISFACTION_METRICS: + title: Customer Satisfaction Metrics + description: Customer experience and satisfaction measurement annotations: - location: company premises - collaboration: in-person collaboration - supervision: direct supervision - equipment: company-provided equipment - culture: office culture participation - REMOTE: - title: Remote Work - description: Work performed away from company facilities + customer: customer-focused measurement + satisfaction: satisfaction and loyalty + experience: customer experience + retention: customer retention + EMPLOYEE_ENGAGEMENT_METRICS: + title: Employee Engagement Metrics + description: Employee satisfaction and engagement measurement annotations: - location: home or remote location - technology: technology-enabled work - flexibility: location flexibility - independence: high independence - communication: virtual communication - HYBRID: - title: Hybrid Work - description: Combination of on-site and remote work + engagement: employee engagement + satisfaction: employee satisfaction + retention: employee retention + productivity: employee productivity + OPERATIONAL_EFFICIENCY_METRICS: + title: Operational Efficiency Metrics + description: Operational performance and efficiency measurement annotations: - flexibility: location flexibility - balance: office and remote balance - collaboration: mixed collaboration modes - scheduling: flexible scheduling - adaptation: adaptive work style - FIELD_WORK: - title: Field Work - description: Work performed at client or field locations + efficiency: operational efficiency + productivity: process productivity + quality: quality metrics + cost: cost efficiency + INNOVATION_METRICS: + title: Innovation Metrics + description: Innovation performance and capability measurement annotations: - location: customer or field locations - travel: travel requirements - independence: field independence - client: client interaction - mobility: mobile work style - TELECOMMUTE: - title: Telecommuting - description: Regular remote work arrangement + innovation: innovation performance + development: new product development + improvement: process improvement + creativity: organizational creativity + SUSTAINABILITY_METRICS: + title: Sustainability Metrics + description: Environmental and social sustainability measurement annotations: - arrangement: formal remote arrangement - technology: telecommunication technology - productivity: productivity focus - work_life: work-life integration - communication: virtual team communication - is_a: HumanResourcesSchemaEnum + sustainability: sustainability performance + environmental: environmental impact + social: social responsibility + governance: governance effectiveness + is_a: ManagementOperationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - BenefitsCategoryEnum: - description: Categories of employee benefits and compensation + source_schema: management_operations + DecisionMakingStyleEnum: + title: Decision Making Style + description: Decision-making approaches and styles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - HEALTH_INSURANCE: - title: Health Insurance - description: Medical, dental, and vision insurance coverage + AUTOCRATIC: + title: Autocratic Decision Making + description: Single decision-maker with full authority annotations: - coverage: medical coverage - family: family coverage options - cost_sharing: employer contribution - networks: provider networks - essential: essential benefit - RETIREMENT_BENEFITS: - title: Retirement Benefits - description: Retirement savings and pension plans + authority: centralized decision authority + speed: fast decision making + control: complete control + input: limited input from others + DEMOCRATIC: + title: Democratic Decision Making + description: Group participation in decision-making process annotations: - savings: 401(k) or retirement savings - matching: employer matching - vesting: vesting schedules - planning: retirement planning - long_term: long-term benefit - PAID_TIME_OFF: - title: Paid Time Off - description: Vacation, sick leave, and personal time + participation: group participation + consensus: consensus building + input: diverse input and perspectives + ownership: shared ownership of decisions + CONSULTATIVE: + title: Consultative Decision Making + description: Leader consults others before deciding annotations: - vacation: vacation time - sick: sick leave - personal: personal days - accrual: accrual systems - work_life: work-life balance - LIFE_INSURANCE: - title: Life Insurance - description: Life and disability insurance coverage + consultation: stakeholder consultation + input: seeks input and advice + authority: leader retains decision authority + informed: informed decision making + CONSENSUS: + title: Consensus Decision Making + description: Agreement reached through group discussion + annotations: + agreement: group agreement required + discussion: extensive group discussion + unanimous: unanimous or near-unanimous agreement + time: time-intensive process + DELEGATED: + title: Delegated Decision Making + description: Decision authority delegated to others annotations: - protection: financial protection - beneficiaries: beneficiary designation - disability: disability coverage - group: group coverage - peace_of_mind: financial security - FLEXIBLE_BENEFITS: - title: Flexible Benefits - description: Flexible spending and benefit choice options + delegation: decision authority delegation + empowerment: employee empowerment + autonomy: decision autonomy + accountability: delegated accountability + DATA_DRIVEN: + title: Data-Driven Decision Making + description: Decisions based on data analysis and evidence annotations: - choice: benefit choice - spending: flexible spending accounts - customization: personalized benefits - tax_advantage: tax advantages - lifestyle: lifestyle accommodation - WELLNESS_PROGRAMS: - title: Wellness Programs - description: Employee health and wellness initiatives + data: data and analytics based + evidence: evidence-based decisions + objectivity: objective decision making + analysis: analytical approach + INTUITIVE: + title: Intuitive Decision Making + description: Decisions based on experience and gut feeling annotations: - health: health promotion - fitness: fitness programs - mental_health: mental health support - prevention: preventive care - culture: wellness culture - PROFESSIONAL_DEVELOPMENT: - title: Professional Development - description: Training, education, and career development benefits + intuition: intuition and experience based + speed: rapid decision making + experience: leverages experience + creativity: creative and innovative + COMMITTEE: + title: Committee Decision Making + description: Formal group decision-making structure annotations: - education: continuing education - training: professional training - career: career development - skill: skill enhancement - growth: professional growth - WORK_LIFE_BALANCE: - title: Work-Life Balance Benefits - description: Benefits supporting work-life integration + structure: formal committee structure + representation: stakeholder representation + process: structured decision process + accountability: shared accountability + COLLABORATIVE: + title: Collaborative Decision Making + description: Joint decision-making with shared responsibility annotations: - flexibility: work flexibility - family: family support - childcare: childcare assistance - elder_care: elder care support - balance: life balance - is_a: HumanResourcesSchemaEnum + collaboration: collaborative approach + shared: shared responsibility + teamwork: team-based decisions + synergy: collective wisdom + CRISIS: + title: Crisis Decision Making + description: Rapid decision-making under crisis conditions + annotations: + urgency: urgent decision making + limited_info: limited information available + speed: rapid response required + risk: high-risk decision making + is_a: ManagementOperationsSchemaEnum annotations: source_domain: business - source_schema: human_resources - IndustryClassificationsSchemaEnum: - description: Schema-level enum for industry_classifications in business - is_a: BusinessDomainEnum - abstract: true - annotations: - source_file: business/industry_classifications.yaml - NAICSSectorEnum: - description: NAICS two-digit sector codes (North American Industry Classification System) + source_schema: management_operations + LeadershipStyleEnum: + title: Leadership Style + description: Leadership approaches and styles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - SECTOR_11: - title: Agriculture, Forestry, Fishing and Hunting - description: Establishments engaged in agriculture, forestry, fishing, and hunting - annotations: - naics_code: '11' - activities: crop production, animal production, forestry, fishing - economic_base: natural resource extraction and production - SECTOR_21: - title: Mining, Quarrying, and Oil and Gas Extraction - description: Establishments engaged in extracting natural resources - annotations: - naics_code: '21' - activities: oil and gas extraction, mining, support activities - economic_base: natural resource extraction - SECTOR_22: - title: Utilities - description: Establishments engaged in providing utilities - annotations: - naics_code: '22' - activities: electric power, natural gas, water, sewage, waste management - regulation: heavily regulated - SECTOR_23: - title: Construction - description: Establishments engaged in construction activities + TRANSFORMATIONAL: + title: Transformational Leadership + description: Inspirational leadership that motivates change annotations: - naics_code: '23' - activities: building construction, heavy construction, specialty trade contractors - cyclical: highly cyclical industry - SECTOR_31_33: - title: Manufacturing - description: Establishments engaged in manufacturing goods + inspiration: inspirational motivation + vision: visionary leadership + development: follower development + change: change-oriented + TRANSACTIONAL: + title: Transactional Leadership + description: Exchange-based leadership with rewards and consequences annotations: - naics_code: 31-33 - activities: food, chemicals, machinery, transportation equipment - value_added: transforms materials into finished goods - SECTOR_42: - title: Wholesale Trade - description: Establishments engaged in wholesale distribution + exchange: reward and consequence based + structure: structured approach + performance: performance-based + management: management by exception + SERVANT: + title: Servant Leadership + description: Leader serves followers and facilitates their growth annotations: - naics_code: '42' - activities: merchant wholesalers, agents and brokers - function: intermediary between manufacturers and retailers - SECTOR_44_45: - title: Retail Trade - description: Establishments engaged in retail sales to consumers + service: service to followers + empowerment: follower empowerment + development: personal development focus + humility: humble leadership approach + AUTHENTIC: + title: Authentic Leadership + description: Genuine and self-aware leadership approach annotations: - naics_code: 44-45 - activities: motor vehicle dealers, food stores, general merchandise - customer: sells to final consumers - SECTOR_48_49: - title: Transportation and Warehousing - description: Establishments providing transportation and warehousing services + authenticity: genuine and authentic + self_awareness: high self-awareness + values: values-based leadership + integrity: personal integrity + CHARISMATIC: + title: Charismatic Leadership + description: Inspiring leadership through personal charisma annotations: - naics_code: 48-49 - activities: air, rail, water, truck transportation, warehousing - infrastructure: transportation infrastructure dependent - SECTOR_51: - title: Information - description: Establishments in information industries + charisma: personal charisma + inspiration: inspirational influence + emotion: emotional appeal + following: devoted following + SITUATIONAL: + title: Situational Leadership + description: Adaptive leadership based on situation requirements annotations: - naics_code: '51' - activities: publishing, broadcasting, telecommunications, data processing - technology: information technology and content - SECTOR_52: - title: Finance and Insurance - description: Establishments providing financial services + adaptation: situational adaptation + flexibility: flexible approach + assessment: situation assessment + style_variation: varying leadership styles + DEMOCRATIC: + title: Democratic Leadership + description: Participative leadership with shared decision-making annotations: - naics_code: '52' - activities: banking, securities, insurance, funds and trusts - regulation: highly regulated financial sector - SECTOR_53: - title: Real Estate and Rental and Leasing - description: Establishments engaged in real estate and rental activities + participation: follower participation + shared: shared decision making + empowerment: team empowerment + collaboration: collaborative approach + AUTOCRATIC: + title: Autocratic Leadership + description: Directive leadership with centralized control annotations: - naics_code: '53' - activities: real estate, rental and leasing services - asset_type: real and personal property - SECTOR_54: - title: Professional, Scientific, and Technical Services - description: Establishments providing professional services + control: centralized control + directive: directive approach + authority: strong authority + efficiency: decision efficiency + LAISSEZ_FAIRE: + title: Laissez-Faire Leadership + description: Hands-off leadership with minimal interference annotations: - naics_code: '54' - activities: legal, accounting, engineering, consulting, research - knowledge_based: knowledge and skill intensive - SECTOR_55: - title: Management of Companies and Enterprises - description: Establishments serving as holding companies or managing enterprises + autonomy: high follower autonomy + minimal: minimal leadership intervention + freedom: freedom to operate + self_direction: self-directed teams + COACHING: + title: Coaching Leadership + description: Development-focused leadership approach annotations: - naics_code: '55' - activities: holding companies, corporate management - function: corporate ownership and management - SECTOR_56: - title: Administrative and Support and Waste Management - description: Establishments providing administrative and support services + development: skill and capability development + guidance: mentoring and guidance + growth: personal and professional growth + support: supportive leadership + is_a: ManagementOperationsSchemaEnum + annotations: + source_domain: business + source_schema: management_operations + BusinessProcessTypeEnum: + title: Business Process Type + description: Types of business processes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CORE_PROCESS: + title: Core Business Process + description: Primary processes that create customer value annotations: - naics_code: '56' - activities: administrative services, waste management, remediation - support_function: business support services - SECTOR_61: - title: Educational Services - description: Establishments providing educational instruction + value: direct customer value creation + primary: primary business activities + competitive: competitive advantage source + strategic: strategic importance + SUPPORT_PROCESS: + title: Support Process + description: Processes that enable core business activities annotations: - naics_code: '61' - activities: schools, colleges, training programs - public_private: public and private education - SECTOR_62: - title: Health Care and Social Assistance - description: Establishments providing health care and social assistance + support: supports core processes + enabling: enabling activities + infrastructure: business infrastructure + indirect: indirect value contribution + MANAGEMENT_PROCESS: + title: Management Process + description: Processes for planning, controlling, and improving annotations: - naics_code: '62' - activities: hospitals, medical practices, social assistance - essential_services: essential public services - SECTOR_71: - title: Arts, Entertainment, and Recreation - description: Establishments in arts, entertainment, and recreation + management: management and governance + planning: planning and control + improvement: process improvement + oversight: organizational oversight + OPERATIONAL_PROCESS: + title: Operational Process + description: Day-to-day operational activities annotations: - naics_code: '71' - activities: performing arts, spectator sports, museums, recreation - discretionary: discretionary consumer spending - SECTOR_72: - title: Accommodation and Food Services - description: Establishments providing accommodation and food services + operations: daily operations + routine: routine activities + execution: operational execution + efficiency: operational efficiency + STRATEGIC_PROCESS: + title: Strategic Process + description: Long-term planning and strategic activities annotations: - naics_code: '72' - activities: hotels, restaurants, food services - consumer_services: consumer hospitality services - SECTOR_81: - title: Other Services (except Public Administration) - description: Establishments providing other services + strategy: strategic planning + long_term: long-term focus + direction: organizational direction + competitive: competitive positioning + INNOVATION_PROCESS: + title: Innovation Process + description: Processes for developing new products or services annotations: - naics_code: '81' - activities: repair, personal care, religious organizations - diverse: diverse service activities - SECTOR_92: - title: Public Administration - description: Government establishments + innovation: innovation and development + creativity: creative processes + new_development: new product/service development + competitive: competitive innovation + CUSTOMER_PROCESS: + title: Customer Process + description: Processes focused on customer interaction and service annotations: - naics_code: '92' - activities: executive, legislative, judicial, public safety - sector: government sector - is_a: IndustryClassificationsSchemaEnum + customer: customer-facing processes + service: customer service + relationship: customer relationship + satisfaction: customer satisfaction + FINANCIAL_PROCESS: + title: Financial Process + description: Processes related to financial management + annotations: + financial: financial management + accounting: accounting and reporting + control: financial control + compliance: financial compliance + is_a: ManagementOperationsSchemaEnum annotations: source_domain: business - source_schema: industry_classifications - EconomicSectorEnum: - description: Broad economic sector classifications + source_schema: management_operations + OrganizationalStructuresSchemaEnum: + description: Schema-level enum for organizational_structures in business + is_a: BusinessDomainEnum + abstract: true + annotations: + source_file: business/organizational_structures.yaml + LegalEntityTypeEnum: + title: Legal Entity Type + description: Legal entity types for business organizations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - PRIMARY_SECTOR: - title: Primary Sector - description: Economic activities extracting natural resources + SOLE_PROPRIETORSHIP: + title: Sole Proprietorship + description: Business owned and operated by single individual annotations: - activities: agriculture, mining, forestry, fishing - output: raw materials and natural resources - employment: typically lower employment share in developed economies - development_stage: dominant in early economic development - SECONDARY_SECTOR: - title: Secondary Sector - description: Economic activities manufacturing and processing goods + legal_separation: no separation from owner + liability: unlimited personal liability + taxation: pass-through to personal returns + complexity: simplest structure + registration: minimal requirements + GENERAL_PARTNERSHIP: + title: General Partnership + description: Business owned by two or more partners sharing responsibilities annotations: - activities: manufacturing, construction, utilities - output: processed and manufactured goods - value_added: transforms raw materials into finished products - employment: historically significant in industrial economies - TERTIARY_SECTOR: - title: Tertiary Sector - description: Economic activities providing services + ownership: shared among general partners + liability: unlimited personal liability for all partners + taxation: pass-through to partners + management: shared management responsibilities + LIMITED_PARTNERSHIP: + title: Limited Partnership (LP) + description: Partnership with general and limited partners annotations: - activities: retail, hospitality, transportation, finance, healthcare - output: services to consumers and businesses - growth: largest and fastest growing sector in developed economies - employment: dominant employment sector - QUATERNARY_SECTOR: - title: Quaternary Sector - description: Knowledge-based economic activities + partner_types: general partners and limited partners + liability: general partners have unlimited liability + limited_liability: limited partners have liability protection + management: general partners manage operations + LIMITED_LIABILITY_PARTNERSHIP: + title: Limited Liability Partnership (LLP) + description: Partnership providing liability protection to all partners annotations: - activities: research, education, information technology, consulting - output: knowledge, information, and intellectual services - characteristics: high skill and education requirements - growth: rapidly growing in knowledge economies - QUINARY_SECTOR: - title: Quinary Sector - description: High-level decision-making and policy services + liability: limited liability for all partners + professional_use: often used by professional services + taxation: pass-through taxation + management: flexible management structure + LIMITED_LIABILITY_COMPANY: + title: Limited Liability Company (LLC) + description: Hybrid entity combining corporation and partnership features annotations: - activities: top-level government, healthcare, education, culture - output: highest level services and decision-making - characteristics: elite services and leadership roles - scope: limited to highest level activities - is_a: IndustryClassificationsSchemaEnum - annotations: - source_domain: business - source_schema: industry_classifications - BusinessActivityTypeEnum: - description: Types of primary business activities - permissible_values: - PRODUCTION: - title: Production/Manufacturing - description: Creating or manufacturing physical goods + liability: limited liability protection + taxation: flexible tax election options + management: flexible management structure + formality: fewer formal requirements than corporations + SINGLE_MEMBER_LLC: + title: Single Member LLC + description: LLC with only one owner/member annotations: - output: physical products and goods - process: transformation of materials - assets: physical assets and equipment intensive - examples: factories, farms, mines - DISTRIBUTION: - title: Distribution/Trade - description: Moving goods from producers to consumers + ownership: single member + liability: limited liability protection + taxation: disregarded entity for tax purposes + simplicity: simpler than multi-member LLC + MULTI_MEMBER_LLC: + title: Multi-Member LLC + description: LLC with multiple owners/members annotations: - function: intermediary between producers and consumers - value_added: place and time utility - examples: wholesalers, retailers, logistics companies - efficiency: improves market efficiency - SERVICES: - title: Service Provision - description: Providing intangible services to customers + ownership: multiple members + liability: limited liability protection + taxation: partnership taxation by default + operating_agreement: recommended operating agreement + C_CORPORATION: + title: C Corporation + description: Traditional corporation with double taxation + annotations: + legal_status: separate legal entity + liability: limited liability for shareholders + taxation: double taxation (corporate and dividend) + governance: formal board and officer structure + stock: can issue multiple classes of stock + S_CORPORATION: + title: S Corporation + description: Corporation electing pass-through taxation + annotations: + taxation: pass-through to shareholders + shareholders: limited to 100 shareholders + stock_types: single class of stock only + eligibility: restrictions on shareholder types + B_CORPORATION: + title: Benefit Corporation (B-Corp) + description: Corporation with social and environmental mission + annotations: + purpose: profit and public benefit + accountability: stakeholder governance requirements + transparency: annual benefit reporting + certification: optional third-party certification + PUBLIC_CORPORATION: + title: Public Corporation + description: Corporation with publicly traded shares + annotations: + shares: publicly traded on stock exchanges + regulation: SEC reporting requirements + governance: extensive governance requirements + liquidity: high share liquidity + PRIVATE_CORPORATION: + title: Private Corporation + description: Corporation with privately held shares annotations: - output: intangible services - characteristics: labor intensive, customized - examples: consulting, healthcare, hospitality - customer_interaction: high customer interaction - TECHNOLOGY: - title: Technology/Innovation - description: Developing and applying technology solutions + shares: privately held shares + shareholders: limited number of shareholders + regulation: fewer regulatory requirements + liquidity: limited share liquidity + NONPROFIT_CORPORATION: + title: Nonprofit Corporation + description: Corporation organized for charitable or public purposes annotations: - focus: technology development and application - innovation: research and development intensive - examples: software companies, biotech, engineering - intellectual_property: high intellectual property content - FINANCE: - title: Financial Services - description: Providing financial and investment services + purpose: charitable, educational, or public benefit + taxation: tax-exempt status possible + profit_distribution: no profit distribution to members + governance: board of directors governance + COOPERATIVE: + title: Cooperative + description: Member-owned and democratically controlled organization annotations: - function: financial intermediation and services - regulation: highly regulated - examples: banks, insurance, investment firms - capital: capital intensive - INFORMATION: - title: Information/Media - description: Creating, processing, and distributing information + ownership: member ownership + control: democratic member control + benefits: benefits proportional to participation + purpose: mutual benefit of members + JOINT_VENTURE: + title: Joint Venture + description: Temporary partnership for specific project or purpose annotations: - output: information and content - channels: various distribution channels - examples: media companies, publishers, data processors - technology_dependent: technology platform dependent - EDUCATION: - title: Education/Training - description: Providing educational and training services + duration: temporary or project-specific + purpose: specific business objective + ownership: shared ownership of venture + liability: depends on structure chosen + HOLDING_COMPANY: + title: Holding Company + description: Company that owns controlling interests in other companies annotations: - function: knowledge and skill development - public_private: public and private providers - examples: schools, universities, training companies - social_impact: high social impact - HEALTHCARE: - title: Healthcare/Medical - description: Providing health and medical services + purpose: own and control subsidiary companies + operations: minimal direct operations + structure: parent-subsidiary relationships + control: controls subsidiaries through ownership + SUBSIDIARY: + title: Subsidiary + description: Company controlled by another company (parent) annotations: - function: health and medical care - regulation: highly regulated - examples: hospitals, clinics, pharmaceutical companies - essential: essential service - ENTERTAINMENT: - title: Entertainment/Recreation - description: Providing entertainment and recreational services + control: controlled by parent company + ownership: majority owned by parent + operations: may operate independently + liability: separate legal entity + FRANCHISE: + title: Franchise + description: Business operating under franchisor's brand and system annotations: - output: entertainment and leisure experiences - discretionary: discretionary consumer spending - examples: media, sports, tourism, gaming - experience_based: experience and emotion based - PROFESSIONAL_SERVICES: - title: Professional Services - description: Providing specialized professional expertise + relationship: franchisor-franchisee relationship + brand: operates under established brand + system: follows franchisor's business system + fees: pays franchise fees and royalties + GOVERNMENT_ENTITY: + title: Government Entity + description: Entity owned and operated by government annotations: - characteristics: high skill and knowledge requirements - customization: highly customized services - examples: law firms, consulting, accounting - expertise: specialized professional expertise - is_a: IndustryClassificationsSchemaEnum + ownership: government ownership + purpose: public service or policy implementation + regulation: government regulations and oversight + funding: government funding sources + is_a: OrganizationalStructuresSchemaEnum annotations: source_domain: business - source_schema: industry_classifications - IndustryMaturityEnum: - description: Industry lifecycle and maturity stages + source_schema: organizational_structures + OrganizationalStructureEnum: + title: Organizational Structure + description: Types of organizational hierarchy and reporting structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - EMERGING: - title: Emerging Industry - description: New industry in early development stage - annotations: - characteristics: high uncertainty, rapid change - growth: high growth potential - technology: new or evolving technology - competition: few competitors, unclear standards - investment: high investment requirements - GROWTH: - title: Growth Industry - description: Industry experiencing rapid expansion + HIERARCHICAL: + title: Hierarchical Structure + description: Traditional pyramid structure with clear chain of command annotations: - characteristics: rapid market expansion - competition: increasing competition - standardization: emerging standards - investment: significant investment opportunities - profitability: improving profitability - MATURE: - title: Mature Industry - description: Established industry with stable growth + authority_flow: top-down authority + communication: vertical communication channels + levels: multiple management levels + control: centralized control + decision_making: centralized decision making + FLAT: + title: Flat Structure + description: Minimal hierarchical levels with broader spans of control annotations: - characteristics: stable market conditions - growth: slower, steady growth - competition: established competitive structure - efficiency: focus on operational efficiency - consolidation: potential for consolidation - DECLINING: - title: Declining Industry - description: Industry experiencing contraction + levels: few hierarchical levels + span_of_control: broad spans of control + communication: direct communication + decision_making: decentralized decision making + flexibility: high flexibility + MATRIX: + title: Matrix Structure + description: Dual reporting relationships combining functional and project lines annotations: - characteristics: decreasing demand - competition: intensifying competition for shrinking market - cost_focus: focus on cost reduction - consolidation: significant consolidation - exit: companies exiting industry - TRANSFORMING: - title: Transforming Industry - description: Industry undergoing fundamental change + reporting: dual reporting relationships + authority: shared authority between managers + flexibility: high project flexibility + complexity: increased complexity + communication: multidirectional communication + FUNCTIONAL: + title: Functional Structure + description: Organization by business functions or departments annotations: - characteristics: disruptive change and innovation - technology: technology-driven transformation - business_models: evolving business models - uncertainty: high uncertainty about future structure - opportunity: opportunities for innovation and disruption - is_a: IndustryClassificationsSchemaEnum - annotations: - source_domain: business - source_schema: industry_classifications - MarketStructureEnum: - description: Competitive structure of industry markets - permissible_values: - PERFECT_COMPETITION: - title: Perfect Competition - description: Many small firms with identical products + grouping: by business function + specialization: functional specialization + efficiency: operational efficiency + coordination: vertical coordination + expertise: concentrated expertise + DIVISIONAL: + title: Divisional Structure + description: Organization by product lines, markets, or geography annotations: - competitors: many small competitors - products: homogeneous products - barriers: no barriers to entry - pricing: price takers - examples: agricultural commodities - MONOPOLISTIC_COMPETITION: - title: Monopolistic Competition - description: Many firms with differentiated products + grouping: by products, markets, or geography + autonomy: divisional autonomy + focus: market or product focus + coordination: horizontal coordination + responsibility: profit center responsibility + NETWORK: + title: Network Structure + description: Flexible structure with interconnected relationships annotations: - competitors: many competitors - products: differentiated products - barriers: low barriers to entry - pricing: some pricing power - examples: restaurants, retail clothing - OLIGOPOLY: - title: Oligopoly - description: Few large firms dominating the market + relationships: network of relationships + flexibility: high flexibility + boundaries: blurred organizational boundaries + collaboration: extensive collaboration + adaptability: high adaptability + TEAM_BASED: + title: Team-Based Structure + description: Organization around self-managing teams annotations: - competitors: few large competitors - concentration: high market concentration - barriers: significant barriers to entry - interdependence: strategic interdependence - examples: automobiles, telecommunications - MONOPOLY: - title: Monopoly - description: Single firm controlling the market + unit: teams as basic organizational unit + management: self-managing teams + collaboration: high collaboration + decision_making: team-based decision making + flexibility: operational flexibility + VIRTUAL: + title: Virtual Structure + description: Geographically dispersed organization connected by technology annotations: - competitors: single market leader - barriers: very high barriers to entry - pricing: price maker - regulation: often regulated - examples: utilities, patented products - DUOPOLY: - title: Duopoly - description: Two firms dominating the market + location: geographically dispersed + technology: technology-enabled communication + flexibility: location flexibility + coordination: virtual coordination + boundaries: minimal physical boundaries + HYBRID: + title: Hybrid Structure + description: Combination of multiple organizational structures annotations: - competitors: two dominant competitors - competition: head-to-head competition - barriers: high barriers to entry - strategy: strategic competition - examples: aircraft manufacturing, some software markets - is_a: IndustryClassificationsSchemaEnum + combination: multiple structure types + flexibility: structural flexibility + adaptation: adaptable to different needs + complexity: increased structural complexity + customization: customized to organization needs + is_a: OrganizationalStructuresSchemaEnum annotations: source_domain: business - source_schema: industry_classifications - IndustryRegulationLevelEnum: - description: Level of government regulation in different industries + source_schema: organizational_structures + ManagementLevelEnum: + title: Management Level + description: Hierarchical levels within organizational management structure + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - HIGHLY_REGULATED: - title: Highly Regulated - description: Industries subject to extensive government oversight + BOARD_OF_DIRECTORS: + title: Board of Directors + description: Governing body elected by shareholders annotations: - oversight: extensive government oversight - compliance: complex compliance requirements - barriers: regulatory barriers to entry - examples: banking, healthcare, utilities, pharmaceuticals - reason: public safety, market power, or systemic risk - MODERATELY_REGULATED: - title: Moderately Regulated - description: Industries with significant but focused regulation + authority: highest governance authority + responsibility: fiduciary responsibility to shareholders + oversight: strategic oversight and control + composition: independent and inside directors + C_SUITE: + title: C-Suite/Chief Officers + description: Top executive leadership team annotations: - oversight: focused regulatory oversight - compliance: specific compliance requirements - areas: targeted regulatory areas - examples: food service, transportation, insurance - balance: balance between oversight and flexibility - LIGHTLY_REGULATED: - title: Lightly Regulated - description: Industries with minimal regulatory oversight + level: top executive level + scope: organization-wide responsibility + titles: CEO, CFO, COO, CTO, etc. + accountability: accountable to board of directors + SENIOR_EXECUTIVE: + title: Senior Executive + description: Senior leadership below C-suite level annotations: - oversight: minimal regulatory oversight - compliance: basic compliance requirements - flexibility: high operational flexibility - examples: technology, consulting, retail - approach: market-based approach - SELF_REGULATED: - title: Self-Regulated - description: Industries primarily regulated by industry organizations + level: senior leadership + scope: major business unit or function + titles: EVP, SVP, General Manager + reporting: reports to C-suite + VICE_PRESIDENT: + title: Vice President + description: Senior management responsible for major divisions annotations: - oversight: industry self-regulation - standards: industry-developed standards - compliance: voluntary compliance - examples: professional services, trade associations - effectiveness: varies by industry - DEREGULATED: - title: Deregulated - description: Industries formerly regulated but now market-based + level: senior management + scope: division or major function + authority: significant decision-making authority + titles: VP, Assistant VP + DIRECTOR: + title: Director + description: Management responsible for departments or major programs annotations: - history: formerly regulated industries - competition: market-based competition - transition: transition from regulation to competition - examples: airlines, telecommunications, energy - benefits: increased competition and efficiency - is_a: IndustryClassificationsSchemaEnum + level: middle management + scope: department or program + responsibility: departmental leadership + oversight: manages multiple managers + MANAGER: + title: Manager + description: Supervisory role managing teams or operations + annotations: + level: middle management + scope: team or operational unit + responsibility: day-to-day operations + supervision: manages individual contributors + SUPERVISOR: + title: Supervisor + description: First-line management overseeing frontline employees + annotations: + level: first-line management + scope: small team or shift + responsibility: direct supervision + interface: employee-management interface + TEAM_LEAD: + title: Team Lead + description: Lead role within team without formal management authority + annotations: + level: senior individual contributor + authority: informal authority + responsibility: team coordination + expertise: technical or project leadership + SENIOR_INDIVIDUAL_CONTRIBUTOR: + title: Senior Individual Contributor + description: Experienced professional without management responsibilities + annotations: + level: senior professional + expertise: specialized expertise + mentoring: may mentor junior staff + projects: leads complex projects + INDIVIDUAL_CONTRIBUTOR: + title: Individual Contributor + description: Professional or specialist role + annotations: + level: professional + responsibility: individual work output + specialization: functional specialization + career_path: professional career track + ENTRY_LEVEL: + title: Entry Level + description: Beginning professional or support roles + annotations: + experience: minimal professional experience + development: learning and development focus + supervision: close supervision + growth_potential: career growth opportunities + is_a: OrganizationalStructuresSchemaEnum annotations: source_domain: business - source_schema: industry_classifications - ManagementOperationsSchemaEnum: - description: Schema-level enum for management_operations in business - is_a: BusinessDomainEnum - abstract: true - annotations: - source_file: business/management_operations.yaml - ManagementMethodologyEnum: - description: Management approaches and methodologies + source_schema: organizational_structures + CorporateGovernanceRoleEnum: + title: Corporate Governance Role + description: Roles within corporate governance structure + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - TRADITIONAL_MANAGEMENT: - title: Traditional Management - description: Hierarchical command-and-control management approach + CHAIRMAN_OF_BOARD: + title: Chairman of the Board + description: Leader of board of directors annotations: - structure: hierarchical structure - authority: centralized authority - communication: top-down communication - control: direct supervision and control - AGILE_MANAGEMENT: - title: Agile Management - description: Flexible, iterative management approach + leadership: board leadership + meetings: chairs board meetings + interface: shareholder interface + governance: governance oversight + LEAD_INDEPENDENT_DIRECTOR: + title: Lead Independent Director + description: Senior independent director when chairman is not independent annotations: - flexibility: adaptive and flexible - iteration: iterative approach - collaboration: cross-functional collaboration - customer_focus: customer-centric - LEAN_MANAGEMENT: - title: Lean Management - description: Waste elimination and value optimization approach + independence: independent from management + leadership: leads independent directors + oversight: additional oversight role + communication: shareholder communication + INDEPENDENT_DIRECTOR: + title: Independent Director + description: Board member independent from company management annotations: - focus: waste elimination - value: value stream optimization - continuous_improvement: kaizen and continuous improvement - efficiency: operational efficiency - PARTICIPATIVE_MANAGEMENT: - title: Participative Management - description: Employee involvement in decision-making + independence: independent from management + objectivity: objective oversight + committees: serves on key committees + governance: independent governance perspective + INSIDE_DIRECTOR: + title: Inside Director + description: Board member who is also company employee or has material relationship annotations: - involvement: employee participation - decision_making: shared decision-making - empowerment: employee empowerment - engagement: increased employee engagement - MATRIX_MANAGEMENT: - title: Matrix Management - description: Dual reporting relationships and shared authority + relationship: material relationship with company + expertise: insider knowledge + perspective: management perspective + potential_conflicts: potential conflicts of interest + AUDIT_COMMITTEE_CHAIR: + title: Audit Committee Chair + description: Chair of board's audit committee annotations: - structure: matrix reporting structure - authority: shared authority - flexibility: organizational flexibility - complexity: increased complexity - PROJECT_MANAGEMENT: - title: Project Management - description: Structured approach to managing projects + committee: audit committee leadership + oversight: financial oversight + independence: must be independent + expertise: financial expertise required + COMPENSATION_COMMITTEE_CHAIR: + title: Compensation Committee Chair + description: Chair of board's compensation committee annotations: - methodology: project management methodology - lifecycle: project lifecycle management - deliverables: deliverable-focused - temporary: temporary organizational structure - RESULTS_ORIENTED_MANAGEMENT: - title: Results-Oriented Management - description: Focus on outcomes and performance results + committee: compensation committee leadership + responsibility: executive compensation oversight + independence: must be independent + alignment: shareholder interest alignment + NOMINATING_COMMITTEE_CHAIR: + title: Nominating Committee Chair + description: Chair of board's nominating and governance committee + annotations: + committee: nominating committee leadership + responsibility: board composition and governance + succession: leadership succession planning + governance: governance best practices + CHIEF_EXECUTIVE_OFFICER: + title: Chief Executive Officer (CEO) + description: Highest-ranking executive officer annotations: - focus: results and outcomes - measurement: performance measurement - accountability: accountability for results - goals: goal-oriented approach - SERVANT_LEADERSHIP: - title: Servant Leadership - description: Leader serves and supports team members + authority: highest executive authority + strategy: strategic leadership + accountability: accountable to board + representation: company representation + CHIEF_FINANCIAL_OFFICER: + title: Chief Financial Officer (CFO) + description: Senior executive responsible for financial management annotations: - philosophy: service-oriented leadership - support: leader supports team - development: people development focus - empowerment: team empowerment - TRANSFORMATIONAL_MANAGEMENT: - title: Transformational Management - description: Change-oriented and inspirational management + responsibility: financial management + reporting: financial reporting oversight + compliance: financial compliance + strategy: financial strategy + CHIEF_OPERATING_OFFICER: + title: Chief Operating Officer (COO) + description: Senior executive responsible for operations annotations: - change: transformation and change focus - inspiration: inspirational leadership - vision: vision-driven - development: follower development - DEMOCRATIC_MANAGEMENT: - title: Democratic Management - description: Collaborative and consensus-building approach + responsibility: operational management + execution: strategy execution + efficiency: operational efficiency + coordination: cross-functional coordination + CORPORATE_SECRETARY: + title: Corporate Secretary + description: Officer responsible for corporate records and governance compliance annotations: - participation: democratic participation - consensus: consensus-building - equality: equal voice in decisions - transparency: transparent processes - is_a: ManagementOperationsSchemaEnum + records: corporate records maintenance + compliance: governance compliance + meetings: board meeting coordination + legal: legal compliance oversight + is_a: OrganizationalStructuresSchemaEnum annotations: source_domain: business - source_schema: management_operations - StrategicFrameworkEnum: - description: Strategic planning and analysis frameworks + source_schema: organizational_structures + BusinessOwnershipTypeEnum: + title: Business Ownership Type + description: Types of business ownership structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - SWOT_ANALYSIS: - title: SWOT Analysis - description: Strengths, Weaknesses, Opportunities, Threats analysis - annotations: - components: strengths, weaknesses, opportunities, threats - purpose: strategic positioning analysis - simplicity: simple and widely used - application: strategic planning and decision-making - PORTERS_FIVE_FORCES: - title: Porter's Five Forces - description: Industry competitiveness analysis framework - annotations: - forces: competitive rivalry, supplier power, buyer power, substitutes, barriers - purpose: industry attractiveness analysis - competition: competitive strategy framework - application: industry analysis and strategy formulation - BALANCED_SCORECARD: - title: Balanced Scorecard - description: Performance measurement from multiple perspectives + PRIVATE_OWNERSHIP: + title: Private Ownership + description: Business owned by private individuals or entities annotations: - perspectives: financial, customer, internal process, learning - purpose: strategic performance measurement - balance: balanced view of performance - alignment: strategy alignment tool - BLUE_OCEAN_STRATEGY: - title: Blue Ocean Strategy - description: Creating uncontested market space strategy + ownership: private individuals or entities + control: private control + capital: private capital sources + disclosure: limited disclosure requirements + PUBLIC_OWNERSHIP: + title: Public Ownership + description: Business with publicly traded ownership shares annotations: - concept: value innovation and market creation - competition: competition avoidance - differentiation: differentiation and low cost - innovation: strategic innovation - ANSOFF_MATRIX: - title: Ansoff Matrix - description: Product and market growth strategy framework + ownership: public shareholders + trading: publicly traded shares + regulation: extensive regulatory requirements + disclosure: public disclosure requirements + FAMILY_OWNERSHIP: + title: Family Ownership + description: Business owned and controlled by family members annotations: - dimensions: products and markets - strategies: market penetration, development, diversification - growth: growth strategy framework - risk: risk assessment of growth options - BCG_MATRIX: - title: BCG Matrix - description: Portfolio analysis of business units + ownership: family members + succession: family succession planning + values: family values integration + long_term: long-term orientation + EMPLOYEE_OWNERSHIP: + title: Employee Ownership + description: Business owned by employees through stock or cooperative structure annotations: - dimensions: market growth and market share - categories: stars, cash cows, question marks, dogs - portfolio: business portfolio analysis - resource_allocation: resource allocation decisions - VALUE_CHAIN_ANALYSIS: - title: Value Chain Analysis - description: Analysis of value-creating activities + ownership: employee owners + participation: employee participation + alignment: ownership-management alignment + structure: ESOP or cooperative structure + INSTITUTIONAL_OWNERSHIP: + title: Institutional Ownership + description: Business owned by institutional investors annotations: - activities: primary and support activities - value: value creation analysis - advantage: competitive advantage source identification - optimization: value chain optimization - SCENARIO_PLANNING: - title: Scenario Planning - description: Multiple future scenario development and planning + ownership: institutional investors + professional: professional management + capital: institutional capital + governance: institutional governance + GOVERNMENT_OWNERSHIP: + title: Government Ownership + description: Business owned by government entities annotations: - scenarios: multiple future scenarios - uncertainty: uncertainty management - planning: strategic contingency planning - flexibility: strategic flexibility - STRATEGIC_CANVAS: - title: Strategy Canvas - description: Visual representation of competitive factors + ownership: government entities + purpose: public policy objectives + regulation: government oversight + funding: public funding + FOREIGN_OWNERSHIP: + title: Foreign Ownership + description: Business owned by foreign individuals or entities annotations: - visualization: visual strategy representation - factors: competitive factors analysis - comparison: competitor comparison - innovation: value innovation identification - CORE_COMPETENCY_ANALYSIS: - title: Core Competency Analysis - description: Identification and development of core competencies + ownership: foreign entities + regulation: foreign investment regulations + capital: foreign capital + compliance: international compliance + JOINT_OWNERSHIP: + title: Joint Ownership + description: Business owned jointly by multiple parties annotations: - competencies: unique organizational capabilities - advantage: sustainable competitive advantage - focus: competency-based strategy - development: capability development - is_a: ManagementOperationsSchemaEnum + ownership: multiple ownership parties + agreements: joint ownership agreements + governance: shared governance + coordination: ownership coordination + is_a: OrganizationalStructuresSchemaEnum annotations: source_domain: business - source_schema: management_operations - OperationalModelEnum: - description: Business operational models and approaches + source_schema: organizational_structures + BusinessSizeClassificationEnum: + title: Business Size Classification + description: Size classifications for business entities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - CENTRALIZED_OPERATIONS: - title: Centralized Operations - description: Centralized operational control and decision-making - annotations: - control: centralized control - efficiency: operational efficiency - standardization: standardized processes - coordination: central coordination - DECENTRALIZED_OPERATIONS: - title: Decentralized Operations - description: Distributed operational control and autonomy - annotations: - autonomy: local autonomy - responsiveness: market responsiveness - flexibility: operational flexibility - empowerment: local empowerment - HYBRID_OPERATIONS: - title: Hybrid Operations - description: Combination of centralized and decentralized elements - annotations: - combination: mixed centralized and decentralized - balance: balance between control and flexibility - optimization: situational optimization - complexity: increased complexity - OUTSOURCED_OPERATIONS: - title: Outsourced Operations - description: External service provider operational model - annotations: - provider: external service providers - focus: core competency focus - cost: cost optimization - expertise: specialized expertise - SHARED_SERVICES: - title: Shared Services - description: Centralized services shared across business units - annotations: - sharing: shared service delivery - efficiency: scale efficiency - standardization: service standardization - cost_effectiveness: cost-effective service delivery - NETWORK_OPERATIONS: - title: Network Operations - description: Collaborative network of partners and suppliers + MICRO_BUSINESS: + title: Micro Business + description: Very small business with minimal employees and revenue annotations: - network: partner and supplier network - collaboration: collaborative operations - flexibility: network flexibility - coordination: network coordination - PLATFORM_OPERATIONS: - title: Platform Operations - description: Platform-based business operational model + employees: typically 1-9 employees + revenue: very low revenue + characteristics: home-based or small office + support: minimal administrative support + SMALL_BUSINESS: + title: Small Business + description: Small business as defined by SBA standards annotations: - platform: platform-based operations - ecosystem: business ecosystem - scalability: scalable operations - network_effects: network effects - AGILE_OPERATIONS: - title: Agile Operations - description: Flexible and responsive operational approach + employees: varies by industry (typically <500) + revenue: varies by industry + sba_definition: meets SBA size standards + characteristics: independently owned and operated + MEDIUM_BUSINESS: + title: Medium Business + description: Mid-sized business between small and large classifications annotations: - agility: operational agility - responsiveness: market responsiveness - adaptation: rapid adaptation - iteration: iterative improvement - LEAN_OPERATIONS: - title: Lean Operations - description: Waste elimination and value-focused operations + employees: typically 500-1500 employees + revenue: moderate revenue levels + characteristics: regional or specialized market presence + structure: more formal organizational structure + LARGE_BUSINESS: + title: Large Business + description: Major corporation with significant operations annotations: - waste: waste elimination - value: value stream focus - efficiency: operational efficiency - continuous_improvement: continuous improvement - DIGITAL_OPERATIONS: - title: Digital Operations - description: Technology-enabled and digital-first operations + employees: '>1500 employees' + revenue: high revenue levels + market_presence: national or international presence + structure: complex organizational structure + MULTINATIONAL_CORPORATION: + title: Multinational Corporation + description: Large corporation operating in multiple countries annotations: - technology: digital technology enabled - automation: process automation - data_driven: data-driven operations - scalability: digital scalability - is_a: ManagementOperationsSchemaEnum + geographic_scope: multiple countries + complexity: high operational complexity + structure: global organizational structure + coordination: international coordination + FORTUNE_500: + title: Fortune 500 Company + description: Among the 500 largest US corporations by revenue + annotations: + ranking: Fortune 500 list + revenue: highest revenue levels + market_position: market leadership positions + recognition: prestigious business recognition + is_a: OrganizationalStructuresSchemaEnum annotations: source_domain: business - source_schema: management_operations - PerformanceMeasurementEnum: - description: Performance measurement systems and approaches + source_schema: organizational_structures + BusinessLifecycleStageEnum: + title: Business Lifecycle Stage + description: Stages in business development lifecycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - KEY_PERFORMANCE_INDICATORS: - title: Key Performance Indicators (KPIs) - description: Specific metrics measuring critical performance areas - annotations: - specificity: specific performance metrics - critical: critical success factors - measurement: quantitative measurement - tracking: performance tracking - OBJECTIVES_KEY_RESULTS: - title: Objectives and Key Results (OKRs) - description: Goal-setting framework with measurable outcomes - annotations: - objectives: qualitative objectives - results: quantitative key results - alignment: organizational alignment - transparency: transparent goal setting - BALANCED_SCORECARD_MEASUREMENT: - title: Balanced Scorecard Measurement - description: Multi-perspective performance measurement system + CONCEPT_STAGE: + title: Concept Stage + description: Initial business idea development and validation annotations: - perspectives: multiple performance perspectives - balance: balanced performance view - strategy: strategy-linked measurement - cause_effect: cause-and-effect relationships - RETURN_ON_INVESTMENT: - title: Return on Investment (ROI) - description: Financial return measurement relative to investment + focus: idea development and validation + activities: market research, business planning + funding: personal or angel funding + risk: highest risk level + STARTUP_STAGE: + title: Startup Stage + description: Business launch and early operations annotations: - financial: financial performance measure - investment: investment-based measurement - efficiency: capital efficiency - comparison: investment comparison - ECONOMIC_VALUE_ADDED: - title: Economic Value Added (EVA) - description: Value creation measurement after cost of capital + focus: product development and market entry + activities: building initial customer base + funding: seed funding, early investments + growth: rapid learning and adaptation + GROWTH_STAGE: + title: Growth Stage + description: Rapid expansion and scaling operations annotations: - value: economic value creation - capital_cost: cost of capital consideration - shareholder: shareholder value focus - performance: true economic performance - CUSTOMER_SATISFACTION_METRICS: - title: Customer Satisfaction Metrics - description: Customer experience and satisfaction measurement + focus: scaling operations and market expansion + activities: increasing market share + funding: venture capital, growth financing + challenges: scaling challenges + EXPANSION_STAGE: + title: Expansion Stage + description: Market expansion and diversification annotations: - customer: customer-focused measurement - satisfaction: satisfaction and loyalty - experience: customer experience - retention: customer retention - EMPLOYEE_ENGAGEMENT_METRICS: - title: Employee Engagement Metrics - description: Employee satisfaction and engagement measurement + focus: market expansion and diversification + activities: new markets, products, or services + funding: growth capital, strategic investments + sophistication: increased operational sophistication + MATURITY_STAGE: + title: Maturity Stage + description: Stable operations with established market position annotations: - engagement: employee engagement - satisfaction: employee satisfaction - retention: employee retention - productivity: employee productivity - OPERATIONAL_EFFICIENCY_METRICS: - title: Operational Efficiency Metrics - description: Operational performance and efficiency measurement + focus: operational efficiency and market defense + activities: defending market position + funding: self-funding, debt financing + stability: stable cash flows + DECLINE_STAGE: + title: Decline Stage + description: Decreasing market relevance or performance annotations: - efficiency: operational efficiency - productivity: process productivity - quality: quality metrics - cost: cost efficiency - INNOVATION_METRICS: - title: Innovation Metrics - description: Innovation performance and capability measurement + focus: cost reduction and restructuring + activities: turnaround efforts or exit planning + challenges: declining revenues or relevance + options: restructuring, sale, or closure + TURNAROUND_STAGE: + title: Turnaround Stage + description: Recovery efforts from decline or crisis annotations: - innovation: innovation performance - development: new product development - improvement: process improvement - creativity: organizational creativity - SUSTAINABILITY_METRICS: - title: Sustainability Metrics - description: Environmental and social sustainability measurement + focus: crisis management and recovery + activities: restructuring and repositioning + leadership: turnaround management + urgency: urgent transformation needs + EXIT_STAGE: + title: Exit Stage + description: Business sale, merger, or closure annotations: - sustainability: sustainability performance - environmental: environmental impact - social: social responsibility - governance: governance effectiveness - is_a: ManagementOperationsSchemaEnum + focus: exit strategy execution + activities: sale, merger, or liquidation + valuation: business valuation + transition: ownership transition + is_a: OrganizationalStructuresSchemaEnum annotations: source_domain: business - source_schema: management_operations - DecisionMakingStyleEnum: - description: Decision-making approaches and styles + source_schema: organizational_structures + QualityManagementSchemaEnum: + description: Schema-level enum for quality_management in business + is_a: BusinessDomainEnum + abstract: true + annotations: + source_file: business/quality_management.yaml + QualityStandardEnum: + title: Quality Standard + description: Quality management standards and frameworks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - AUTOCRATIC: - title: Autocratic Decision Making - description: Single decision-maker with full authority + ISO_9001: + title: ISO 9001 Quality Management Systems + description: International standard for quality management systems annotations: - authority: centralized decision authority - speed: fast decision making - control: complete control - input: limited input from others - DEMOCRATIC: - title: Democratic Decision Making - description: Group participation in decision-making process + standard: ISO 9001:2015 + focus: quality management systems + approach: process-based approach + certification: third-party certification available + scope: applicable to all organizations + ISO_14001: + title: ISO 14001 Environmental Management + description: International standard for environmental management systems annotations: - participation: group participation - consensus: consensus building - input: diverse input and perspectives - ownership: shared ownership of decisions - CONSULTATIVE: - title: Consultative Decision Making - description: Leader consults others before deciding + standard: ISO 14001:2015 + focus: environmental management + integration: integrates with quality management + compliance: environmental compliance + sustainability: environmental sustainability + ISO_45001: + title: ISO 45001 Occupational Health and Safety + description: International standard for occupational health and safety + annotations: + standard: ISO 45001:2018 + focus: occupational health and safety + integration: integrates with other management systems + prevention: injury and illness prevention + workplace: workplace safety + ISO_27001: + title: ISO 27001 Information Security Management + description: International standard for information security management annotations: - consultation: stakeholder consultation - input: seeks input and advice - authority: leader retains decision authority - informed: informed decision making - CONSENSUS: - title: Consensus Decision Making - description: Agreement reached through group discussion + standard: ISO 27001:2013 + focus: information security + risk: risk-based approach + confidentiality: confidentiality, integrity, availability + compliance: regulatory compliance + TQM: + title: Total Quality Management + description: Comprehensive quality management philosophy annotations: - agreement: group agreement required - discussion: extensive group discussion - unanimous: unanimous or near-unanimous agreement - time: time-intensive process - DELEGATED: - title: Delegated Decision Making - description: Decision authority delegated to others + philosophy: total quality philosophy + scope: organization-wide approach + customer: customer focus + improvement: continuous improvement + involvement: total employee involvement + EFQM: + title: European Foundation for Quality Management + description: European excellence model for organizational performance annotations: - delegation: decision authority delegation - empowerment: employee empowerment - autonomy: decision autonomy - accountability: delegated accountability - DATA_DRIVEN: - title: Data-Driven Decision Making - description: Decisions based on data analysis and evidence + model: excellence model + assessment: self-assessment framework + improvement: organizational improvement + excellence: business excellence + europe: European standard + MALCOLM_BALDRIGE: + title: Malcolm Baldrige National Quality Award + description: US national quality framework and award annotations: - data: data and analytics based - evidence: evidence-based decisions - objectivity: objective decision making - analysis: analytical approach - INTUITIVE: - title: Intuitive Decision Making - description: Decisions based on experience and gut feeling + framework: performance excellence framework + award: national quality award + assessment: organizational assessment + excellence: performance excellence + united_states: US standard + SIX_SIGMA: + title: Six Sigma Quality Management + description: Data-driven quality improvement methodology annotations: - intuition: intuition and experience based - speed: rapid decision making - experience: leverages experience - creativity: creative and innovative - COMMITTEE: - title: Committee Decision Making - description: Formal group decision-making structure + methodology: statistical quality improvement + data_driven: data and measurement focused + defect_reduction: defect and variation reduction + belt_system: belt certification system + tools: statistical tools and techniques + LEAN_QUALITY: + title: Lean Quality Management + description: Waste elimination and value-focused quality approach annotations: - structure: formal committee structure - representation: stakeholder representation - process: structured decision process - accountability: shared accountability - COLLABORATIVE: - title: Collaborative Decision Making - description: Joint decision-making with shared responsibility + philosophy: lean philosophy + waste: waste elimination + value: value stream focus + efficiency: operational efficiency + improvement: continuous improvement + AS9100: + title: AS9100 Aerospace Quality Standard + description: Quality standard for aerospace industry annotations: - collaboration: collaborative approach - shared: shared responsibility - teamwork: team-based decisions - synergy: collective wisdom - CRISIS: - title: Crisis Decision Making - description: Rapid decision-making under crisis conditions + industry: aerospace and defense + based_on: based on ISO 9001 + requirements: additional aerospace requirements + certification: aerospace certification + safety: safety and reliability focus + TS16949: + title: TS 16949 Automotive Quality Standard + description: Quality standard for automotive industry annotations: - urgency: urgent decision making - limited_info: limited information available - speed: rapid response required - risk: high-risk decision making - is_a: ManagementOperationsSchemaEnum + industry: automotive industry + based_on: based on ISO 9001 + requirements: automotive-specific requirements + supply_chain: automotive supply chain + defect_prevention: defect prevention focus + ISO_13485: + title: ISO 13485 Medical Device Quality + description: Quality standard for medical device industry + annotations: + industry: medical device industry + regulatory: regulatory compliance + safety: patient safety focus + design_controls: design controls + risk_management: risk management + is_a: QualityManagementSchemaEnum annotations: source_domain: business - source_schema: management_operations - LeadershipStyleEnum: - description: Leadership approaches and styles + source_schema: quality_management + QualityMethodologyEnum: + title: Quality Methodology + description: Quality improvement methodologies and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - TRANSFORMATIONAL: - title: Transformational Leadership - description: Inspirational leadership that motivates change + DMAIC: + title: DMAIC (Define, Measure, Analyze, Improve, Control) + description: Six Sigma problem-solving methodology annotations: - inspiration: inspirational motivation - vision: visionary leadership - development: follower development - change: change-oriented - TRANSACTIONAL: - title: Transactional Leadership - description: Exchange-based leadership with rewards and consequences + phases: Define, Measure, Analyze, Improve, Control + approach: data-driven problem solving + structured: structured improvement process + statistical: statistical analysis + six_sigma: Six Sigma methodology + DMADV: + title: DMADV (Define, Measure, Analyze, Design, Verify) + description: Six Sigma design methodology for new processes annotations: - exchange: reward and consequence based - structure: structured approach - performance: performance-based - management: management by exception - SERVANT: - title: Servant Leadership - description: Leader serves followers and facilitates their growth + phases: Define, Measure, Analyze, Design, Verify + purpose: new process or product design + design: design for Six Sigma + verification: design verification + prevention: defect prevention + PDCA: + title: PDCA (Plan, Do, Check, Act) + description: Continuous improvement cycle methodology annotations: - service: service to followers - empowerment: follower empowerment - development: personal development focus - humility: humble leadership approach - AUTHENTIC: - title: Authentic Leadership - description: Genuine and self-aware leadership approach + cycle: Plan, Do, Check, Act + continuous: continuous improvement + iterative: iterative process + deming: Deming cycle + simple: simple and versatile + KAIZEN: + title: Kaizen Continuous Improvement + description: Japanese philosophy of continuous improvement annotations: - authenticity: genuine and authentic - self_awareness: high self-awareness - values: values-based leadership - integrity: personal integrity - CHARISMATIC: - title: Charismatic Leadership - description: Inspiring leadership through personal charisma + philosophy: continuous improvement philosophy + incremental: small incremental improvements + employee: employee-driven improvement + culture: improvement culture + daily: daily improvement activities + LEAN_SIX_SIGMA: + title: Lean Six Sigma + description: Combined methodology integrating Lean and Six Sigma annotations: - charisma: personal charisma - inspiration: inspirational influence - emotion: emotional appeal - following: devoted following - SITUATIONAL: - title: Situational Leadership - description: Adaptive leadership based on situation requirements + combination: Lean and Six Sigma integration + waste: waste elimination + variation: variation reduction + speed: speed and quality + comprehensive: comprehensive improvement + FIVE_S: + title: 5S Workplace Organization + description: Workplace organization and standardization methodology annotations: - adaptation: situational adaptation - flexibility: flexible approach - assessment: situation assessment - style_variation: varying leadership styles - DEMOCRATIC: - title: Democratic Leadership - description: Participative leadership with shared decision-making + components: Sort, Set in Order, Shine, Standardize, Sustain + workplace: workplace organization + visual: visual management + foundation: improvement foundation + safety: safety and efficiency + ROOT_CAUSE_ANALYSIS: + title: Root Cause Analysis + description: Systematic approach to identifying problem root causes annotations: - participation: follower participation - shared: shared decision making - empowerment: team empowerment - collaboration: collaborative approach - AUTOCRATIC: - title: Autocratic Leadership - description: Directive leadership with centralized control + systematic: systematic problem analysis + causes: root cause identification + prevention: problem prevention + tools: various analytical tools + thorough: thorough investigation + STATISTICAL_PROCESS_CONTROL: + title: Statistical Process Control (SPC) + description: Statistical methods for process monitoring and control annotations: - control: centralized control - directive: directive approach - authority: strong authority - efficiency: decision efficiency - LAISSEZ_FAIRE: - title: Laissez-Faire Leadership - description: Hands-off leadership with minimal interference + statistical: statistical monitoring + control_charts: control charts + variation: variation monitoring + prevention: problem prevention + real_time: real-time monitoring + FAILURE_MODE_ANALYSIS: + title: Failure Mode and Effects Analysis (FMEA) + description: Systematic analysis of potential failure modes annotations: - autonomy: high follower autonomy - minimal: minimal leadership intervention - freedom: freedom to operate - self_direction: self-directed teams - COACHING: - title: Coaching Leadership - description: Development-focused leadership approach + analysis: failure mode analysis + prevention: failure prevention + risk: risk assessment + systematic: systematic approach + design: design and process FMEA + BENCHMARKING: + title: Benchmarking + description: Performance comparison with best practices annotations: - development: skill and capability development - guidance: mentoring and guidance - growth: personal and professional growth - support: supportive leadership - is_a: ManagementOperationsSchemaEnum + comparison: performance comparison + best_practices: best practice identification + improvement: improvement opportunities + external: external benchmarking + internal: internal benchmarking + is_a: QualityManagementSchemaEnum annotations: source_domain: business - source_schema: management_operations - BusinessProcessTypeEnum: - description: Types of business processes + source_schema: quality_management + QualityControlTechniqueEnum: + title: Quality Control Technique + description: Quality control techniques and tools + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - CORE_PROCESS: - title: Core Business Process - description: Primary processes that create customer value + CONTROL_CHARTS: + title: Control Charts + description: Statistical charts for monitoring process variation annotations: - value: direct customer value creation - primary: primary business activities - competitive: competitive advantage source - strategic: strategic importance - SUPPORT_PROCESS: - title: Support Process - description: Processes that enable core business activities + statistical: statistical process monitoring + variation: variation tracking + limits: control limits + trends: trend identification + real_time: real-time monitoring + PARETO_ANALYSIS: + title: Pareto Analysis + description: 80/20 rule analysis for problem prioritization annotations: - support: supports core processes - enabling: enabling activities - infrastructure: business infrastructure - indirect: indirect value contribution - MANAGEMENT_PROCESS: - title: Management Process - description: Processes for planning, controlling, and improving + prioritization: problem prioritization + rule: 80/20 rule + focus: focus on vital few + impact: impact analysis + resources: resource allocation + FISHBONE_DIAGRAM: + title: Fishbone Diagram (Ishikawa) + description: Cause-and-effect analysis diagram annotations: - management: management and governance - planning: planning and control - improvement: process improvement - oversight: organizational oversight - OPERATIONAL_PROCESS: - title: Operational Process - description: Day-to-day operational activities + cause_effect: cause and effect analysis + brainstorming: structured brainstorming + categories: cause categories + visual: visual analysis tool + team: team analysis tool + HISTOGRAM: + title: Histogram + description: Frequency distribution chart for data analysis annotations: - operations: daily operations - routine: routine activities - execution: operational execution - efficiency: operational efficiency - STRATEGIC_PROCESS: - title: Strategic Process - description: Long-term planning and strategic activities + distribution: data distribution + frequency: frequency analysis + patterns: pattern identification + visual: visual data representation + analysis: statistical analysis + SCATTER_DIAGRAM: + title: Scatter Diagram + description: Correlation analysis between two variables annotations: - strategy: strategic planning - long_term: long-term focus - direction: organizational direction - competitive: competitive positioning - INNOVATION_PROCESS: - title: Innovation Process - description: Processes for developing new products or services + correlation: correlation analysis + relationship: variable relationship + pattern: pattern identification + statistical: statistical relationship + visual: visual correlation + CHECK_SHEET: + title: Check Sheet + description: Data collection and recording tool annotations: - innovation: innovation and development - creativity: creative processes - new_development: new product/service development - competitive: competitive innovation - CUSTOMER_PROCESS: - title: Customer Process - description: Processes focused on customer interaction and service + collection: data collection + recording: systematic recording + tracking: problem tracking + simple: simple data tool + standardized: standardized format + FLOW_CHART: + title: Flow Chart + description: Process flow visualization and analysis annotations: - customer: customer-facing processes - service: customer service - relationship: customer relationship - satisfaction: customer satisfaction - FINANCIAL_PROCESS: - title: Financial Process - description: Processes related to financial management + process: process visualization + flow: workflow analysis + steps: process steps + improvement: process improvement + understanding: process understanding + DESIGN_OF_EXPERIMENTS: + title: Design of Experiments (DOE) + description: Statistical method for process optimization annotations: - financial: financial management - accounting: accounting and reporting - control: financial control - compliance: financial compliance - is_a: ManagementOperationsSchemaEnum + statistical: statistical experimentation + optimization: process optimization + factors: factor analysis + interaction: interaction effects + efficiency: experimental efficiency + SAMPLING_PLANS: + title: Statistical Sampling Plans + description: Systematic approach to quality sampling + annotations: + sampling: statistical sampling + plans: sampling plans + acceptance: acceptance sampling + risk: risk control + efficiency: sampling efficiency + GAUGE_R_AND_R: + title: Gauge R&R (Repeatability and Reproducibility) + description: Measurement system analysis technique + annotations: + measurement: measurement system analysis + repeatability: measurement repeatability + reproducibility: measurement reproducibility + variation: measurement variation + capability: measurement capability + is_a: QualityManagementSchemaEnum annotations: source_domain: business - source_schema: management_operations - OrganizationalStructuresSchemaEnum: - description: Schema-level enum for organizational_structures in business - is_a: BusinessDomainEnum - abstract: true - annotations: - source_file: business/organizational_structures.yaml - LegalEntityTypeEnum: - description: Legal entity types for business organizations + source_schema: quality_management + QualityAssuranceLevelEnum: + title: Quality Assurance Level + description: Levels of quality assurance implementation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - SOLE_PROPRIETORSHIP: - title: Sole Proprietorship - description: Business owned and operated by single individual - annotations: - legal_separation: no separation from owner - liability: unlimited personal liability - taxation: pass-through to personal returns - complexity: simplest structure - registration: minimal requirements - GENERAL_PARTNERSHIP: - title: General Partnership - description: Business owned by two or more partners sharing responsibilities + BASIC_QA: + title: Basic Quality Assurance + description: Fundamental quality assurance practices annotations: - ownership: shared among general partners - liability: unlimited personal liability for all partners - taxation: pass-through to partners - management: shared management responsibilities - LIMITED_PARTNERSHIP: - title: Limited Partnership (LP) - description: Partnership with general and limited partners + level: basic implementation + practices: fundamental QA practices + inspection: inspection-based approach + reactive: reactive quality approach + compliance: basic compliance + INTERMEDIATE_QA: + title: Intermediate Quality Assurance + description: Systematic quality assurance with documented processes annotations: - partner_types: general partners and limited partners - liability: general partners have unlimited liability - limited_liability: limited partners have liability protection - management: general partners manage operations - LIMITED_LIABILITY_PARTNERSHIP: - title: Limited Liability Partnership (LLP) - description: Partnership providing liability protection to all partners + level: intermediate implementation + systematic: systematic approach + documentation: documented processes + prevention: some prevention focus + training: quality training programs + ADVANCED_QA: + title: Advanced Quality Assurance + description: Comprehensive quality management system annotations: - liability: limited liability for all partners - professional_use: often used by professional services - taxation: pass-through taxation - management: flexible management structure - LIMITED_LIABILITY_COMPANY: - title: Limited Liability Company (LLC) - description: Hybrid entity combining corporation and partnership features + level: advanced implementation + comprehensive: comprehensive QMS + integration: integrated approach + prevention: prevention-focused + measurement: quality measurement systems + WORLD_CLASS_QA: + title: World-Class Quality Assurance + description: Excellence-oriented quality management annotations: - liability: limited liability protection - taxation: flexible tax election options - management: flexible management structure - formality: fewer formal requirements than corporations - SINGLE_MEMBER_LLC: - title: Single Member LLC - description: LLC with only one owner/member + level: world-class implementation + excellence: quality excellence + innovation: quality innovation + leadership: quality leadership + benchmarking: best practice benchmarking + TOTAL_QUALITY: + title: Total Quality Management + description: Organization-wide quality culture and commitment annotations: - ownership: single member - liability: limited liability protection - taxation: disregarded entity for tax purposes - simplicity: simpler than multi-member LLC - MULTI_MEMBER_LLC: - title: Multi-Member LLC - description: LLC with multiple owners/members + level: total quality implementation + culture: quality culture + organization_wide: entire organization + customer: customer-focused + continuous: continuous improvement + is_a: QualityManagementSchemaEnum + annotations: + source_domain: business + source_schema: quality_management + ProcessImprovementApproachEnum: + title: Process Improvement Approach + description: Process improvement methodologies and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BUSINESS_PROCESS_REENGINEERING: + title: Business Process Reengineering (BPR) + description: Radical redesign of business processes annotations: - ownership: multiple members - liability: limited liability protection - taxation: partnership taxation by default - operating_agreement: recommended operating agreement - C_CORPORATION: - title: C Corporation - description: Traditional corporation with double taxation + approach: radical process redesign + dramatic: dramatic improvement + technology: technology-enabled + fundamental: fundamental rethinking + breakthrough: breakthrough performance + CONTINUOUS_IMPROVEMENT: + title: Continuous Improvement + description: Ongoing incremental process improvement annotations: - legal_status: separate legal entity - liability: limited liability for shareholders - taxation: double taxation (corporate and dividend) - governance: formal board and officer structure - stock: can issue multiple classes of stock - S_CORPORATION: - title: S Corporation - description: Corporation electing pass-through taxation + approach: incremental improvement + ongoing: continuous effort + culture: improvement culture + employee: employee involvement + sustainable: sustainable improvement + PROCESS_STANDARDIZATION: + title: Process Standardization + description: Establishing consistent process standards annotations: - taxation: pass-through to shareholders - shareholders: limited to 100 shareholders - stock_types: single class of stock only - eligibility: restrictions on shareholder types - B_CORPORATION: - title: Benefit Corporation (B-Corp) - description: Corporation with social and environmental mission + standardization: process standardization + consistency: consistent execution + documentation: process documentation + training: standard training + compliance: standard compliance + AUTOMATION: + title: Process Automation + description: Technology-driven process automation annotations: - purpose: profit and public benefit - accountability: stakeholder governance requirements - transparency: annual benefit reporting - certification: optional third-party certification - PUBLIC_CORPORATION: - title: Public Corporation - description: Corporation with publicly traded shares + technology: automation technology + efficiency: operational efficiency + consistency: consistent execution + cost: cost reduction + quality: quality improvement + DIGITALIZATION: + title: Digital Process Transformation + description: Digital technology-enabled process transformation annotations: - shares: publicly traded on stock exchanges - regulation: SEC reporting requirements - governance: extensive governance requirements - liquidity: high share liquidity - PRIVATE_CORPORATION: - title: Private Corporation - description: Corporation with privately held shares + digital: digital transformation + technology: digital technology + data: data-driven processes + integration: system integration + innovation: digital innovation + OUTSOURCING: + title: Process Outsourcing + description: External provider process management annotations: - shares: privately held shares - shareholders: limited number of shareholders - regulation: fewer regulatory requirements - liquidity: limited share liquidity - NONPROFIT_CORPORATION: - title: Nonprofit Corporation - description: Corporation organized for charitable or public purposes + external: external process management + specialization: specialized providers + cost: cost optimization + focus: core competency focus + expertise: external expertise + SHARED_SERVICES: + title: Shared Services Model + description: Centralized shared process delivery annotations: - purpose: charitable, educational, or public benefit - taxation: tax-exempt status possible - profit_distribution: no profit distribution to members - governance: board of directors governance - COOPERATIVE: - title: Cooperative - description: Member-owned and democratically controlled organization + centralization: centralized delivery + sharing: shared across units + efficiency: scale efficiency + standardization: service standardization + optimization: cost optimization + AGILE_PROCESS_IMPROVEMENT: + title: Agile Process Improvement + description: Flexible and iterative process improvement annotations: - ownership: member ownership - control: democratic member control - benefits: benefits proportional to participation - purpose: mutual benefit of members - JOINT_VENTURE: - title: Joint Venture - description: Temporary partnership for specific project or purpose + agile: agile methodology + iterative: iterative improvement + flexible: flexible approach + responsive: responsive to change + collaboration: collaborative improvement + is_a: QualityManagementSchemaEnum + annotations: + source_domain: business + source_schema: quality_management + QualityMaturityLevelEnum: + title: Quality Maturity Level + description: Organizational quality maturity levels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AD_HOC: + title: Ad Hoc Quality Approach + description: Informal and unstructured quality practices annotations: - duration: temporary or project-specific - purpose: specific business objective - ownership: shared ownership of venture - liability: depends on structure chosen - HOLDING_COMPANY: - title: Holding Company - description: Company that owns controlling interests in other companies + maturity: initial maturity level + structure: unstructured approach + informal: informal practices + reactive: reactive quality + inconsistent: inconsistent results + DEFINED: + title: Defined Quality Processes + description: Documented and standardized quality processes annotations: - purpose: own and control subsidiary companies - operations: minimal direct operations - structure: parent-subsidiary relationships - control: controls subsidiaries through ownership - SUBSIDIARY: - title: Subsidiary - description: Company controlled by another company (parent) + maturity: defined maturity level + documentation: documented processes + standardization: standardized approach + training: process training + consistency: consistent execution + MANAGED: + title: Managed Quality System + description: Measured and controlled quality management annotations: - control: controlled by parent company - ownership: majority owned by parent - operations: may operate independently - liability: separate legal entity - FRANCHISE: - title: Franchise - description: Business operating under franchisor's brand and system + maturity: managed maturity level + measurement: quality measurement + control: process control + monitoring: performance monitoring + improvement: targeted improvement + OPTIMIZED: + title: Optimized Quality Performance + description: Continuously improving quality excellence annotations: - relationship: franchisor-franchisee relationship - brand: operates under established brand - system: follows franchisor's business system - fees: pays franchise fees and royalties - GOVERNMENT_ENTITY: - title: Government Entity - description: Entity owned and operated by government + maturity: optimized maturity level + optimization: continuous optimization + innovation: quality innovation + excellence: quality excellence + benchmarking: best practice adoption + WORLD_CLASS: + title: World-Class Quality Leadership + description: Industry-leading quality performance and innovation annotations: - ownership: government ownership - purpose: public service or policy implementation - regulation: government regulations and oversight - funding: government funding sources - is_a: OrganizationalStructuresSchemaEnum + maturity: world-class maturity level + leadership: industry leadership + innovation: quality innovation + excellence: sustained excellence + recognition: external recognition + is_a: QualityManagementSchemaEnum annotations: source_domain: business - source_schema: organizational_structures - OrganizationalStructureEnum: - description: Types of organizational hierarchy and reporting structures + source_schema: quality_management + SupplyChainSchemaEnum: + description: Schema-level enum for supply_chain in business + is_a: BusinessDomainEnum + abstract: true + annotations: + source_file: business/supply_chain.yaml + ProcurementTypeEnum: + title: Procurement Type + description: Types of procurement activities and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - HIERARCHICAL: - title: Hierarchical Structure - description: Traditional pyramid structure with clear chain of command + DIRECT_PROCUREMENT: + title: Direct Procurement + description: Procurement of materials directly used in production annotations: - authority_flow: top-down authority - communication: vertical communication channels - levels: multiple management levels - control: centralized control - decision_making: centralized decision making - FLAT: - title: Flat Structure - description: Minimal hierarchical levels with broader spans of control + category: direct materials + purpose: production input + impact: direct impact on product + examples: raw materials, components, subassemblies + strategic: strategically important + INDIRECT_PROCUREMENT: + title: Indirect Procurement + description: Procurement of goods and services supporting operations annotations: - levels: few hierarchical levels - span_of_control: broad spans of control - communication: direct communication - decision_making: decentralized decision making - flexibility: high flexibility - MATRIX: - title: Matrix Structure - description: Dual reporting relationships combining functional and project lines + category: indirect materials and services + purpose: operational support + impact: indirect impact on product + examples: office supplies, maintenance, professional services + cost_focus: cost optimization focus + SERVICES_PROCUREMENT: + title: Services Procurement + description: Procurement of professional and business services annotations: - reporting: dual reporting relationships - authority: shared authority between managers - flexibility: high project flexibility - complexity: increased complexity - communication: multidirectional communication - FUNCTIONAL: - title: Functional Structure - description: Organization by business functions or departments + category: services + intangible: intangible deliverables + examples: consulting, IT services, maintenance + relationship: relationship-based + management: service level management + CAPITAL_PROCUREMENT: + title: Capital Procurement + description: Procurement of capital equipment and assets annotations: - grouping: by business function - specialization: functional specialization - efficiency: operational efficiency - coordination: vertical coordination - expertise: concentrated expertise - DIVISIONAL: - title: Divisional Structure - description: Organization by product lines, markets, or geography + category: capital expenditure + long_term: long-term assets + high_value: high value purchases + examples: machinery, equipment, facilities + approval: capital approval process + STRATEGIC_PROCUREMENT: + title: Strategic Procurement + description: Procurement of strategically important items annotations: - grouping: by products, markets, or geography - autonomy: divisional autonomy - focus: market or product focus - coordination: horizontal coordination - responsibility: profit center responsibility - NETWORK: - title: Network Structure - description: Flexible structure with interconnected relationships + importance: strategic importance + risk: high business risk + value: high value impact + partnership: strategic partnerships + long_term: long-term relationships + TACTICAL_PROCUREMENT: + title: Tactical Procurement + description: Routine procurement of standard items annotations: - relationships: network of relationships - flexibility: high flexibility - boundaries: blurred organizational boundaries - collaboration: extensive collaboration - adaptability: high adaptability - TEAM_BASED: - title: Team-Based Structure - description: Organization around self-managing teams + routine: routine purchases + standard: standardized items + efficiency: efficiency focused + transactional: transactional approach + volume: volume-based + EMERGENCY_PROCUREMENT: + title: Emergency Procurement + description: Urgent procurement due to immediate needs annotations: - unit: teams as basic organizational unit - management: self-managing teams - collaboration: high collaboration - decision_making: team-based decision making - flexibility: operational flexibility - VIRTUAL: - title: Virtual Structure - description: Geographically dispersed organization connected by technology + urgency: urgent requirements + expedited: expedited process + higher_cost: potentially higher costs + risk_mitigation: business continuity + limited_sourcing: limited supplier options + FRAMEWORK_PROCUREMENT: + title: Framework Procurement + description: Pre-negotiated procurement agreements annotations: - location: geographically dispersed - technology: technology-enabled communication - flexibility: location flexibility - coordination: virtual coordination - boundaries: minimal physical boundaries - HYBRID: - title: Hybrid Structure - description: Combination of multiple organizational structures + agreement: pre-negotiated terms + efficiency: procurement efficiency + compliance: standardized compliance + multiple_suppliers: multiple approved suppliers + call_off: call-off contracts + E_PROCUREMENT: + title: Electronic Procurement + description: Technology-enabled procurement processes annotations: - combination: multiple structure types - flexibility: structural flexibility - adaptation: adaptable to different needs - complexity: increased structural complexity - customization: customized to organization needs - is_a: OrganizationalStructuresSchemaEnum + technology: electronic platforms + automation: process automation + efficiency: operational efficiency + transparency: process transparency + data: procurement data analytics + SUSTAINABLE_PROCUREMENT: + title: Sustainable Procurement + description: Environmentally and socially responsible procurement + annotations: + sustainability: environmental and social criteria + responsibility: corporate responsibility + lifecycle: lifecycle considerations + certification: sustainability certifications + stakeholder: stakeholder value + is_a: SupplyChainSchemaEnum annotations: source_domain: business - source_schema: organizational_structures - ManagementLevelEnum: - description: Hierarchical levels within organizational management structure + source_schema: supply_chain + VendorCategoryEnum: + title: Vendor Category + description: Vendor classification categories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BOARD_OF_DIRECTORS: - title: Board of Directors - description: Governing body elected by shareholders - annotations: - authority: highest governance authority - responsibility: fiduciary responsibility to shareholders - oversight: strategic oversight and control - composition: independent and inside directors - C_SUITE: - title: C-Suite/Chief Officers - description: Top executive leadership team + STRATEGIC_SUPPLIER: + title: Strategic Supplier + description: Critical suppliers with strategic importance annotations: - level: top executive level - scope: organization-wide responsibility - titles: CEO, CFO, COO, CTO, etc. - accountability: accountable to board of directors - SENIOR_EXECUTIVE: - title: Senior Executive - description: Senior leadership below C-suite level + importance: strategic business importance + relationship: partnership relationship + risk: high business risk if disrupted + collaboration: collaborative planning + long_term: long-term agreements + PREFERRED_SUPPLIER: + title: Preferred Supplier + description: Suppliers with proven performance and preferred status annotations: - level: senior leadership - scope: major business unit or function - titles: EVP, SVP, General Manager - reporting: reports to C-suite - VICE_PRESIDENT: - title: Vice President - description: Senior management responsible for major divisions + performance: proven performance history + preferred: preferred supplier status + reliability: reliable delivery + quality: consistent quality + relationship: ongoing relationship + APPROVED_SUPPLIER: + title: Approved Supplier + description: Suppliers meeting qualification requirements annotations: - level: senior management - scope: division or major function - authority: significant decision-making authority - titles: VP, Assistant VP - DIRECTOR: - title: Director - description: Management responsible for departments or major programs + qualification: meets qualification criteria + approved: approved for business + standards: meets quality standards + compliance: regulatory compliance + monitoring: performance monitoring + TRANSACTIONAL_SUPPLIER: + title: Transactional Supplier + description: Suppliers for routine, low-risk purchases annotations: - level: middle management - scope: department or program - responsibility: departmental leadership - oversight: manages multiple managers - MANAGER: - title: Manager - description: Supervisory role managing teams or operations + routine: routine transactions + low_risk: low business risk + standard: standard products/services + efficiency: cost and efficiency focus + limited_relationship: limited relationship + SINGLE_SOURCE: + title: Single Source Supplier + description: Only available supplier for specific requirement annotations: - level: middle management - scope: team or operational unit - responsibility: day-to-day operations - supervision: manages individual contributors - SUPERVISOR: - title: Supervisor - description: First-line management overseeing frontline employees + uniqueness: unique product or service + monopoly: single source situation + dependency: high dependency + risk: supply risk concentration + relationship: close relationship management + SOLE_SOURCE: + title: Sole Source Supplier + description: Deliberately chosen single supplier annotations: - level: first-line management - scope: small team or shift - responsibility: direct supervision - interface: employee-management interface - TEAM_LEAD: - title: Team Lead - description: Lead role within team without formal management authority + choice: deliberate single supplier choice + partnership: strategic partnership + specialization: specialized capability + integration: integrated operations + exclusive: exclusive relationship + MINORITY_SUPPLIER: + title: Minority/Diverse Supplier + description: Suppliers meeting diversity criteria annotations: - level: senior individual contributor - authority: informal authority - responsibility: team coordination - expertise: technical or project leadership - SENIOR_INDIVIDUAL_CONTRIBUTOR: - title: Senior Individual Contributor - description: Experienced professional without management responsibilities + diversity: supplier diversity program + certification: diversity certification + inclusion: supplier inclusion + social_responsibility: corporate social responsibility + development: supplier development + LOCAL_SUPPLIER: + title: Local Supplier + description: Geographically local suppliers annotations: - level: senior professional - expertise: specialized expertise - mentoring: may mentor junior staff - projects: leads complex projects - INDIVIDUAL_CONTRIBUTOR: - title: Individual Contributor - description: Professional or specialist role + geography: local geographic proximity + community: local community support + logistics: reduced logistics costs + responsiveness: quick response capability + sustainability: reduced carbon footprint + GLOBAL_SUPPLIER: + title: Global Supplier + description: Suppliers with global capabilities annotations: - level: professional - responsibility: individual work output - specialization: functional specialization - career_path: professional career track - ENTRY_LEVEL: - title: Entry Level - description: Beginning professional or support roles + global: global presence and capability + scale: economies of scale + standardization: global standardization + complexity: complex management + risk: global supply chain risk + SPOT_SUPPLIER: + title: Spot Market Supplier + description: Suppliers for one-time or spot purchases annotations: - experience: minimal professional experience - development: learning and development focus - supervision: close supervision - growth_potential: career growth opportunities - is_a: OrganizationalStructuresSchemaEnum + spot_market: spot market transactions + one_time: one-time purchases + price_driven: price-driven selection + no_relationship: no ongoing relationship + market_based: market-based pricing + is_a: SupplyChainSchemaEnum annotations: source_domain: business - source_schema: organizational_structures - CorporateGovernanceRoleEnum: - description: Roles within corporate governance structure + source_schema: supply_chain + SupplyChainStrategyEnum: + title: Supply Chain Strategy + description: Supply chain strategic approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - CHAIRMAN_OF_BOARD: - title: Chairman of the Board - description: Leader of board of directors - annotations: - leadership: board leadership - meetings: chairs board meetings - interface: shareholder interface - governance: governance oversight - LEAD_INDEPENDENT_DIRECTOR: - title: Lead Independent Director - description: Senior independent director when chairman is not independent + LEAN_SUPPLY_CHAIN: + title: Lean Supply Chain + description: Waste elimination and efficiency-focused supply chain annotations: - independence: independent from management - leadership: leads independent directors - oversight: additional oversight role - communication: shareholder communication - INDEPENDENT_DIRECTOR: - title: Independent Director - description: Board member independent from company management + philosophy: lean philosophy + waste: waste elimination + efficiency: operational efficiency + flow: smooth material flow + inventory: minimal inventory + AGILE_SUPPLY_CHAIN: + title: Agile Supply Chain + description: Flexible and responsive supply chain annotations: - independence: independent from management - objectivity: objective oversight - committees: serves on key committees - governance: independent governance perspective - INSIDE_DIRECTOR: - title: Inside Director - description: Board member who is also company employee or has material relationship + flexibility: high flexibility + responsiveness: rapid response capability + adaptation: quick adaptation + variability: handles demand variability + customer: customer responsiveness + RESILIENT_SUPPLY_CHAIN: + title: Resilient Supply Chain + description: Risk-resistant and robust supply chain annotations: - relationship: material relationship with company - expertise: insider knowledge - perspective: management perspective - potential_conflicts: potential conflicts of interest - AUDIT_COMMITTEE_CHAIR: - title: Audit Committee Chair - description: Chair of board's audit committee + resilience: supply chain resilience + risk_management: comprehensive risk management + redundancy: built-in redundancy + recovery: quick recovery capability + continuity: business continuity focus + SUSTAINABLE_SUPPLY_CHAIN: + title: Sustainable Supply Chain + description: Environmentally and socially responsible supply chain annotations: - committee: audit committee leadership - oversight: financial oversight - independence: must be independent - expertise: financial expertise required - COMPENSATION_COMMITTEE_CHAIR: - title: Compensation Committee Chair - description: Chair of board's compensation committee + sustainability: environmental and social sustainability + responsibility: corporate responsibility + lifecycle: lifecycle assessment + circular: circular economy principles + stakeholder: stakeholder value + GLOBAL_SUPPLY_CHAIN: + title: Global Supply Chain + description: Internationally distributed supply chain annotations: - committee: compensation committee leadership - responsibility: executive compensation oversight - independence: must be independent - alignment: shareholder interest alignment - NOMINATING_COMMITTEE_CHAIR: - title: Nominating Committee Chair - description: Chair of board's nominating and governance committee + global: global geographic distribution + scale: economies of scale + complexity: increased complexity + risk: global risks + coordination: global coordination + LOCAL_SUPPLY_CHAIN: + title: Local/Regional Supply Chain + description: Geographically concentrated supply chain annotations: - committee: nominating committee leadership - responsibility: board composition and governance - succession: leadership succession planning - governance: governance best practices - CHIEF_EXECUTIVE_OFFICER: - title: Chief Executive Officer (CEO) - description: Highest-ranking executive officer + local: local or regional focus + proximity: geographic proximity + responsiveness: local responsiveness + community: community support + sustainability: reduced transportation + DIGITAL_SUPPLY_CHAIN: + title: Digital Supply Chain + description: Technology-enabled and data-driven supply chain annotations: - authority: highest executive authority - strategy: strategic leadership - accountability: accountable to board - representation: company representation - CHIEF_FINANCIAL_OFFICER: - title: Chief Financial Officer (CFO) - description: Senior executive responsible for financial management + digital: digital transformation + technology: advanced technology + data: data-driven decisions + automation: process automation + visibility: end-to-end visibility + COLLABORATIVE_SUPPLY_CHAIN: + title: Collaborative Supply Chain + description: Partnership-based collaborative supply chain annotations: - responsibility: financial management - reporting: financial reporting oversight - compliance: financial compliance - strategy: financial strategy - CHIEF_OPERATING_OFFICER: - title: Chief Operating Officer (COO) - description: Senior executive responsible for operations + collaboration: supply chain collaboration + partnership: strategic partnerships + integration: process integration + sharing: information sharing + joint_planning: collaborative planning + COST_FOCUSED_SUPPLY_CHAIN: + title: Cost-Focused Supply Chain + description: Cost optimization-focused supply chain annotations: - responsibility: operational management - execution: strategy execution - efficiency: operational efficiency - coordination: cross-functional coordination - CORPORATE_SECRETARY: - title: Corporate Secretary - description: Officer responsible for corporate records and governance compliance + cost: cost optimization + efficiency: cost efficiency + standardization: process standardization + scale: economies of scale + procurement: cost-focused procurement + CUSTOMER_FOCUSED_SUPPLY_CHAIN: + title: Customer-Focused Supply Chain + description: Customer service-oriented supply chain annotations: - records: corporate records maintenance - compliance: governance compliance - meetings: board meeting coordination - legal: legal compliance oversight - is_a: OrganizationalStructuresSchemaEnum + customer: customer-centric + service: customer service focus + customization: product customization + responsiveness: customer responsiveness + satisfaction: customer satisfaction + is_a: SupplyChainSchemaEnum annotations: source_domain: business - source_schema: organizational_structures - BusinessOwnershipTypeEnum: - description: Types of business ownership structures + source_schema: supply_chain + LogisticsOperationEnum: + title: Logistics Operation + description: Types of logistics operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - PRIVATE_OWNERSHIP: - title: Private Ownership - description: Business owned by private individuals or entities + INBOUND_LOGISTICS: + title: Inbound Logistics + description: Management of incoming materials and supplies annotations: - ownership: private individuals or entities - control: private control - capital: private capital sources - disclosure: limited disclosure requirements - PUBLIC_OWNERSHIP: - title: Public Ownership - description: Business with publicly traded ownership shares + direction: inbound to organization + materials: raw materials and supplies + suppliers: supplier coordination + receiving: receiving operations + quality: incoming quality control + OUTBOUND_LOGISTICS: + title: Outbound Logistics + description: Management of finished goods distribution + annotations: + direction: outbound from organization + products: finished goods + customers: customer delivery + distribution: distribution management + service: customer service + REVERSE_LOGISTICS: + title: Reverse Logistics + description: Management of product returns and recycling + annotations: + direction: reverse flow + returns: product returns + recycling: recycling and disposal + recovery: value recovery + sustainability: environmental responsibility + THIRD_PARTY_LOGISTICS: + title: Third-Party Logistics (3PL) + description: Outsourced logistics services annotations: - ownership: public shareholders - trading: publicly traded shares - regulation: extensive regulatory requirements - disclosure: public disclosure requirements - FAMILY_OWNERSHIP: - title: Family Ownership - description: Business owned and controlled by family members + outsourcing: logistics outsourcing + service_provider: third-party provider + specialization: logistics specialization + cost: cost optimization + expertise: logistics expertise + FOURTH_PARTY_LOGISTICS: + title: Fourth-Party Logistics (4PL) + description: Supply chain integration and management services annotations: - ownership: family members - succession: family succession planning - values: family values integration - long_term: long-term orientation - EMPLOYEE_OWNERSHIP: - title: Employee Ownership - description: Business owned by employees through stock or cooperative structure + integration: supply chain integration + management: end-to-end management + coordination: multi-provider coordination + strategy: strategic logistics + technology: technology integration + WAREHOUSING: + title: Warehousing Operations + description: Storage and inventory management operations annotations: - ownership: employee owners - participation: employee participation - alignment: ownership-management alignment - structure: ESOP or cooperative structure - INSTITUTIONAL_OWNERSHIP: - title: Institutional Ownership - description: Business owned by institutional investors + storage: product storage + inventory: inventory management + handling: material handling + distribution: distribution center + automation: warehouse automation + TRANSPORTATION: + title: Transportation Management + description: Movement of goods between locations annotations: - ownership: institutional investors - professional: professional management - capital: institutional capital - governance: institutional governance - GOVERNMENT_OWNERSHIP: - title: Government Ownership - description: Business owned by government entities + movement: goods movement + modes: transportation modes + routing: route optimization + scheduling: delivery scheduling + cost: transportation cost + CROSS_DOCKING: + title: Cross-Docking Operations + description: Direct transfer without storage annotations: - ownership: government entities - purpose: public policy objectives - regulation: government oversight - funding: public funding - FOREIGN_OWNERSHIP: - title: Foreign Ownership - description: Business owned by foreign individuals or entities + transfer: direct transfer + minimal_storage: minimal inventory storage + efficiency: operational efficiency + speed: fast throughput + consolidation: shipment consolidation + DISTRIBUTION: + title: Distribution Management + description: Product distribution and delivery operations annotations: - ownership: foreign entities - regulation: foreign investment regulations - capital: foreign capital - compliance: international compliance - JOINT_OWNERSHIP: - title: Joint Ownership - description: Business owned jointly by multiple parties + distribution: product distribution + network: distribution network + delivery: customer delivery + service: delivery service + coverage: market coverage + FREIGHT_FORWARDING: + title: Freight Forwarding + description: International shipping and customs management annotations: - ownership: multiple ownership parties - agreements: joint ownership agreements - governance: shared governance - coordination: ownership coordination - is_a: OrganizationalStructuresSchemaEnum + international: international shipping + customs: customs clearance + documentation: shipping documentation + coordination: multi-modal coordination + compliance: regulatory compliance + is_a: SupplyChainSchemaEnum annotations: source_domain: business - source_schema: organizational_structures - BusinessSizeClassificationEnum: - description: Size classifications for business entities + source_schema: supply_chain + SourcingStrategyEnum: + title: Sourcing Strategy + description: Sourcing strategy approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - MICRO_BUSINESS: - title: Micro Business - description: Very small business with minimal employees and revenue + SINGLE_SOURCING: + title: Single Sourcing + description: Deliberate use of one supplier for strategic reasons annotations: - employees: typically 1-9 employees - revenue: very low revenue - characteristics: home-based or small office - support: minimal administrative support - SMALL_BUSINESS: - title: Small Business - description: Small business as defined by SBA standards + suppliers: single supplier + strategic: strategic decision + partnership: close partnership + risk: supply concentration risk + benefits: economies of scale + MULTIPLE_SOURCING: + title: Multiple Sourcing + description: Use of multiple suppliers for risk mitigation annotations: - employees: varies by industry (typically <500) - revenue: varies by industry - sba_definition: meets SBA size standards - characteristics: independently owned and operated - MEDIUM_BUSINESS: - title: Medium Business - description: Mid-sized business between small and large classifications + suppliers: multiple suppliers + risk_mitigation: supply risk mitigation + competition: supplier competition + flexibility: sourcing flexibility + management: complex supplier management + DUAL_SOURCING: + title: Dual Sourcing + description: Use of two suppliers for balance of risk and efficiency annotations: - employees: typically 500-1500 employees - revenue: moderate revenue levels - characteristics: regional or specialized market presence - structure: more formal organizational structure - LARGE_BUSINESS: - title: Large Business - description: Major corporation with significant operations + suppliers: two suppliers + balance: risk and efficiency balance + backup: backup supply capability + competition: limited competition + management: manageable complexity + GLOBAL_SOURCING: + title: Global Sourcing + description: Worldwide sourcing for best value annotations: - employees: '>1500 employees' - revenue: high revenue levels - market_presence: national or international presence - structure: complex organizational structure - MULTINATIONAL_CORPORATION: - title: Multinational Corporation - description: Large corporation operating in multiple countries + geographic: global geographic scope + cost: cost optimization + capability: access to capabilities + complexity: increased complexity + risk: global supply risks + DOMESTIC_SOURCING: + title: Domestic Sourcing + description: Sourcing within domestic market annotations: - geographic_scope: multiple countries - complexity: high operational complexity - structure: global organizational structure - coordination: international coordination - FORTUNE_500: - title: Fortune 500 Company - description: Among the 500 largest US corporations by revenue + geographic: domestic market only + proximity: geographic proximity + responsiveness: local responsiveness + compliance: regulatory compliance + support: domestic economy support + NEAR_SOURCING: + title: Near Sourcing + description: Sourcing from nearby geographic regions annotations: - ranking: Fortune 500 list - revenue: highest revenue levels - market_position: market leadership positions - recognition: prestigious business recognition - is_a: OrganizationalStructuresSchemaEnum + geographic: nearby regions + balance: cost and proximity balance + risk: reduced supply chain risk + responsiveness: improved responsiveness + cost: moderate cost advantage + VERTICAL_INTEGRATION: + title: Vertical Integration + description: Internal production instead of external sourcing + annotations: + internal: internal production + control: direct control + capability: internal capability development + investment: significant investment + flexibility: reduced flexibility + OUTSOURCING: + title: Outsourcing + description: External sourcing of non-core activities + annotations: + external: external providers + focus: core competency focus + cost: cost optimization + expertise: access to expertise + dependency: external dependency + INSOURCING: + title: Insourcing + description: Bringing previously outsourced activities internal + annotations: + internal: bring activities internal + control: increased control + capability: internal capability building + cost: potential cost increase + strategic: strategic importance + CONSORTIUM_SOURCING: + title: Consortium Sourcing + description: Collaborative sourcing with other organizations + annotations: + collaboration: multi-organization collaboration + leverage: increased buying leverage + cost: cost reduction through scale + complexity: coordination complexity + relationships: multi-party relationships + is_a: SupplyChainSchemaEnum annotations: source_domain: business - source_schema: organizational_structures - BusinessLifecycleStageEnum: - description: Stages in business development lifecycle + source_schema: supply_chain + SupplierRelationshipTypeEnum: + title: Supplier Relationship Type + description: Types of supplier relationship management + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - CONCEPT_STAGE: - title: Concept Stage - description: Initial business idea development and validation + TRANSACTIONAL: + title: Transactional Relationship + description: Arms-length, price-focused supplier relationship + annotations: + focus: price and terms focus + interaction: minimal interaction + duration: short-term orientation + switching: easy supplier switching + competition: competitive bidding + PREFERRED_SUPPLIER: + title: Preferred Supplier Relationship + description: Ongoing relationship with proven suppliers annotations: - focus: idea development and validation - activities: market research, business planning - funding: personal or angel funding - risk: highest risk level - STARTUP_STAGE: - title: Startup Stage - description: Business launch and early operations + status: preferred supplier status + performance: proven performance + priority: priority consideration + benefits: preferential treatment + stability: stable relationship + STRATEGIC_PARTNERSHIP: + title: Strategic Partnership + description: Collaborative long-term strategic relationship annotations: - focus: product development and market entry - activities: building initial customer base - funding: seed funding, early investments - growth: rapid learning and adaptation - GROWTH_STAGE: - title: Growth Stage - description: Rapid expansion and scaling operations + collaboration: strategic collaboration + integration: business integration + planning: joint planning + development: joint development + mutual_benefit: mutual value creation + ALLIANCE: + title: Strategic Alliance + description: Formal alliance with shared objectives annotations: - focus: scaling operations and market expansion - activities: increasing market share - funding: venture capital, growth financing - challenges: scaling challenges - EXPANSION_STAGE: - title: Expansion Stage - description: Market expansion and diversification + formal: formal alliance agreement + objectives: shared strategic objectives + resources: shared resources + risks: shared risks and rewards + governance: joint governance + JOINT_VENTURE: + title: Joint Venture + description: Separate entity created with supplier annotations: - focus: market expansion and diversification - activities: new markets, products, or services - funding: growth capital, strategic investments - sophistication: increased operational sophistication - MATURITY_STAGE: - title: Maturity Stage - description: Stable operations with established market position + entity: separate legal entity + ownership: shared ownership + investment: joint investment + control: shared control + separate: separate business unit + VENDOR_MANAGED_INVENTORY: + title: Vendor Managed Inventory (VMI) + description: Supplier manages customer inventory annotations: - focus: operational efficiency and market defense - activities: defending market position - funding: self-funding, debt financing - stability: stable cash flows - DECLINE_STAGE: - title: Decline Stage - description: Decreasing market relevance or performance + management: supplier manages inventory + visibility: demand visibility + responsibility: supplier responsibility + efficiency: inventory efficiency + integration: systems integration + CONSIGNMENT: + title: Consignment Relationship + description: Supplier owns inventory until consumption annotations: - focus: cost reduction and restructuring - activities: turnaround efforts or exit planning - challenges: declining revenues or relevance - options: restructuring, sale, or closure - TURNAROUND_STAGE: - title: Turnaround Stage - description: Recovery efforts from decline or crisis + ownership: supplier retains ownership + location: customer location + payment: payment on consumption + cash_flow: improved customer cash flow + risk: supplier inventory risk + COLLABORATIVE_PLANNING: + title: Collaborative Planning Relationship + description: Joint planning and forecasting relationship annotations: - focus: crisis management and recovery - activities: restructuring and repositioning - leadership: turnaround management - urgency: urgent transformation needs - EXIT_STAGE: - title: Exit Stage - description: Business sale, merger, or closure + planning: collaborative planning + forecasting: joint forecasting + information: information sharing + coordination: demand coordination + efficiency: supply chain efficiency + DEVELOPMENT_PARTNERSHIP: + title: Supplier Development Partnership + description: Investment in supplier capability development annotations: - focus: exit strategy execution - activities: sale, merger, or liquidation - valuation: business valuation - transition: ownership transition - is_a: OrganizationalStructuresSchemaEnum + development: supplier capability development + investment: customer investment + improvement: supplier improvement + capability: capability building + long_term: long-term commitment + RISK_SHARING: + title: Risk Sharing Partnership + description: Shared risk and reward relationship + annotations: + risk: shared risk and reward + incentives: aligned incentives + performance: performance-based + outcomes: shared outcomes + collaboration: collaborative approach + is_a: SupplyChainSchemaEnum annotations: source_domain: business - source_schema: organizational_structures - QualityManagementSchemaEnum: - description: Schema-level enum for quality_management in business - is_a: BusinessDomainEnum - abstract: true - annotations: - source_file: business/quality_management.yaml - QualityStandardEnum: - description: Quality management standards and frameworks + source_schema: supply_chain + InventoryManagementApproachEnum: + title: Inventory Management Approach + description: Inventory management methodologies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ISO_9001: - title: ISO 9001 Quality Management Systems - description: International standard for quality management systems - annotations: - standard: ISO 9001:2015 - focus: quality management systems - approach: process-based approach - certification: third-party certification available - scope: applicable to all organizations - ISO_14001: - title: ISO 14001 Environmental Management - description: International standard for environmental management systems - annotations: - standard: ISO 14001:2015 - focus: environmental management - integration: integrates with quality management - compliance: environmental compliance - sustainability: environmental sustainability - ISO_45001: - title: ISO 45001 Occupational Health and Safety - description: International standard for occupational health and safety + JUST_IN_TIME: + title: Just-in-Time (JIT) + description: Minimal inventory with precise timing annotations: - standard: ISO 45001:2018 - focus: occupational health and safety - integration: integrates with other management systems - prevention: injury and illness prevention - workplace: workplace safety - ISO_27001: - title: ISO 27001 Information Security Management - description: International standard for information security management + timing: precise delivery timing + waste: inventory waste elimination + flow: continuous flow + supplier: supplier integration + quality: zero defect requirement + ECONOMIC_ORDER_QUANTITY: + title: Economic Order Quantity (EOQ) + description: Optimal order quantity calculation annotations: - standard: ISO 27001:2013 - focus: information security - risk: risk-based approach - confidentiality: confidentiality, integrity, availability - compliance: regulatory compliance - TQM: - title: Total Quality Management - description: Comprehensive quality management philosophy + optimization: cost optimization + calculation: mathematical calculation + trade_off: ordering vs holding cost trade-off + static: static demand assumption + classical: classical inventory model + ABC_ANALYSIS: + title: ABC Analysis + description: Inventory classification by value importance annotations: - philosophy: total quality philosophy - scope: organization-wide approach - customer: customer focus - improvement: continuous improvement - involvement: total employee involvement - EFQM: - title: European Foundation for Quality Management - description: European excellence model for organizational performance + classification: value-based classification + focus: priority focus on high-value items + management: differentiated management + efficiency: resource allocation efficiency + pareto: Pareto principle application + SAFETY_STOCK: + title: Safety Stock Management + description: Buffer inventory for demand/supply uncertainty annotations: - model: excellence model - assessment: self-assessment framework - improvement: organizational improvement - excellence: business excellence - europe: European standard - MALCOLM_BALDRIGE: - title: Malcolm Baldrige National Quality Award - description: US national quality framework and award + buffer: inventory buffer + uncertainty: demand and supply uncertainty + service_level: service level protection + cost: additional holding cost + risk: stockout risk mitigation + VENDOR_MANAGED_INVENTORY: + title: Vendor Managed Inventory (VMI) + description: Supplier-controlled inventory management annotations: - framework: performance excellence framework - award: national quality award - assessment: organizational assessment - excellence: performance excellence - united_states: US standard - SIX_SIGMA: - title: Six Sigma Quality Management - description: Data-driven quality improvement methodology + control: supplier inventory control + visibility: demand visibility + automation: automated replenishment + efficiency: inventory efficiency + partnership: supplier partnership + CONSIGNMENT_INVENTORY: + title: Consignment Inventory + description: Supplier-owned inventory at customer location annotations: - methodology: statistical quality improvement - data_driven: data and measurement focused - defect_reduction: defect and variation reduction - belt_system: belt certification system - tools: statistical tools and techniques - LEAN_QUALITY: - title: Lean Quality Management - description: Waste elimination and value-focused quality approach + ownership: supplier ownership + location: customer location + cash_flow: improved cash flow + availability: immediate availability + risk: supplier risk + KANBAN: + title: Kanban System + description: Visual pull-based inventory system annotations: - philosophy: lean philosophy - waste: waste elimination - value: value stream focus - efficiency: operational efficiency - improvement: continuous improvement - AS9100: - title: AS9100 Aerospace Quality Standard - description: Quality standard for aerospace industry + visual: visual control system + pull: pull-based replenishment + lean: lean methodology + signals: kanban signals + flow: smooth material flow + TWO_BIN_SYSTEM: + title: Two-Bin System + description: Simple reorder point system using two bins annotations: - industry: aerospace and defense - based_on: based on ISO 9001 - requirements: additional aerospace requirements - certification: aerospace certification - safety: safety and reliability focus - TS16949: - title: TS 16949 Automotive Quality Standard - description: Quality standard for automotive industry + simplicity: simple reorder system + visual: visual reorder point + bins: two-bin methodology + automatic: automatic reordering + low_cost: low-cost implementation + CONTINUOUS_REVIEW: + title: Continuous Review System + description: Continuous monitoring with fixed reorder point annotations: - industry: automotive industry - based_on: based on ISO 9001 - requirements: automotive-specific requirements - supply_chain: automotive supply chain - defect_prevention: defect prevention focus - ISO_13485: - title: ISO 13485 Medical Device Quality - description: Quality standard for medical device industry + monitoring: continuous inventory monitoring + reorder_point: fixed reorder point + quantity: fixed order quantity + responsiveness: responsive to demand + cost: higher monitoring cost + PERIODIC_REVIEW: + title: Periodic Review System + description: Periodic inventory review with variable order quantity annotations: - industry: medical device industry - regulatory: regulatory compliance - safety: patient safety focus - design_controls: design controls - risk_management: risk management - is_a: QualityManagementSchemaEnum + periodic: periodic review intervals + variable: variable order quantity + target: target inventory level + aggregation: order aggregation + efficiency: administrative efficiency + is_a: SupplyChainSchemaEnum annotations: source_domain: business - source_schema: quality_management - QualityMethodologyEnum: - description: Quality improvement methodologies and approaches + source_schema: supply_chain + ChemistryDomainEnum: + description: Domain-level enum for chemistry value sets + is_a: ValueSetEnum + abstract: true + ChemicalEntitiesSchemaEnum: + description: Schema-level enum for chemical_entities in chemistry + is_a: ChemistryDomainEnum + abstract: true + annotations: + source_file: chemistry/chemical_entities.yaml + SubatomicParticleEnum: + title: Subatomic Particle + description: Fundamental and composite subatomic particles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - DMAIC: - title: DMAIC (Define, Measure, Analyze, Improve, Control) - description: Six Sigma problem-solving methodology + ELECTRON: + description: Elementary particle with -1 charge, spin 1/2 + meaning: CHEBI:10545 annotations: - phases: Define, Measure, Analyze, Improve, Control - approach: data-driven problem solving - structured: structured improvement process - statistical: statistical analysis - six_sigma: Six Sigma methodology - DMADV: - title: DMADV (Define, Measure, Analyze, Design, Verify) - description: Six Sigma design methodology for new processes + mass: 0.51099895 MeV/c² + charge: '-1' + spin: 1/2 + type: lepton + POSITRON: + description: Antiparticle of electron with +1 charge + meaning: CHEBI:30225 annotations: - phases: Define, Measure, Analyze, Design, Verify - purpose: new process or product design - design: design for Six Sigma - verification: design verification - prevention: defect prevention - PDCA: - title: PDCA (Plan, Do, Check, Act) - description: Continuous improvement cycle methodology + mass: 0.51099895 MeV/c² + charge: '+1' + spin: 1/2 + type: lepton + MUON: + description: Heavy lepton with -1 charge + meaning: CHEBI:36356 annotations: - cycle: Plan, Do, Check, Act - continuous: continuous improvement - iterative: iterative process - deming: Deming cycle - simple: simple and versatile - KAIZEN: - title: Kaizen Continuous Improvement - description: Japanese philosophy of continuous improvement + mass: 105.658 MeV/c² + charge: '-1' + spin: 1/2 + type: lepton + TAU_LEPTON: + description: Heaviest lepton with -1 charge + meaning: CHEBI:36355 annotations: - philosophy: continuous improvement philosophy - incremental: small incremental improvements - employee: employee-driven improvement - culture: improvement culture - daily: daily improvement activities - LEAN_SIX_SIGMA: - title: Lean Six Sigma - description: Combined methodology integrating Lean and Six Sigma + mass: 1777.05 MeV/c² + charge: '-1' + spin: 1/2 + type: lepton + ELECTRON_NEUTRINO: + description: Electron neutrino, nearly massless + meaning: CHEBI:30223 annotations: - combination: Lean and Six Sigma integration - waste: waste elimination - variation: variation reduction - speed: speed and quality - comprehensive: comprehensive improvement - FIVE_S: - title: 5S Workplace Organization - description: Workplace organization and standardization methodology + mass: <2.2 eV/c² + charge: '0' + spin: 1/2 + type: lepton + MUON_NEUTRINO: + description: Muon neutrino + meaning: CHEBI:36353 annotations: - components: Sort, Set in Order, Shine, Standardize, Sustain - workplace: workplace organization - visual: visual management - foundation: improvement foundation - safety: safety and efficiency - ROOT_CAUSE_ANALYSIS: - title: Root Cause Analysis - description: Systematic approach to identifying problem root causes + mass: <0.17 MeV/c² + charge: '0' + spin: 1/2 + type: lepton + TAU_NEUTRINO: + description: Tau neutrino + meaning: CHEBI:36354 annotations: - systematic: systematic problem analysis - causes: root cause identification - prevention: problem prevention - tools: various analytical tools - thorough: thorough investigation - STATISTICAL_PROCESS_CONTROL: - title: Statistical Process Control (SPC) - description: Statistical methods for process monitoring and control + mass: <15.5 MeV/c² + charge: '0' + spin: 1/2 + type: lepton + UP_QUARK: + title: up quark + description: First generation quark with +2/3 charge + meaning: CHEBI:36366 annotations: - statistical: statistical monitoring - control_charts: control charts - variation: variation monitoring - prevention: problem prevention - real_time: real-time monitoring - FAILURE_MODE_ANALYSIS: - title: Failure Mode and Effects Analysis (FMEA) - description: Systematic analysis of potential failure modes + mass: 2.16 MeV/c² + charge: +2/3 + spin: 1/2 + type: quark + generation: '1' + DOWN_QUARK: + description: First generation quark with -1/3 charge + meaning: CHEBI:36367 annotations: - analysis: failure mode analysis - prevention: failure prevention - risk: risk assessment - systematic: systematic approach - design: design and process FMEA - BENCHMARKING: - title: Benchmarking - description: Performance comparison with best practices + mass: 4.67 MeV/c² + charge: -1/3 + spin: 1/2 + type: quark + generation: '1' + CHARM_QUARK: + title: charm quark + description: Second generation quark with +2/3 charge + meaning: CHEBI:36369 annotations: - comparison: performance comparison - best_practices: best practice identification - improvement: improvement opportunities - external: external benchmarking - internal: internal benchmarking - is_a: QualityManagementSchemaEnum - annotations: - source_domain: business - source_schema: quality_management - QualityControlTechniqueEnum: - description: Quality control techniques and tools - permissible_values: - CONTROL_CHARTS: - title: Control Charts - description: Statistical charts for monitoring process variation + mass: 1.27 GeV/c² + charge: +2/3 + spin: 1/2 + type: quark + generation: '2' + STRANGE_QUARK: + title: strange quark + description: Second generation quark with -1/3 charge + meaning: CHEBI:36368 + annotations: + mass: 93.4 MeV/c² + charge: -1/3 + spin: 1/2 + type: quark + generation: '2' + TOP_QUARK: + description: Third generation quark with +2/3 charge + meaning: CHEBI:36371 annotations: - statistical: statistical process monitoring - variation: variation tracking - limits: control limits - trends: trend identification - real_time: real-time monitoring - PARETO_ANALYSIS: - title: Pareto Analysis - description: 80/20 rule analysis for problem prioritization + mass: 172.76 GeV/c² + charge: +2/3 + spin: 1/2 + type: quark + generation: '3' + BOTTOM_QUARK: + title: bottom quark + description: Third generation quark with -1/3 charge + meaning: CHEBI:36370 annotations: - prioritization: problem prioritization - rule: 80/20 rule - focus: focus on vital few - impact: impact analysis - resources: resource allocation - FISHBONE_DIAGRAM: - title: Fishbone Diagram (Ishikawa) - description: Cause-and-effect analysis diagram + mass: 4.18 GeV/c² + charge: -1/3 + spin: 1/2 + type: quark + generation: '3' + PHOTON: + description: Force carrier for electromagnetic interaction + meaning: CHEBI:30212 annotations: - cause_effect: cause and effect analysis - brainstorming: structured brainstorming - categories: cause categories - visual: visual analysis tool - team: team analysis tool - HISTOGRAM: - title: Histogram - description: Frequency distribution chart for data analysis + mass: '0' + charge: '0' + spin: '1' + type: gauge boson + W_BOSON: + title: composite particle + description: Force carrier for weak interaction + meaning: CHEBI:36343 annotations: - distribution: data distribution - frequency: frequency analysis - patterns: pattern identification - visual: visual data representation - analysis: statistical analysis - SCATTER_DIAGRAM: - title: Scatter Diagram - description: Correlation analysis between two variables + mass: 80.379 GeV/c² + charge: ±1 + spin: '1' + type: gauge boson + Z_BOSON: + title: hadron + description: Force carrier for weak interaction + meaning: CHEBI:36344 annotations: - correlation: correlation analysis - relationship: variable relationship - pattern: pattern identification - statistical: statistical relationship - visual: visual correlation - CHECK_SHEET: - title: Check Sheet - description: Data collection and recording tool + mass: 91.1876 GeV/c² + charge: '0' + spin: '1' + type: gauge boson + GLUON: + description: Force carrier for strong interaction annotations: - collection: data collection - recording: systematic recording - tracking: problem tracking - simple: simple data tool - standardized: standardized format - FLOW_CHART: - title: Flow Chart - description: Process flow visualization and analysis + mass: '0' + charge: '0' + spin: '1' + type: gauge boson + color_charge: 'yes' + HIGGS_BOSON: + description: Scalar boson responsible for mass + meaning: CHEBI:146278 annotations: - process: process visualization - flow: workflow analysis - steps: process steps - improvement: process improvement - understanding: process understanding - DESIGN_OF_EXPERIMENTS: - title: Design of Experiments (DOE) - description: Statistical method for process optimization + mass: 125.25 GeV/c² + charge: '0' + spin: '0' + type: scalar boson + PROTON: + description: Positively charged nucleon + meaning: CHEBI:24636 annotations: - statistical: statistical experimentation - optimization: process optimization - factors: factor analysis - interaction: interaction effects - efficiency: experimental efficiency - SAMPLING_PLANS: - title: Statistical Sampling Plans - description: Systematic approach to quality sampling + mass: 938.272 MeV/c² + charge: '+1' + spin: 1/2 + type: baryon + composition: uud + NEUTRON: + description: Neutral nucleon + meaning: CHEBI:30222 annotations: - sampling: statistical sampling - plans: sampling plans - acceptance: acceptance sampling - risk: risk control - efficiency: sampling efficiency - GAUGE_R_AND_R: - title: Gauge R&R (Repeatability and Reproducibility) - description: Measurement system analysis technique + mass: 939.565 MeV/c² + charge: '0' + spin: 1/2 + type: baryon + composition: udd + ALPHA_PARTICLE: + description: Helium-4 nucleus + meaning: CHEBI:30216 annotations: - measurement: measurement system analysis - repeatability: measurement repeatability - reproducibility: measurement reproducibility - variation: measurement variation - capability: measurement capability - is_a: QualityManagementSchemaEnum + mass: 3727.379 MeV/c² + charge: '+2' + composition: 2 protons, 2 neutrons + DEUTERON: + description: Hydrogen-2 nucleus + meaning: CHEBI:29233 + annotations: + mass: 1875.613 MeV/c² + charge: '+1' + composition: 1 proton, 1 neutron + TRITON: + description: Hydrogen-3 nucleus + meaning: CHEBI:29234 + annotations: + mass: 2808.921 MeV/c² + charge: '+1' + composition: 1 proton, 2 neutrons + is_a: ChemicalEntitiesSchemaEnum annotations: - source_domain: business - source_schema: quality_management - QualityAssuranceLevelEnum: - description: Levels of quality assurance implementation + source_domain: chemistry + source_schema: chemical_entities + BondTypeEnum: + title: Bond Type + description: Types of chemical bonds + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BASIC_QA: - title: Basic Quality Assurance - description: Fundamental quality assurance practices - annotations: - level: basic implementation - practices: fundamental QA practices - inspection: inspection-based approach - reactive: reactive quality approach - compliance: basic compliance - INTERMEDIATE_QA: - title: Intermediate Quality Assurance - description: Systematic quality assurance with documented processes + SINGLE: + description: Single covalent bond + meaning: gc:Single annotations: - level: intermediate implementation - systematic: systematic approach - documentation: documented processes - prevention: some prevention focus - training: quality training programs - ADVANCED_QA: - title: Advanced Quality Assurance - description: Comprehensive quality management system + bond_order: '1' + electrons_shared: '2' + DOUBLE: + description: Double covalent bond + meaning: gc:Double annotations: - level: advanced implementation - comprehensive: comprehensive QMS - integration: integrated approach - prevention: prevention-focused - measurement: quality measurement systems - WORLD_CLASS_QA: - title: World-Class Quality Assurance - description: Excellence-oriented quality management + bond_order: '2' + electrons_shared: '4' + TRIPLE: + description: Triple covalent bond + meaning: gc:Triple annotations: - level: world-class implementation - excellence: quality excellence - innovation: quality innovation - leadership: quality leadership - benchmarking: best practice benchmarking - TOTAL_QUALITY: - title: Total Quality Management - description: Organization-wide quality culture and commitment + bond_order: '3' + electrons_shared: '6' + QUADRUPLE: + description: Quadruple bond (rare, in transition metals) + meaning: gc:Quadruple annotations: - level: total quality implementation - culture: quality culture - organization_wide: entire organization - customer: customer-focused - continuous: continuous improvement - is_a: QualityManagementSchemaEnum - annotations: - source_domain: business - source_schema: quality_management - ProcessImprovementApproachEnum: - description: Process improvement methodologies and approaches - permissible_values: - BUSINESS_PROCESS_REENGINEERING: - title: Business Process Reengineering (BPR) - description: Radical redesign of business processes + bond_order: '4' + electrons_shared: '8' + AROMATIC: + description: Aromatic bond + meaning: gc:AromaticBond annotations: - approach: radical process redesign - dramatic: dramatic improvement - technology: technology-enabled - fundamental: fundamental rethinking - breakthrough: breakthrough performance - CONTINUOUS_IMPROVEMENT: - title: Continuous Improvement - description: Ongoing incremental process improvement + bond_order: '1.5' + delocalized: 'true' + IONIC: + title: organic molecular entity + description: Ionic bond + meaning: CHEBI:50860 annotations: - approach: incremental improvement - ongoing: continuous effort - culture: improvement culture - employee: employee involvement - sustainable: sustainable improvement - PROCESS_STANDARDIZATION: - title: Process Standardization - description: Establishing consistent process standards + type: electrostatic + HYDROGEN: + description: Hydrogen bond annotations: - standardization: process standardization - consistency: consistent execution - documentation: process documentation - training: standard training - compliance: standard compliance - AUTOMATION: - title: Process Automation - description: Technology-driven process automation + type: weak interaction + energy: 5-30 kJ/mol + METALLIC: + description: Metallic bond annotations: - technology: automation technology - efficiency: operational efficiency - consistency: consistent execution - cost: cost reduction - quality: quality improvement - DIGITALIZATION: - title: Digital Process Transformation - description: Digital technology-enabled process transformation + type: delocalized electrons + VAN_DER_WAALS: + description: Van der Waals interaction annotations: - digital: digital transformation - technology: digital technology - data: data-driven processes - integration: system integration - innovation: digital innovation - OUTSOURCING: - title: Process Outsourcing - description: External provider process management + type: weak interaction + energy: 0.4-4 kJ/mol + COORDINATE: + title: coordination entity + description: Coordinate/dative covalent bond + meaning: CHEBI:33240 annotations: - external: external process management - specialization: specialized providers - cost: cost optimization - focus: core competency focus - expertise: external expertise - SHARED_SERVICES: - title: Shared Services Model - description: Centralized shared process delivery + electrons_from: one atom + PI: + description: Pi bond annotations: - centralization: centralized delivery - sharing: shared across units - efficiency: scale efficiency - standardization: service standardization - optimization: cost optimization - AGILE_PROCESS_IMPROVEMENT: - title: Agile Process Improvement - description: Flexible and iterative process improvement + orbital_overlap: side-to-side + SIGMA: + description: Sigma bond annotations: - agile: agile methodology - iterative: iterative improvement - flexible: flexible approach - responsive: responsive to change - collaboration: collaborative improvement - is_a: QualityManagementSchemaEnum + orbital_overlap: head-to-head + is_a: ChemicalEntitiesSchemaEnum annotations: - source_domain: business - source_schema: quality_management - QualityMaturityLevelEnum: - description: Organizational quality maturity levels + source_domain: chemistry + source_schema: chemical_entities + PeriodicTableBlockEnum: + title: Periodic Table Block + description: Blocks of the periodic table + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - AD_HOC: - title: Ad Hoc Quality Approach - description: Informal and unstructured quality practices - annotations: - maturity: initial maturity level - structure: unstructured approach - informal: informal practices - reactive: reactive quality - inconsistent: inconsistent results - DEFINED: - title: Defined Quality Processes - description: Documented and standardized quality processes + S_BLOCK: + title: s-block molecular entity + description: s-block elements (groups 1 and 2) + meaning: CHEBI:33674 annotations: - maturity: defined maturity level - documentation: documented processes - standardization: standardized approach - training: process training - consistency: consistent execution - MANAGED: - title: Managed Quality System - description: Measured and controlled quality management + valence_orbital: s + groups: 1,2 + P_BLOCK: + title: p-block molecular entity + description: p-block elements (groups 13-18) + meaning: CHEBI:33675 annotations: - maturity: managed maturity level - measurement: quality measurement - control: process control - monitoring: performance monitoring - improvement: targeted improvement - OPTIMIZED: - title: Optimized Quality Performance - description: Continuously improving quality excellence + valence_orbital: p + groups: 13,14,15,16,17,18 + D_BLOCK: + title: d-block element atom + description: d-block elements (transition metals) + meaning: CHEBI:33561 annotations: - maturity: optimized maturity level - optimization: continuous optimization - innovation: quality innovation - excellence: quality excellence - benchmarking: best practice adoption - WORLD_CLASS: - title: World-Class Quality Leadership - description: Industry-leading quality performance and innovation + valence_orbital: d + groups: 3-12 + F_BLOCK: + title: f-block element atom + description: f-block elements (lanthanides and actinides) + meaning: CHEBI:33562 annotations: - maturity: world-class maturity level - leadership: industry leadership - innovation: quality innovation - excellence: sustained excellence - recognition: external recognition - is_a: QualityManagementSchemaEnum - annotations: - source_domain: business - source_schema: quality_management - SupplyChainSchemaEnum: - description: Schema-level enum for supply_chain in business - is_a: BusinessDomainEnum - abstract: true + valence_orbital: f + series: lanthanides, actinides + is_a: ChemicalEntitiesSchemaEnum annotations: - source_file: business/supply_chain.yaml - ProcurementTypeEnum: - description: Types of procurement activities and approaches + source_domain: chemistry + source_schema: chemical_entities + ElementFamilyEnum: + title: Element Family + description: Chemical element families/groups + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - DIRECT_PROCUREMENT: - title: Direct Procurement - description: Procurement of materials directly used in production + ALKALI_METALS: + title: alkali metal atom + description: Group 1 elements (except hydrogen) + meaning: CHEBI:22314 annotations: - category: direct materials - purpose: production input - impact: direct impact on product - examples: raw materials, components, subassemblies - strategic: strategically important - INDIRECT_PROCUREMENT: - title: Indirect Procurement - description: Procurement of goods and services supporting operations + group: '1' + elements: Li, Na, K, Rb, Cs, Fr + ALKALINE_EARTH_METALS: + title: alkaloid + description: Group 2 elements + meaning: CHEBI:22315 annotations: - category: indirect materials and services - purpose: operational support - impact: indirect impact on product - examples: office supplies, maintenance, professional services - cost_focus: cost optimization focus - SERVICES_PROCUREMENT: - title: Services Procurement - description: Procurement of professional and business services + group: '2' + elements: Be, Mg, Ca, Sr, Ba, Ra + TRANSITION_METALS: + title: transition element atom + description: d-block elements + meaning: CHEBI:27081 annotations: - category: services - intangible: intangible deliverables - examples: consulting, IT services, maintenance - relationship: relationship-based - management: service level management - CAPITAL_PROCUREMENT: - title: Capital Procurement - description: Procurement of capital equipment and assets + groups: 3-12 + LANTHANIDES: + title: titanium group molecular entity + description: Lanthanide series + meaning: CHEBI:33768 annotations: - category: capital expenditure - long_term: long-term assets - high_value: high value purchases - examples: machinery, equipment, facilities - approval: capital approval process - STRATEGIC_PROCUREMENT: - title: Strategic Procurement - description: Procurement of strategically important items + atomic_numbers: 57-71 + ACTINIDES: + title: fuconates + description: Actinide series + meaning: CHEBI:33769 annotations: - importance: strategic importance - risk: high business risk - value: high value impact - partnership: strategic partnerships - long_term: long-term relationships - TACTICAL_PROCUREMENT: - title: Tactical Procurement - description: Routine procurement of standard items + atomic_numbers: 89-103 + CHALCOGENS: + title: chalcogen + description: Group 16 elements + meaning: CHEBI:33303 annotations: - routine: routine purchases - standard: standardized items - efficiency: efficiency focused - transactional: transactional approach - volume: volume-based - EMERGENCY_PROCUREMENT: - title: Emergency Procurement - description: Urgent procurement due to immediate needs + group: '16' + elements: O, S, Se, Te, Po + HALOGENS: + title: idopyranuronic acid + description: Group 17 elements + meaning: CHEBI:47902 annotations: - urgency: urgent requirements - expedited: expedited process - higher_cost: potentially higher costs - risk_mitigation: business continuity - limited_sourcing: limited supplier options - FRAMEWORK_PROCUREMENT: - title: Framework Procurement - description: Pre-negotiated procurement agreements + group: '17' + elements: F, Cl, Br, I, At + NOBLE_GASES: + title: neon atom + description: Group 18 elements + meaning: CHEBI:33310 annotations: - agreement: pre-negotiated terms - efficiency: procurement efficiency - compliance: standardized compliance - multiple_suppliers: multiple approved suppliers - call_off: call-off contracts - E_PROCUREMENT: - title: Electronic Procurement - description: Technology-enabled procurement processes + group: '18' + elements: He, Ne, Ar, Kr, Xe, Rn + METALLOIDS: + title: s-block element atom + description: Elements with intermediate properties + meaning: CHEBI:33559 annotations: - technology: electronic platforms - automation: process automation - efficiency: operational efficiency - transparency: process transparency - data: procurement data analytics - SUSTAINABLE_PROCUREMENT: - title: Sustainable Procurement - description: Environmentally and socially responsible procurement + elements: B, Si, Ge, As, Sb, Te, Po + POST_TRANSITION_METALS: + description: Metals after the transition series annotations: - sustainability: environmental and social criteria - responsibility: corporate responsibility - lifecycle: lifecycle considerations - certification: sustainability certifications - stakeholder: stakeholder value - is_a: SupplyChainSchemaEnum + elements: Al, Ga, In, Tl, Sn, Pb, Bi + NONMETALS: + title: nonmetal atom + description: Non-metallic elements + meaning: CHEBI:25585 + annotations: + elements: H, C, N, O, F, P, S, Cl, Se, Br, I + is_a: ChemicalEntitiesSchemaEnum annotations: - source_domain: business - source_schema: supply_chain - VendorCategoryEnum: - description: Vendor classification categories + source_domain: chemistry + source_schema: chemical_entities + ElementMetallicClassificationEnum: + title: Element Metallic Classification + description: Metallic character classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - STRATEGIC_SUPPLIER: - title: Strategic Supplier - description: Critical suppliers with strategic importance + METALLIC: + description: Metallic elements + meaning: damlpt:Metallic annotations: - importance: strategic business importance - relationship: partnership relationship - risk: high business risk if disrupted - collaboration: collaborative planning - long_term: long-term agreements - PREFERRED_SUPPLIER: - title: Preferred Supplier - description: Suppliers with proven performance and preferred status + properties: conductive, malleable, ductile + NON_METALLIC: + description: Non-metallic elements + meaning: damlpt:Non-Metallic annotations: - performance: proven performance history - preferred: preferred supplier status - reliability: reliable delivery - quality: consistent quality - relationship: ongoing relationship - APPROVED_SUPPLIER: - title: Approved Supplier - description: Suppliers meeting qualification requirements + properties: poor conductors, brittle + SEMI_METALLIC: + description: Semi-metallic/metalloid elements + meaning: damlpt:Semi-Metallic annotations: - qualification: meets qualification criteria - approved: approved for business - standards: meets quality standards - compliance: regulatory compliance - monitoring: performance monitoring - TRANSACTIONAL_SUPPLIER: - title: Transactional Supplier - description: Suppliers for routine, low-risk purchases + properties: intermediate properties + is_a: ChemicalEntitiesSchemaEnum + annotations: + source_domain: chemistry + source_schema: chemical_entities + HardOrSoftEnum: + title: Hard Or Soft + description: HSAB (Hard Soft Acid Base) classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + HARD: + description: Hard acids/bases (small, high charge density) annotations: - routine: routine transactions - low_risk: low business risk - standard: standard products/services - efficiency: cost and efficiency focus - limited_relationship: limited relationship - SINGLE_SOURCE: - title: Single Source Supplier - description: Only available supplier for specific requirement + examples: H+, Li+, Mg2+, Al3+, F-, OH- + polarizability: low + SOFT: + description: Soft acids/bases (large, low charge density) annotations: - uniqueness: unique product or service - monopoly: single source situation - dependency: high dependency - risk: supply risk concentration - relationship: close relationship management - SOLE_SOURCE: - title: Sole Source Supplier - description: Deliberately chosen single supplier + examples: Cu+, Ag+, Au+, I-, S2- + polarizability: high + BORDERLINE: + description: Borderline acids/bases annotations: - choice: deliberate single supplier choice - partnership: strategic partnership - specialization: specialized capability - integration: integrated operations - exclusive: exclusive relationship - MINORITY_SUPPLIER: - title: Minority/Diverse Supplier - description: Suppliers meeting diversity criteria + examples: Fe2+, Co2+, Ni2+, Cu2+, Zn2+ + polarizability: intermediate + is_a: ChemicalEntitiesSchemaEnum + annotations: + source_domain: chemistry + source_schema: chemical_entities + BronstedAcidBaseRoleEnum: + title: Bronsted Acid Base Role + description: Brønsted-Lowry acid-base roles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ACID: + title: Bronsted acid + description: Proton donor + meaning: CHEBI:39141 annotations: - diversity: supplier diversity program - certification: diversity certification - inclusion: supplier inclusion - social_responsibility: corporate social responsibility - development: supplier development - LOCAL_SUPPLIER: - title: Local Supplier - description: Geographically local suppliers + definition: species that donates H+ + BASE: + title: Bronsted base + description: Proton acceptor + meaning: CHEBI:39142 annotations: - geography: local geographic proximity - community: local community support - logistics: reduced logistics costs - responsiveness: quick response capability - sustainability: reduced carbon footprint - GLOBAL_SUPPLIER: - title: Global Supplier - description: Suppliers with global capabilities + definition: species that accepts H+ + AMPHOTERIC: + description: Can act as both acid and base annotations: - global: global presence and capability - scale: economies of scale - standardization: global standardization - complexity: complex management - risk: global supply chain risk - SPOT_SUPPLIER: - title: Spot Market Supplier - description: Suppliers for one-time or spot purchases + definition: species that can donate or accept H+ + examples: H2O, HSO4-, H2PO4- + is_a: ChemicalEntitiesSchemaEnum + annotations: + source_domain: chemistry + source_schema: chemical_entities + LewisAcidBaseRoleEnum: + title: Lewis Acid Base Role + description: Lewis acid-base roles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LEWIS_ACID: + description: Electron pair acceptor annotations: - spot_market: spot market transactions - one_time: one-time purchases - price_driven: price-driven selection - no_relationship: no ongoing relationship - market_based: market-based pricing - is_a: SupplyChainSchemaEnum + definition: species that accepts electron pair + examples: BF3, AlCl3, H+ + LEWIS_BASE: + description: Electron pair donor + annotations: + definition: species that donates electron pair + examples: NH3, OH-, H2O + is_a: ChemicalEntitiesSchemaEnum annotations: - source_domain: business - source_schema: supply_chain - SupplyChainStrategyEnum: - description: Supply chain strategic approaches + source_domain: chemistry + source_schema: chemical_entities + OxidationStateEnum: + title: Oxidation State + description: Common oxidation states + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - LEAN_SUPPLY_CHAIN: - title: Lean Supply Chain - description: Waste elimination and efficiency-focused supply chain + MINUS_4: + description: Oxidation state -4 annotations: - philosophy: lean philosophy - waste: waste elimination - efficiency: operational efficiency - flow: smooth material flow - inventory: minimal inventory - AGILE_SUPPLY_CHAIN: - title: Agile Supply Chain - description: Flexible and responsive supply chain + value: '-4' + example: C in CH4 + MINUS_3: + description: Oxidation state -3 + annotations: + value: '-3' + example: N in NH3 + MINUS_2: + description: Oxidation state -2 + annotations: + value: '-2' + example: O in H2O + MINUS_1: + description: Oxidation state -1 + annotations: + value: '-1' + example: Cl in NaCl + ZERO: + description: Oxidation state 0 annotations: - flexibility: high flexibility - responsiveness: rapid response capability - adaptation: quick adaptation - variability: handles demand variability - customer: customer responsiveness - RESILIENT_SUPPLY_CHAIN: - title: Resilient Supply Chain - description: Risk-resistant and robust supply chain + value: '0' + example: elemental forms + PLUS_1: + description: Oxidation state +1 annotations: - resilience: supply chain resilience - risk_management: comprehensive risk management - redundancy: built-in redundancy - recovery: quick recovery capability - continuity: business continuity focus - SUSTAINABLE_SUPPLY_CHAIN: - title: Sustainable Supply Chain - description: Environmentally and socially responsible supply chain + value: '+1' + example: Na in NaCl + PLUS_2: + description: Oxidation state +2 annotations: - sustainability: environmental and social sustainability - responsibility: corporate responsibility - lifecycle: lifecycle assessment - circular: circular economy principles - stakeholder: stakeholder value - GLOBAL_SUPPLY_CHAIN: - title: Global Supply Chain - description: Internationally distributed supply chain + value: '+2' + example: Ca in CaCl2 + PLUS_3: + description: Oxidation state +3 annotations: - global: global geographic distribution - scale: economies of scale - complexity: increased complexity - risk: global risks - coordination: global coordination - LOCAL_SUPPLY_CHAIN: - title: Local/Regional Supply Chain - description: Geographically concentrated supply chain + value: '+3' + example: Al in Al2O3 + PLUS_4: + description: Oxidation state +4 annotations: - local: local or regional focus - proximity: geographic proximity - responsiveness: local responsiveness - community: community support - sustainability: reduced transportation - DIGITAL_SUPPLY_CHAIN: - title: Digital Supply Chain - description: Technology-enabled and data-driven supply chain + value: '+4' + example: C in CO2 + PLUS_5: + description: Oxidation state +5 annotations: - digital: digital transformation - technology: advanced technology - data: data-driven decisions - automation: process automation - visibility: end-to-end visibility - COLLABORATIVE_SUPPLY_CHAIN: - title: Collaborative Supply Chain - description: Partnership-based collaborative supply chain + value: '+5' + example: P in PO4³⁻ + PLUS_6: + description: Oxidation state +6 annotations: - collaboration: supply chain collaboration - partnership: strategic partnerships - integration: process integration - sharing: information sharing - joint_planning: collaborative planning - COST_FOCUSED_SUPPLY_CHAIN: - title: Cost-Focused Supply Chain - description: Cost optimization-focused supply chain + value: '+6' + example: S in SO4²⁻ + PLUS_7: + description: Oxidation state +7 annotations: - cost: cost optimization - efficiency: cost efficiency - standardization: process standardization - scale: economies of scale - procurement: cost-focused procurement - CUSTOMER_FOCUSED_SUPPLY_CHAIN: - title: Customer-Focused Supply Chain - description: Customer service-oriented supply chain + value: '+7' + example: Mn in MnO4⁻ + PLUS_8: + description: Oxidation state +8 annotations: - customer: customer-centric - service: customer service focus - customization: product customization - responsiveness: customer responsiveness - satisfaction: customer satisfaction - is_a: SupplyChainSchemaEnum + value: '+8' + example: Os in OsO4 + is_a: ChemicalEntitiesSchemaEnum annotations: - source_domain: business - source_schema: supply_chain - LogisticsOperationEnum: - description: Types of logistics operations + source_domain: chemistry + source_schema: chemical_entities + ChiralityEnum: + title: Chirality + description: Chirality/stereochemistry descriptors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - INBOUND_LOGISTICS: - title: Inbound Logistics - description: Management of incoming materials and supplies - annotations: - direction: inbound to organization - materials: raw materials and supplies - suppliers: supplier coordination - receiving: receiving operations - quality: incoming quality control - OUTBOUND_LOGISTICS: - title: Outbound Logistics - description: Management of finished goods distribution - annotations: - direction: outbound from organization - products: finished goods - customers: customer delivery - distribution: distribution management - service: customer service - REVERSE_LOGISTICS: - title: Reverse Logistics - description: Management of product returns and recycling + R: + description: Rectus (right) configuration annotations: - direction: reverse flow - returns: product returns - recycling: recycling and disposal - recovery: value recovery - sustainability: environmental responsibility - THIRD_PARTY_LOGISTICS: - title: Third-Party Logistics (3PL) - description: Outsourced logistics services + cahn_ingold_prelog: 'true' + S: + description: Sinister (left) configuration annotations: - outsourcing: logistics outsourcing - service_provider: third-party provider - specialization: logistics specialization - cost: cost optimization - expertise: logistics expertise - FOURTH_PARTY_LOGISTICS: - title: Fourth-Party Logistics (4PL) - description: Supply chain integration and management services + cahn_ingold_prelog: 'true' + D: + description: Dextrorotatory annotations: - integration: supply chain integration - management: end-to-end management - coordination: multi-provider coordination - strategy: strategic logistics - technology: technology integration - WAREHOUSING: - title: Warehousing Operations - description: Storage and inventory management operations + fischer_projection: 'true' + optical_rotation: positive + L: + description: Levorotatory annotations: - storage: product storage - inventory: inventory management - handling: material handling - distribution: distribution center - automation: warehouse automation - TRANSPORTATION: - title: Transportation Management - description: Movement of goods between locations + fischer_projection: 'true' + optical_rotation: negative + RACEMIC: + description: Racemic mixture (50:50 of enantiomers) annotations: - movement: goods movement - modes: transportation modes - routing: route optimization - scheduling: delivery scheduling - cost: transportation cost - CROSS_DOCKING: - title: Cross-Docking Operations - description: Direct transfer without storage + optical_rotation: zero + MESO: + description: Meso compound (achiral despite stereocenters) annotations: - transfer: direct transfer - minimal_storage: minimal inventory storage - efficiency: operational efficiency - speed: fast throughput - consolidation: shipment consolidation - DISTRIBUTION: - title: Distribution Management - description: Product distribution and delivery operations + internal_symmetry: 'true' + E: + description: Entgegen (opposite) configuration annotations: - distribution: product distribution - network: distribution network - delivery: customer delivery - service: delivery service - coverage: market coverage - FREIGHT_FORWARDING: - title: Freight Forwarding - description: International shipping and customs management + geometric_isomer: 'true' + Z: + description: Zusammen (together) configuration annotations: - international: international shipping - customs: customs clearance - documentation: shipping documentation - coordination: multi-modal coordination - compliance: regulatory compliance - is_a: SupplyChainSchemaEnum + geometric_isomer: 'true' + is_a: ChemicalEntitiesSchemaEnum annotations: - source_domain: business - source_schema: supply_chain - SourcingStrategyEnum: - description: Sourcing strategy approaches + source_domain: chemistry + source_schema: chemical_entities + NanostructureMorphologyEnum: + title: Nanostructure Morphology + description: Types of nanostructure morphologies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - SINGLE_SOURCING: - title: Single Sourcing - description: Deliberate use of one supplier for strategic reasons + NANOTUBE: + description: Cylindrical nanostructure + meaning: CHEBI:50796 + annotations: + dimensions: 1D + examples: carbon nanotubes + NANOPARTICLE: + description: Particle with nanoscale dimensions + meaning: CHEBI:50803 + annotations: + dimensions: 0D + size_range: 1-100 nm + NANOROD: + description: Rod-shaped nanostructure + meaning: CHEBI:50805 + annotations: + dimensions: 1D + aspect_ratio: 3-20 + QUANTUM_DOT: + description: Semiconductor nanocrystal + meaning: CHEBI:50853 + annotations: + dimensions: 0D + property: quantum confinement + NANOWIRE: + description: Wire with nanoscale diameter annotations: - suppliers: single supplier - strategic: strategic decision - partnership: close partnership - risk: supply concentration risk - benefits: economies of scale - MULTIPLE_SOURCING: - title: Multiple Sourcing - description: Use of multiple suppliers for risk mitigation + dimensions: 1D + diameter: <100 nm + NANOSHEET: + description: Two-dimensional nanostructure annotations: - suppliers: multiple suppliers - risk_mitigation: supply risk mitigation - competition: supplier competition - flexibility: sourcing flexibility - management: complex supplier management - DUAL_SOURCING: - title: Dual Sourcing - description: Use of two suppliers for balance of risk and efficiency + dimensions: 2D + thickness: <100 nm + NANOFIBER: + description: Fiber with nanoscale diameter annotations: - suppliers: two suppliers - balance: risk and efficiency balance - backup: backup supply capability - competition: limited competition - management: manageable complexity - GLOBAL_SOURCING: - title: Global Sourcing - description: Worldwide sourcing for best value + dimensions: 1D + diameter: <1000 nm + is_a: ChemicalEntitiesSchemaEnum + annotations: + source_domain: chemistry + source_schema: chemical_entities + ReactionDirectionalitySchemaEnum: + description: Schema-level enum for reaction_directionality in chemistry + is_a: ChemistryDomainEnum + abstract: true + annotations: + source_file: chemistry/reaction_directionality.yaml + ReactionDirectionality: + title: Reaction Directionality + description: The directionality of a chemical reaction or process + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LEFT_TO_RIGHT: + description: Reaction proceeds from left to right (forward direction) + aliases: + - LR + - forward + - --> + RIGHT_TO_LEFT: + description: Reaction proceeds from right to left (reverse direction) + aliases: + - RL + - reverse + - backward + - <-- + BIDIRECTIONAL: + description: Reaction can proceed in both directions + aliases: + - BIDI + - reversible + - <--> + exact_mappings: + - SBO:0000650 + AGNOSTIC: + description: Direction is unknown or not specified + aliases: + - unknown + - unspecified + IRREVERSIBLE_LEFT_TO_RIGHT: + description: Reaction proceeds only from left to right and cannot be reversed + aliases: + - irreversible forward + - ->> + exact_mappings: + - SBO:0000651 + IRREVERSIBLE_RIGHT_TO_LEFT: + description: Reaction proceeds only from right to left and cannot be reversed + aliases: + - irreversible reverse + - <<- + is_a: ReactionDirectionalitySchemaEnum + annotations: + source_domain: chemistry + source_schema: reaction_directionality + ReactionsSchemaEnum: + description: Schema-level enum for reactions in chemistry + is_a: ChemistryDomainEnum + abstract: true + annotations: + source_file: chemistry/reactions.yaml + ReactionTypeEnum: + title: Reaction Type + description: Types of chemical reactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SYNTHESIS: + description: Combination reaction (A + B → AB) annotations: - geographic: global geographic scope - cost: cost optimization - capability: access to capabilities - complexity: increased complexity - risk: global supply risks - DOMESTIC_SOURCING: - title: Domestic Sourcing - description: Sourcing within domestic market + aliases: combination, addition + pattern: A + B → AB + DECOMPOSITION: + description: Breakdown reaction (AB → A + B) annotations: - geographic: domestic market only - proximity: geographic proximity - responsiveness: local responsiveness - compliance: regulatory compliance - support: domestic economy support - NEAR_SOURCING: - title: Near Sourcing - description: Sourcing from nearby geographic regions + aliases: analysis + pattern: AB → A + B + SINGLE_DISPLACEMENT: + description: Single replacement reaction (A + BC → AC + B) annotations: - geographic: nearby regions - balance: cost and proximity balance - risk: reduced supply chain risk - responsiveness: improved responsiveness - cost: moderate cost advantage - VERTICAL_INTEGRATION: - title: Vertical Integration - description: Internal production instead of external sourcing + aliases: single replacement + pattern: A + BC → AC + B + DOUBLE_DISPLACEMENT: + description: Double replacement reaction (AB + CD → AD + CB) annotations: - internal: internal production - control: direct control - capability: internal capability development - investment: significant investment - flexibility: reduced flexibility - OUTSOURCING: - title: Outsourcing - description: External sourcing of non-core activities + aliases: double replacement, metathesis + pattern: AB + CD → AD + CB + COMBUSTION: + description: Reaction with oxygen producing heat and light annotations: - external: external providers - focus: core competency focus - cost: cost optimization - expertise: access to expertise - dependency: external dependency - INSOURCING: - title: Insourcing - description: Bringing previously outsourced activities internal + reactant: oxygen + products: usually CO2 and H2O + SUBSTITUTION: + title: substitution reaction + description: Replacement of one group by another + meaning: MOP:0000790 annotations: - internal: bring activities internal - control: increased control - capability: internal capability building - cost: potential cost increase - strategic: strategic importance - CONSORTIUM_SOURCING: - title: Consortium Sourcing - description: Collaborative sourcing with other organizations + subtypes: SN1, SN2, SNAr + ELIMINATION: + title: elimination reaction + description: Removal of atoms/groups forming double bond + meaning: MOP:0000656 annotations: - collaboration: multi-organization collaboration - leverage: increased buying leverage - cost: cost reduction through scale - complexity: coordination complexity - relationships: multi-party relationships - is_a: SupplyChainSchemaEnum - annotations: - source_domain: business - source_schema: supply_chain - SupplierRelationshipTypeEnum: - description: Types of supplier relationship management - permissible_values: - TRANSACTIONAL: - title: Transactional Relationship - description: Arms-length, price-focused supplier relationship + subtypes: E1, E2, E1cB + ADDITION: + title: addition reaction + description: Addition to multiple bond + meaning: MOP:0000642 annotations: - focus: price and terms focus - interaction: minimal interaction - duration: short-term orientation - switching: easy supplier switching - competition: competitive bidding - PREFERRED_SUPPLIER: - title: Preferred Supplier Relationship - description: Ongoing relationship with proven suppliers + subtypes: electrophilic, nucleophilic, radical + REARRANGEMENT: + description: Reorganization of molecular structure annotations: - status: preferred supplier status - performance: proven performance - priority: priority consideration - benefits: preferential treatment - stability: stable relationship - STRATEGIC_PARTNERSHIP: - title: Strategic Partnership - description: Collaborative long-term strategic relationship + examples: Claisen, Cope, Wagner-Meerwein + OXIDATION: + description: Loss of electrons or increase in oxidation state annotations: - collaboration: strategic collaboration - integration: business integration - planning: joint planning - development: joint development - mutual_benefit: mutual value creation - ALLIANCE: - title: Strategic Alliance - description: Formal alliance with shared objectives + electron_change: loss + REDUCTION: + description: Gain of electrons or decrease in oxidation state annotations: - formal: formal alliance agreement - objectives: shared strategic objectives - resources: shared resources - risks: shared risks and rewards - governance: joint governance - JOINT_VENTURE: - title: Joint Venture - description: Separate entity created with supplier + electron_change: gain + DIELS_ALDER: + title: Diels-Alder reaction + description: '[4+2] cycloaddition reaction' + meaning: RXNO:0000006 annotations: - entity: separate legal entity - ownership: shared ownership - investment: joint investment - control: shared control - separate: separate business unit - VENDOR_MANAGED_INVENTORY: - title: Vendor Managed Inventory (VMI) - description: Supplier manages customer inventory + type: pericyclic + components: diene + dienophile + FRIEDEL_CRAFTS: + title: Friedel-Crafts reaction + description: Electrophilic aromatic substitution + meaning: RXNO:0000369 annotations: - management: supplier manages inventory - visibility: demand visibility - responsibility: supplier responsibility - efficiency: inventory efficiency - integration: systems integration - CONSIGNMENT: - title: Consignment Relationship - description: Supplier owns inventory until consumption + subtypes: alkylation, acylation + GRIGNARD: + title: Grignard reaction + description: Organometallic addition reaction + meaning: RXNO:0000014 annotations: - ownership: supplier retains ownership - location: customer location - payment: payment on consumption - cash_flow: improved customer cash flow - risk: supplier inventory risk - COLLABORATIVE_PLANNING: - title: Collaborative Planning Relationship - description: Joint planning and forecasting relationship + reagent: RMgX + WITTIG: + title: Wittig reaction + description: Alkene formation from phosphonium ylide + meaning: RXNO:0000015 annotations: - planning: collaborative planning - forecasting: joint forecasting - information: information sharing - coordination: demand coordination - efficiency: supply chain efficiency - DEVELOPMENT_PARTNERSHIP: - title: Supplier Development Partnership - description: Investment in supplier capability development + product: alkene + ALDOL: + title: aldol condensation + description: Condensation forming β-hydroxy carbonyl + meaning: RXNO:0000017 annotations: - development: supplier capability development - investment: customer investment - improvement: supplier improvement - capability: capability building - long_term: long-term commitment - RISK_SHARING: - title: Risk Sharing Partnership - description: Shared risk and reward relationship + mechanism: enolate addition + MICHAEL_ADDITION: + title: Michael addition + description: 1,4-addition to α,β-unsaturated carbonyl + meaning: RXNO:0000009 annotations: - risk: shared risk and reward - incentives: aligned incentives - performance: performance-based - outcomes: shared outcomes - collaboration: collaborative approach - is_a: SupplyChainSchemaEnum + type: conjugate addition + is_a: ReactionsSchemaEnum annotations: - source_domain: business - source_schema: supply_chain - InventoryManagementApproachEnum: - description: Inventory management methodologies + source_domain: chemistry + source_schema: reactions + ReactionMechanismEnum: + title: Reaction Mechanism + description: Reaction mechanism types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - JUST_IN_TIME: - title: Just-in-Time (JIT) - description: Minimal inventory with precise timing + SN1: + description: Unimolecular nucleophilic substitution annotations: - timing: precise delivery timing - waste: inventory waste elimination - flow: continuous flow - supplier: supplier integration - quality: zero defect requirement - ECONOMIC_ORDER_QUANTITY: - title: Economic Order Quantity (EOQ) - description: Optimal order quantity calculation + rate_determining: carbocation formation + stereochemistry: racemization + SN2: + description: Bimolecular nucleophilic substitution annotations: - optimization: cost optimization - calculation: mathematical calculation - trade_off: ordering vs holding cost trade-off - static: static demand assumption - classical: classical inventory model - ABC_ANALYSIS: - title: ABC Analysis - description: Inventory classification by value importance + rate_determining: concerted + stereochemistry: inversion + E1: + description: Unimolecular elimination annotations: - classification: value-based classification - focus: priority focus on high-value items - management: differentiated management - efficiency: resource allocation efficiency - pareto: Pareto principle application - SAFETY_STOCK: - title: Safety Stock Management - description: Buffer inventory for demand/supply uncertainty + intermediate: carbocation + E2: + description: Bimolecular elimination annotations: - buffer: inventory buffer - uncertainty: demand and supply uncertainty - service_level: service level protection - cost: additional holding cost - risk: stockout risk mitigation - VENDOR_MANAGED_INVENTORY: - title: Vendor Managed Inventory (VMI) - description: Supplier-controlled inventory management + requirement: antiperiplanar + E1CB: + description: Elimination via conjugate base annotations: - control: supplier inventory control - visibility: demand visibility - automation: automated replenishment - efficiency: inventory efficiency - partnership: supplier partnership - CONSIGNMENT_INVENTORY: - title: Consignment Inventory - description: Supplier-owned inventory at customer location + intermediate: carbanion + RADICAL: + description: Free radical mechanism annotations: - ownership: supplier ownership - location: customer location - cash_flow: improved cash flow - availability: immediate availability - risk: supplier risk - KANBAN: - title: Kanban System - description: Visual pull-based inventory system + initiation: homolytic cleavage + PERICYCLIC: + description: Concerted cyclic electron reorganization annotations: - visual: visual control system - pull: pull-based replenishment - lean: lean methodology - signals: kanban signals - flow: smooth material flow - TWO_BIN_SYSTEM: - title: Two-Bin System - description: Simple reorder point system using two bins + examples: Diels-Alder, Cope + ELECTROPHILIC_AROMATIC: + description: Electrophilic aromatic substitution annotations: - simplicity: simple reorder system - visual: visual reorder point - bins: two-bin methodology - automatic: automatic reordering - low_cost: low-cost implementation - CONTINUOUS_REVIEW: - title: Continuous Review System - description: Continuous monitoring with fixed reorder point + intermediate: arenium ion + NUCLEOPHILIC_AROMATIC: + description: Nucleophilic aromatic substitution annotations: - monitoring: continuous inventory monitoring - reorder_point: fixed reorder point - quantity: fixed order quantity - responsiveness: responsive to demand - cost: higher monitoring cost - PERIODIC_REVIEW: - title: Periodic Review System - description: Periodic inventory review with variable order quantity + requirement: electron-withdrawing groups + ADDITION_ELIMINATION: + description: Addition followed by elimination annotations: - periodic: periodic review intervals - variable: variable order quantity - target: target inventory level - aggregation: order aggregation - efficiency: administrative efficiency - is_a: SupplyChainSchemaEnum - annotations: - source_domain: business - source_schema: supply_chain - ChemistryDomainEnum: - description: Domain-level enum for chemistry value sets - is_a: ValueSetEnum - abstract: true - ChemicalEntitiesSchemaEnum: - description: Schema-level enum for chemical_entities in chemistry - is_a: ChemistryDomainEnum - abstract: true + intermediate: tetrahedral + is_a: ReactionsSchemaEnum annotations: - source_file: chemistry/chemical_entities.yaml - SubatomicParticleEnum: - description: Fundamental and composite subatomic particles + source_domain: chemistry + source_schema: reactions + CatalystTypeEnum: + title: Catalyst Type + description: Types of catalysts + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ELECTRON: - description: Elementary particle with -1 charge, spin 1/2 - meaning: CHEBI:10545 - annotations: - mass: 0.51099895 MeV/c² - charge: '-1' - spin: 1/2 - type: lepton - POSITRON: - description: Antiparticle of electron with +1 charge - meaning: CHEBI:30225 - annotations: - mass: 0.51099895 MeV/c² - charge: '+1' - spin: 1/2 - type: lepton - MUON: - description: Heavy lepton with -1 charge - meaning: CHEBI:36356 + HOMOGENEOUS: + description: Catalyst in same phase as reactants annotations: - mass: 105.658 MeV/c² - charge: '-1' - spin: 1/2 - type: lepton - TAU_LEPTON: - description: Heaviest lepton with -1 charge - meaning: CHEBI:36355 + phase: same as reactants + examples: acid, base, metal complexes + HETEROGENEOUS: + description: Catalyst in different phase from reactants annotations: - mass: 1777.05 MeV/c² - charge: '-1' - spin: 1/2 - type: lepton - ELECTRON_NEUTRINO: - description: Electron neutrino, nearly massless - meaning: CHEBI:30223 + phase: different from reactants + examples: Pt/Pd on carbon, zeolites + ENZYME: + title: cofactor + description: Biological catalyst + meaning: CHEBI:23357 annotations: - mass: <2.2 eV/c² - charge: '0' - spin: 1/2 - type: lepton - MUON_NEUTRINO: - description: Muon neutrino - meaning: CHEBI:36353 + type: protein + specificity: high + ORGANOCATALYST: + description: Small organic molecule catalyst annotations: - mass: <0.17 MeV/c² - charge: '0' - spin: 1/2 - type: lepton - TAU_NEUTRINO: - description: Tau neutrino - meaning: CHEBI:36354 + metal_free: 'true' + examples: proline, thiourea + PHOTOCATALYST: + description: Light-activated catalyst annotations: - mass: <15.5 MeV/c² - charge: '0' - spin: 1/2 - type: lepton - UP_QUARK: - title: up quark - description: First generation quark with +2/3 charge - meaning: CHEBI:36366 + activation: light + examples: TiO2, Ru complexes + PHASE_TRANSFER: + description: Catalyst facilitating reaction between phases annotations: - mass: 2.16 MeV/c² - charge: +2/3 - spin: 1/2 - type: quark - generation: '1' - DOWN_QUARK: - description: First generation quark with -1/3 charge - meaning: CHEBI:36367 + function: transfers reactant between phases + ACID: + description: Acid catalyst annotations: - mass: 4.67 MeV/c² - charge: -1/3 - spin: 1/2 - type: quark - generation: '1' - CHARM_QUARK: - title: charm quark - description: Second generation quark with +2/3 charge - meaning: CHEBI:36369 + mechanism: proton donation + BASE: + description: Base catalyst annotations: - mass: 1.27 GeV/c² - charge: +2/3 - spin: 1/2 - type: quark - generation: '2' - STRANGE_QUARK: - title: strange quark - description: Second generation quark with -1/3 charge - meaning: CHEBI:36368 + mechanism: proton abstraction + METAL: + description: Metal catalyst annotations: - mass: 93.4 MeV/c² - charge: -1/3 - spin: 1/2 - type: quark - generation: '2' - TOP_QUARK: - description: Third generation quark with +2/3 charge - meaning: CHEBI:36371 + examples: Pd, Pt, Ni, Ru + BIFUNCTIONAL: + description: Catalyst with two active sites annotations: - mass: 172.76 GeV/c² - charge: +2/3 - spin: 1/2 - type: quark - generation: '3' - BOTTOM_QUARK: - title: bottom quark - description: Third generation quark with -1/3 charge - meaning: CHEBI:36370 + sites: multiple + is_a: ReactionsSchemaEnum + annotations: + source_domain: chemistry + source_schema: reactions + ReactionConditionEnum: + title: Reaction Condition + description: Reaction conditions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ROOM_TEMPERATURE: + description: Standard room temperature (20-25°C) annotations: - mass: 4.18 GeV/c² - charge: -1/3 - spin: 1/2 - type: quark - generation: '3' - PHOTON: - description: Force carrier for electromagnetic interaction - meaning: CHEBI:30212 + temperature: 20-25°C + REFLUX: + description: Boiling with condensation return annotations: - mass: '0' - charge: '0' - spin: '1' - type: gauge boson - W_BOSON: - title: composite particle - description: Force carrier for weak interaction - meaning: CHEBI:36343 + temperature: solvent boiling point + CRYOGENIC: + description: Very low temperature conditions annotations: - mass: 80.379 GeV/c² - charge: ±1 - spin: '1' - type: gauge boson - Z_BOSON: - title: hadron - description: Force carrier for weak interaction - meaning: CHEBI:36344 + temperature: <-150°C + examples: liquid N2, liquid He + HIGH_PRESSURE: + description: Elevated pressure conditions annotations: - mass: 91.1876 GeV/c² - charge: '0' - spin: '1' - type: gauge boson - GLUON: - description: Force carrier for strong interaction + pressure: '>10 atm' + VACUUM: + description: Reduced pressure conditions annotations: - mass: '0' - charge: '0' - spin: '1' - type: gauge boson - color_charge: 'yes' - HIGGS_BOSON: - description: Scalar boson responsible for mass - meaning: CHEBI:146278 + pressure: <1 atm + INERT_ATMOSPHERE: + description: Non-reactive gas atmosphere annotations: - mass: 125.25 GeV/c² - charge: '0' - spin: '0' - type: scalar boson - PROTON: - description: Positively charged nucleon - meaning: CHEBI:24636 + gases: N2, Ar + MICROWAVE: + description: Microwave heating annotations: - mass: 938.272 MeV/c² - charge: '+1' - spin: 1/2 - type: baryon - composition: uud - NEUTRON: - description: Neutral nucleon - meaning: CHEBI:30222 + heating: microwave irradiation + ULTRASOUND: + description: Ultrasonic conditions annotations: - mass: 939.565 MeV/c² - charge: '0' - spin: 1/2 - type: baryon - composition: udd - ALPHA_PARTICLE: - description: Helium-4 nucleus - meaning: CHEBI:30216 + activation: ultrasound + PHOTOCHEMICAL: + description: Light-induced conditions annotations: - mass: 3727.379 MeV/c² - charge: '+2' - composition: 2 protons, 2 neutrons - DEUTERON: - description: Hydrogen-2 nucleus - meaning: CHEBI:29233 + activation: UV or visible light + ELECTROCHEMICAL: + description: Electrically driven conditions annotations: - mass: 1875.613 MeV/c² - charge: '+1' - composition: 1 proton, 1 neutron - TRITON: - description: Hydrogen-3 nucleus - meaning: CHEBI:29234 + activation: electric current + FLOW: + description: Continuous flow conditions annotations: - mass: 2808.921 MeV/c² - charge: '+1' - composition: 1 proton, 2 neutrons - is_a: ChemicalEntitiesSchemaEnum + type: continuous process + BATCH: + description: Batch reaction conditions + annotations: + type: batch process + is_a: ReactionsSchemaEnum annotations: source_domain: chemistry - source_schema: chemical_entities - BondTypeEnum: - description: Types of chemical bonds + source_schema: reactions + ReactionRateOrderEnum: + title: Reaction Rate Order + description: Reaction rate orders + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - SINGLE: - description: Single covalent bond - meaning: gc:Single + ZERO_ORDER: + description: Rate independent of concentration annotations: - bond_order: '1' - electrons_shared: '2' - DOUBLE: - description: Double covalent bond - meaning: gc:Double + rate_law: rate = k + integrated: '[A] = [A]₀ - kt' + FIRST_ORDER: + description: Rate proportional to concentration annotations: - bond_order: '2' - electrons_shared: '4' - TRIPLE: - description: Triple covalent bond - meaning: gc:Triple + rate_law: rate = k[A] + integrated: ln[A] = ln[A]₀ - kt + SECOND_ORDER: + description: Rate proportional to concentration squared annotations: - bond_order: '3' - electrons_shared: '6' - QUADRUPLE: - description: Quadruple bond (rare, in transition metals) - meaning: gc:Quadruple + rate_law: rate = k[A]² + integrated: 1/[A] = 1/[A]₀ + kt + PSEUDO_FIRST_ORDER: + description: Apparent first order (excess reagent) annotations: - bond_order: '4' - electrons_shared: '8' - AROMATIC: - description: Aromatic bond - meaning: gc:AromaticBond + condition: one reagent in large excess + FRACTIONAL_ORDER: + description: Non-integer order + annotations: + indicates: complex mechanism + MIXED_ORDER: + description: Different orders for different reactants annotations: - bond_order: '1.5' - delocalized: 'true' - IONIC: - title: organic molecular entity - description: Ionic bond - meaning: CHEBI:50860 + example: rate = k[A][B]² + is_a: ReactionsSchemaEnum + annotations: + source_domain: chemistry + source_schema: reactions + EnzymeClassEnum: + title: Enzyme Class + description: EC enzyme classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + OXIDOREDUCTASE: + title: Oxidoreductases + description: Catalyzes oxidation-reduction reactions + meaning: EC:1 annotations: - type: electrostatic - HYDROGEN: - description: Hydrogen bond + EC_class: '1' + examples: dehydrogenases, oxidases + TRANSFERASE: + title: Transferases + description: Catalyzes group transfer reactions + meaning: EC:2 annotations: - type: weak interaction - energy: 5-30 kJ/mol - METALLIC: - description: Metallic bond + EC_class: '2' + examples: kinases, transaminases + HYDROLASE: + title: Hydrolases + description: Catalyzes hydrolysis reactions + meaning: EC:3 annotations: - type: delocalized electrons - VAN_DER_WAALS: - description: Van der Waals interaction + EC_class: '3' + examples: proteases, lipases + LYASE: + title: Lyases + description: Catalyzes non-hydrolytic additions/removals + meaning: EC:4 annotations: - type: weak interaction - energy: 0.4-4 kJ/mol - COORDINATE: - title: coordination entity - description: Coordinate/dative covalent bond - meaning: CHEBI:33240 + EC_class: '4' + examples: decarboxylases, aldolases + ISOMERASE: + title: Isomerases + description: Catalyzes isomerization reactions + meaning: EC:5 annotations: - electrons_from: one atom - PI: - description: Pi bond + EC_class: '5' + examples: racemases, epimerases + LIGASE: + title: Ligases + description: Catalyzes formation of bonds with ATP + meaning: EC:6 annotations: - orbital_overlap: side-to-side - SIGMA: - description: Sigma bond + EC_class: '6' + examples: synthetases, carboxylases + TRANSLOCASE: + title: Translocases + description: Catalyzes movement across membranes + meaning: EC:7 annotations: - orbital_overlap: head-to-head - is_a: ChemicalEntitiesSchemaEnum + EC_class: '7' + examples: ATPases, ion pumps + is_a: ReactionsSchemaEnum annotations: source_domain: chemistry - source_schema: chemical_entities - PeriodicTableBlockEnum: - description: Blocks of the periodic table + source_schema: reactions + SolventClassEnum: + title: Solvent Class + description: Classes of solvents + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - S_BLOCK: - title: s-block molecular entity - description: s-block elements (groups 1 and 2) - meaning: CHEBI:33674 + PROTIC: + description: Solvents with acidic hydrogen annotations: - valence_orbital: s - groups: 1,2 - P_BLOCK: - title: p-block molecular entity - description: p-block elements (groups 13-18) - meaning: CHEBI:33675 + H_bonding: donor + examples: water, alcohols, acids + APROTIC_POLAR: + description: Polar solvents without acidic H annotations: - valence_orbital: p - groups: 13,14,15,16,17,18 - D_BLOCK: - title: d-block element atom - description: d-block elements (transition metals) - meaning: CHEBI:33561 + H_bonding: acceptor only + examples: DMSO, DMF, acetone + APROTIC_NONPOLAR: + description: Nonpolar solvents annotations: - valence_orbital: d - groups: 3-12 - F_BLOCK: - title: f-block element atom - description: f-block elements (lanthanides and actinides) - meaning: CHEBI:33562 + H_bonding: none + examples: hexane, benzene, CCl4 + IONIC_LIQUID: + description: Room temperature ionic liquids annotations: - valence_orbital: f - series: lanthanides, actinides - is_a: ChemicalEntitiesSchemaEnum + state: liquid salt + examples: imidazolium salts + SUPERCRITICAL: + description: Supercritical fluids + annotations: + state: supercritical + examples: scCO2, scH2O + AQUEOUS: + description: Water-based solvents + annotations: + base: water + ORGANIC: + description: Organic solvents + annotations: + base: organic compounds + GREEN: + description: Environmentally friendly solvents + annotations: + property: low environmental impact + examples: water, ethanol, scCO2 + is_a: ReactionsSchemaEnum annotations: source_domain: chemistry - source_schema: chemical_entities - ElementFamilyEnum: - description: Chemical element families/groups + source_schema: reactions + ThermodynamicParameterEnum: + title: Thermodynamic Parameter + description: Thermodynamic parameters + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ALKALI_METALS: - title: alkali metal atom - description: Group 1 elements (except hydrogen) - meaning: CHEBI:22314 + ENTHALPY: + description: Heat content (ΔH) annotations: - group: '1' - elements: Li, Na, K, Rb, Cs, Fr - ALKALINE_EARTH_METALS: - title: alkaloid - description: Group 2 elements - meaning: CHEBI:22315 + symbol: ΔH + units: kJ/mol + ENTROPY: + description: Disorder (ΔS) annotations: - group: '2' - elements: Be, Mg, Ca, Sr, Ba, Ra - TRANSITION_METALS: - title: transition element atom - description: d-block elements - meaning: CHEBI:27081 + symbol: ΔS + units: J/mol·K + GIBBS_ENERGY: + description: Free energy (ΔG) annotations: - groups: 3-12 - LANTHANIDES: - title: titanium group molecular entity - description: Lanthanide series - meaning: CHEBI:33768 + symbol: ΔG + units: kJ/mol + ACTIVATION_ENERGY: + description: Energy barrier (Ea) annotations: - atomic_numbers: 57-71 - ACTINIDES: - title: fuconates - description: Actinide series - meaning: CHEBI:33769 + symbol: Ea + units: kJ/mol + HEAT_CAPACITY: + description: Heat capacity (Cp) annotations: - atomic_numbers: 89-103 - CHALCOGENS: - title: chalcogen - description: Group 16 elements - meaning: CHEBI:33303 + symbol: Cp + units: J/mol·K + INTERNAL_ENERGY: + description: Internal energy (ΔU) annotations: - group: '16' - elements: O, S, Se, Te, Po - HALOGENS: - title: idopyranuronic acid - description: Group 17 elements - meaning: CHEBI:47902 + symbol: ΔU + units: kJ/mol + is_a: ReactionsSchemaEnum + annotations: + source_domain: chemistry + source_schema: reactions + RolesSchemaEnum: + description: Schema-level enum for roles in chemistry + is_a: ChemistryDomainEnum + abstract: true + annotations: + source_file: chemistry/roles.yaml + ChemicalRole: + title: Chemical Role + description: Roles played by molecular entities within a chemical context, dynamically populated from ChEBI. Includes + roles such as catalyst, reagent, solvent, indicator, buffer, and other chemical functions. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.ebi.ac.uk/chebi + publishers: https://www.ebi.ac.uk/chebi + source_domain: chemistry + source_schema: roles + reachable_from: + source_nodes: + - CHEBI:51086 + is_direct: false + relationship_types: + - rdfs:subClassOf + is_a: RolesSchemaEnum + ClinicalDomainEnum: + description: Domain-level enum for clinical value sets + is_a: ValueSetEnum + abstract: true + GeneticsSchemaEnum: + description: Schema-level enum for genetics in clinical + is_a: ClinicalDomainEnum + abstract: true + annotations: + source_file: clinical/genetics.yaml + ModeOfInheritance: + title: Mode of Inheritance + description: Patterns of genetic inheritance describing how traits or disorders are passed between generations. Based + on HP:0000005 (Mode of inheritance). + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://hpo.jax.org + publishers: https://hpo.jax.org + source_domain: clinical + source_schema: genetics + permissible_values: + AUTOSOMAL_DOMINANT: + title: Autosomal dominant inheritance + description: A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes in + which a trait manifests in heterozygotes. + meaning: HP:0000006 + AUTOSOMAL_RECESSIVE: + title: Autosomal recessive inheritance + description: A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes in + which a trait manifests in individuals with two pathogenic alleles. + meaning: HP:0000007 + X_LINKED: + title: X-linked inheritance + description: A mode of inheritance that is observed for traits related to a gene encoded on the X chromosome. + meaning: HP:0001417 + X_LINKED_DOMINANT: + title: X-linked dominant inheritance + description: A mode of inheritance that is observed for dominant traits related to a gene encoded on the X chromosome. + meaning: HP:0001423 + is_a: X_LINKED + X_LINKED_RECESSIVE: + title: X-linked recessive inheritance + description: A mode of inheritance that is observed for recessive traits related to a gene encoded on the X chromosome. + meaning: HP:0001419 + is_a: X_LINKED + Y_LINKED: + title: Y-linked inheritance + description: A mode of inheritance that is observed for traits related to a gene encoded on the Y chromosome. + meaning: HP:0001450 + MITOCHONDRIAL: + title: Mitochondrial inheritance + description: A mode of inheritance that is observed for traits related to a gene encoded on the mitochondrial genome. + Maternally inherited. + meaning: HP:0001427 + MENDELIAN: + title: Mendelian inheritance + description: A mode of inheritance of diseases whose pathophysiology can be traced back to deleterious variants in + a single gene. + meaning: HP:0034345 + NON_MENDELIAN: + title: Non-Mendelian inheritance + description: A mode of inheritance that depends on genetic determinants in more than one gene. + meaning: HP:0001426 + DIGENIC: + title: Digenic inheritance + description: A type of multifactorial inheritance governed by the simultaneous action of two gene loci. + meaning: HP:0010984 + is_a: NON_MENDELIAN + OLIGOGENIC: + title: Oligogenic inheritance + description: A type of multifactorial inheritance governed by the simultaneous action of a few gene loci (typically + three). + meaning: HP:0010983 + is_a: NON_MENDELIAN + POLYGENIC: + title: Polygenic inheritance + description: A mode of inheritance that depends on a mixture of major and minor genetic determinants possibly together + with environmental factors. + meaning: HP:0010982 + is_a: NON_MENDELIAN + SEMIDOMINANT: + title: Semidominant inheritance + description: A mode of inheritance for traits that can manifest in both monoallelic and biallelic states, with similar + or differing phenotype severity. + meaning: HP:0032113 + PSEUDOAUTOSOMAL: + title: Pseudoautosomal inheritance + description: A pattern of inheritance observed for alleles in the X-Y identical regions, resembling autosomal inheritance. + meaning: HP:0034339 + PSEUDOAUTOSOMAL_DOMINANT: + title: Pseudoautosomal dominant inheritance + description: A type of pseudoautosomal inheritance that is dominant. + meaning: HP:0034340 + is_a: PSEUDOAUTOSOMAL + PSEUDOAUTOSOMAL_RECESSIVE: + title: Pseudoautosomal recessive inheritance + description: A type of pseudoautosomal inheritance that is recessive. + meaning: HP:0034341 + is_a: PSEUDOAUTOSOMAL + is_a: GeneticsSchemaEnum + NihDemographicsSchemaEnum: + description: Schema-level enum for nih_demographics in clinical + is_a: ClinicalDomainEnum + abstract: true + annotations: + source_file: clinical/nih_demographics.yaml + RaceOMB1997Enum: + title: Race OMB1997 + description: 'Race categories following OMB 1997 standards used by NIH and federal agencies. + + Respondents may select multiple races.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AMERICAN_INDIAN_OR_ALASKA_NATIVE: + description: A person having origins in any of the original peoples of North and South America (including Central + America), and who maintains tribal affiliation or community attachment + meaning: NCIT:C41259 + annotations: + omb_code: 1002-5 + related_mappings: + - ExO:0000134 + - ExO:0000133 + ASIAN: + description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian + subcontinent + meaning: NCIT:C41260 annotations: - group: '17' - elements: F, Cl, Br, I, At - NOBLE_GASES: - title: neon atom - description: Group 18 elements - meaning: CHEBI:33310 + omb_code: 2028-9 + includes: Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, Philippine Islands, Thailand, Vietnam + related_mappings: + - ExO:0000135 + - ExO:0000136 + - ExO:0000139 + - ExO:0000143 + - ExO:0000147 + - ExO:0000148 + - ExO:0000157 + BLACK_OR_AFRICAN_AMERICAN: + description: A person having origins in any of the black racial groups of Africa + meaning: NCIT:C16352 annotations: - group: '18' - elements: He, Ne, Ar, Kr, Xe, Rn - METALLOIDS: - title: s-block element atom - description: Elements with intermediate properties - meaning: CHEBI:33559 + omb_code: 2054-5 + related_mappings: + - ExO:0000132 + NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER: + description: A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands + meaning: NCIT:C41219 annotations: - elements: B, Si, Ge, As, Sb, Te, Po - POST_TRANSITION_METALS: - description: Metals after the transition series + omb_code: 2076-8 + related_mappings: + - ExO:0000152 + - ExO:0000154 + - ExO:0000144 + - ExO:0000156 + WHITE: + description: A person having origins in any of the original peoples of Europe, the Middle East, or North Africa + meaning: NCIT:C41261 annotations: - elements: Al, Ga, In, Tl, Sn, Pb, Bi - NONMETALS: - title: nonmetal atom - description: Non-metallic elements - meaning: CHEBI:25585 + omb_code: 2106-3 + related_mappings: + - ExO:0000158 + MORE_THAN_ONE_RACE: + description: Person identifies with more than one race category + meaning: NCIT:C67109 + title: Multiracial annotations: - elements: H, C, N, O, F, P, S, Cl, Se, Br, I - is_a: ChemicalEntitiesSchemaEnum + note: Added after 1997 revision to allow multiple race reporting + UNKNOWN_OR_NOT_REPORTED: + description: Race not known, not reported, or declined to answer + meaning: NCIT:C17998 + title: Unknown + annotations: + aliases: Unknown, Not Reported, Prefer not to answer + is_a: NihDemographicsSchemaEnum annotations: - source_domain: chemistry - source_schema: chemical_entities - ElementMetallicClassificationEnum: - description: Metallic character classification + source_domain: clinical + source_schema: nih_demographics + EthnicityOMB1997Enum: + title: Ethnicity OMB1997 + description: Ethnicity categories following OMB 1997 standards used by NIH and federal agencies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - METALLIC: - description: Metallic elements - meaning: damlpt:Metallic + HISPANIC_OR_LATINO: + description: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, + regardless of race + meaning: NCIT:C17459 annotations: - properties: conductive, malleable, ductile - NON_METALLIC: - description: Non-metallic elements - meaning: damlpt:Non-Metallic + omb_code: 2135-2 + related_mappings: + - ExO:0000145 + - ExO:0000149 + - ExO:0000137 + - ExO:0000138 + - ExO:0000140 + - ExO:0000141 + - ExO:0000142 + - ExO:0000150 + - ExO:0000151 + - ExO:0000155 + NOT_HISPANIC_OR_LATINO: + description: A person not of Hispanic or Latino origin + meaning: NCIT:C41222 annotations: - properties: poor conductors, brittle - SEMI_METALLIC: - description: Semi-metallic/metalloid elements - meaning: damlpt:Semi-Metallic + omb_code: 2186-5 + UNKNOWN_OR_NOT_REPORTED: + description: Ethnicity not known, not reported, or declined to answer + meaning: NCIT:C17998 + title: Unknown annotations: - properties: intermediate properties - is_a: ChemicalEntitiesSchemaEnum + aliases: Unknown, Not Reported, Prefer not to answer + is_a: NihDemographicsSchemaEnum annotations: - source_domain: chemistry - source_schema: chemical_entities - HardOrSoftEnum: - description: HSAB (Hard Soft Acid Base) classification + source_domain: clinical + source_schema: nih_demographics + BiologicalSexEnum: + title: Biological Sex + description: 'Biological sex assigned at birth based on anatomical and physiological traits. + + Required by NIH as a biological variable in research.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - HARD: - description: Hard acids/bases (small, high charge density) + MALE: + description: Male sex assigned at birth + meaning: PATO:0000384 + exact_mappings: + - NCIT:C20197 + - GSSO:000371 + related_mappings: + - ExO:0000112 + FEMALE: + description: Female sex assigned at birth + meaning: PATO:0000383 + exact_mappings: + - NCIT:C16576 + - GSSO:000369 + related_mappings: + - ExO:0000111 + INTERSEX: + description: Born with reproductive or sexual anatomy that doesn't fit typical definitions of male or female + meaning: NCIT:C45908 annotations: - examples: H+, Li+, Mg2+, Al3+, F-, OH- - polarizability: low - SOFT: - description: Soft acids/bases (large, low charge density) + prevalence: 0.018% to 1.7% + note: May be assigned male or female at birth + UNKNOWN_OR_NOT_REPORTED: + description: Sex not known, not reported, or declined to answer + meaning: NCIT:C17998 + title: Unknown + is_a: NihDemographicsSchemaEnum + annotations: + source_domain: clinical + source_schema: nih_demographics + AgeGroupEnum: + title: Age Group + description: Standard age groups used in NIH clinical research, particularly NINDS CDEs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NEONATE: + description: Birth to 28 days + meaning: NCIT:C16731 + title: Newborn annotations: - examples: Cu+, Ag+, Au+, I-, S2- - polarizability: high - BORDERLINE: - description: Borderline acids/bases + max_age_days: 28 + INFANT: + description: 29 days to less than 1 year + meaning: NCIT:C27956 annotations: - examples: Fe2+, Co2+, Ni2+, Cu2+, Zn2+ - polarizability: intermediate - is_a: ChemicalEntitiesSchemaEnum + min_age_days: 29 + max_age_years: 1 + YOUNG_PEDIATRIC: + description: 0 to 5 years (NINDS CDE definition) + meaning: NCIT:C39299 + title: Pediatric + annotations: + min_age_years: 0 + max_age_years: 5 + ninds_category: true + PEDIATRIC: + description: 6 to 12 years (NINDS CDE definition) + meaning: NCIT:C16423 + title: Child + annotations: + min_age_years: 6 + max_age_years: 12 + ninds_category: true + ADOLESCENT: + description: 13 to 17 years + meaning: NCIT:C27954 + annotations: + min_age_years: 13 + max_age_years: 17 + YOUNG_ADULT: + description: 18 to 24 years + meaning: NCIT:C91107 + annotations: + min_age_years: 18 + max_age_years: 24 + ADULT: + description: 25 to 64 years + meaning: NCIT:C17600 + annotations: + min_age_years: 25 + max_age_years: 64 + OLDER_ADULT: + description: 65 years and older + meaning: NCIT:C16268 + title: Elderly + annotations: + min_age_years: 65 + aliases: Geriatric, Elderly, Senior + is_a: NihDemographicsSchemaEnum annotations: - source_domain: chemistry - source_schema: chemical_entities - BronstedAcidBaseRoleEnum: - description: Brønsted-Lowry acid-base roles + source_domain: clinical + source_schema: nih_demographics + ParticipantVitalStatusEnum: + title: Participant Vital Status + description: Vital status of a research participant in clinical studies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ALIVE: + description: Participant is living + meaning: NCIT:C37987 + exact_mappings: + - PATO:0001421 + DECEASED: + title: Dead + description: Participant is deceased + meaning: NCIT:C28554 + exact_mappings: + - PATO:0001422 + UNKNOWN: + description: Vital status unknown or lost to follow-up + meaning: NCIT:C17998 + is_a: NihDemographicsSchemaEnum + annotations: + source_domain: clinical + source_schema: nih_demographics + RecruitmentStatusEnum: + title: Recruitment Status + description: Clinical trial or study recruitment status per NIH/ClinicalTrials.gov + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NOT_YET_RECRUITING: + description: Study has not started recruiting participants + meaning: NCIT:C211610 + title: Not Yet Enrolling + RECRUITING: + description: Currently recruiting participants + meaning: NCIT:C142621 + title: Open To Enrollment + ENROLLING_BY_INVITATION: + description: Enrolling participants by invitation only + meaning: NCIT:C211611 + ACTIVE_NOT_RECRUITING: + description: Study ongoing but not recruiting new participants + meaning: NCIT:C211612 + title: Study Active, Not Enrolling + SUSPENDED: + description: Study temporarily stopped + meaning: NCIT:C211613 + title: Study Enrollment Suspended + TERMINATED: + description: Study stopped early and will not resume + meaning: NCIT:C70757 + title: Study Terminated + COMPLETED: + description: Study has ended normally + meaning: NCIT:C70756 + title: Completed Clinical Study + WITHDRAWN: + description: Study withdrawn before enrollment + meaning: NCIT:C70758 + title: Study Withdrawn + is_a: NihDemographicsSchemaEnum + annotations: + source_domain: clinical + source_schema: nih_demographics + StudyPhaseEnum: + title: Study Phase + description: Clinical trial phases per FDA and NIH definitions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ACID: - title: Bronsted acid - description: Proton donor - meaning: CHEBI:39141 + EARLY_PHASE_1: + description: Exploratory trials before traditional Phase 1 + meaning: NCIT:C54721 + title: Phase 0 Trial annotations: - definition: species that donates H+ - BASE: - title: Bronsted base - description: Proton acceptor - meaning: CHEBI:39142 + aliases: Phase 0 + PHASE_1: + title: Phase I Trial + description: Initial safety and dosage studies + meaning: NCIT:C15600 annotations: - definition: species that accepts H+ - AMPHOTERIC: - description: Can act as both acid and base + participants: 20-100 + PHASE_1_2: + title: Phase II/III Trial + description: Combined Phase 1 and Phase 2 trial + meaning: NCIT:C15694 + PHASE_2: + title: Phase II Trial + description: Efficacy and side effects studies + meaning: NCIT:C15601 annotations: - definition: species that can donate or accept H+ - examples: H2O, HSO4-, H2PO4- - is_a: ChemicalEntitiesSchemaEnum - annotations: - source_domain: chemistry - source_schema: chemical_entities - LewisAcidBaseRoleEnum: - description: Lewis acid-base roles - permissible_values: - LEWIS_ACID: - description: Electron pair acceptor + participants: 100-300 + PHASE_2_3: + title: Phase IIa Trial + description: Combined Phase 2 and Phase 3 trial + meaning: NCIT:C49686 + PHASE_3: + title: Phase III Trial + description: Efficacy comparison with standard treatment + meaning: NCIT:C15602 annotations: - definition: species that accepts electron pair - examples: BF3, AlCl3, H+ - LEWIS_BASE: - description: Electron pair donor + participants: 300-3000 + PHASE_4: + title: Phase IV Trial + description: Post-marketing surveillance + meaning: NCIT:C15603 annotations: - definition: species that donates electron pair - examples: NH3, OH-, H2O - is_a: ChemicalEntitiesSchemaEnum + note: After FDA approval + NOT_APPLICABLE: + description: Not a phased clinical trial + meaning: NCIT:C48660 + annotations: + note: For observational studies, device trials, etc. + is_a: NihDemographicsSchemaEnum annotations: - source_domain: chemistry - source_schema: chemical_entities - OxidationStateEnum: - description: Common oxidation states + source_domain: clinical + source_schema: nih_demographics + PhenopacketsSchemaEnum: + description: Schema-level enum for phenopackets in clinical + is_a: ClinicalDomainEnum + abstract: true + annotations: + source_file: clinical/phenopackets.yaml + KaryotypicSexEnum: + title: Karyotypic Sex + description: Karyotypic sex of an individual based on chromosome composition + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets permissible_values: - MINUS_4: - description: Oxidation state -4 - annotations: - value: '-4' - example: C in CH4 - MINUS_3: - description: Oxidation state -3 - annotations: - value: '-3' - example: N in NH3 - MINUS_2: - description: Oxidation state -2 - annotations: - value: '-2' - example: O in H2O - MINUS_1: - description: Oxidation state -1 + XX: + description: Female karyotype (46,XX) + meaning: NCIT:C45976 + title: XX Genotype annotations: - value: '-1' - example: Cl in NaCl - ZERO: - description: Oxidation state 0 + chromosome_count: 46 + typical_phenotypic_sex: female + XY: + description: Male karyotype (46,XY) + meaning: NCIT:C45977 + title: XY Genotype annotations: - value: '0' - example: elemental forms - PLUS_1: - description: Oxidation state +1 + chromosome_count: 46 + typical_phenotypic_sex: male + XO: + description: Turner syndrome karyotype (45,X) + meaning: NCIT:C176780 + title: 45,XO Karyotype annotations: - value: '+1' - example: Na in NaCl - PLUS_2: - description: Oxidation state +2 + chromosome_count: 45 + condition: Turner syndrome + XXY: + description: Klinefelter syndrome karyotype (47,XXY) + meaning: NCIT:C176784 + title: 47,XXY Karyotype annotations: - value: '+2' - example: Ca in CaCl2 - PLUS_3: - description: Oxidation state +3 + chromosome_count: 47 + condition: Klinefelter syndrome + XXX: + description: Triple X syndrome karyotype (47,XXX) + meaning: NCIT:C176785 + title: 47,XXX Karyotype annotations: - value: '+3' - example: Al in Al2O3 - PLUS_4: - description: Oxidation state +4 + chromosome_count: 47 + condition: Triple X syndrome + XXXY: + description: XXXY syndrome karyotype (48,XXXY) + meaning: NCIT:C176786 + title: 48,XXXY Karyotype annotations: - value: '+4' - example: C in CO2 - PLUS_5: - description: Oxidation state +5 + chromosome_count: 48 + condition: XXXY syndrome + XXXX: + description: Tetrasomy X karyotype (48,XXXX) + meaning: NCIT:C176787 + title: 48,XXXX Karyotype annotations: - value: '+5' - example: P in PO4³⁻ - PLUS_6: - description: Oxidation state +6 + chromosome_count: 48 + condition: Tetrasomy X + XXYY: + description: XXYY syndrome karyotype (48,XXYY) + meaning: NCIT:C89801 + title: XXYY Syndrome annotations: - value: '+6' - example: S in SO4²⁻ - PLUS_7: - description: Oxidation state +7 + chromosome_count: 48 + condition: XXYY syndrome + XYY: + description: Jacob's syndrome karyotype (47,XYY) + meaning: NCIT:C176782 + title: 47,XYY Karyotype annotations: - value: '+7' - example: Mn in MnO4⁻ - PLUS_8: - description: Oxidation state +8 + chromosome_count: 47 + condition: Jacob's syndrome + OTHER_KARYOTYPE: + description: Other karyotypic sex not listed annotations: - value: '+8' - example: Os in OsO4 - is_a: ChemicalEntitiesSchemaEnum - annotations: - source_domain: chemistry - source_schema: chemical_entities - ChiralityEnum: - description: Chirality/stereochemistry descriptors + note: May include complex chromosomal arrangements + UNKNOWN_KARYOTYPE: + description: Karyotype not determined or unknown + meaning: NCIT:C17998 + title: Unknown + is_a: PhenopacketsSchemaEnum + PhenotypicSexEnum: + title: Phenotypic Sex + description: 'Phenotypic sex of an individual based on observable characteristics. + + FHIR mapping: AdministrativeGender' + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets permissible_values: - R: - description: Rectus (right) configuration - annotations: - cahn_ingold_prelog: 'true' - S: - description: Sinister (left) configuration + MALE: + description: Male phenotypic sex + meaning: PATO:0000384 + exact_mappings: + - NCIT:C20197 + FEMALE: + description: Female phenotypic sex + meaning: PATO:0000383 + exact_mappings: + - NCIT:C16576 + OTHER_SEX: + description: Sex characteristics not clearly male or female + meaning: NCIT:C45908 + title: Intersex annotations: - cahn_ingold_prelog: 'true' - D: - description: Dextrorotatory + note: Includes differences of sex development (DSD) + UNKNOWN_SEX: + description: Sex not assessed or not available + meaning: NCIT:C17998 + title: Unknown + is_a: PhenopacketsSchemaEnum + AllelicStateEnum: + title: Allelic State + description: Allelic state/zygosity of a variant or genetic feature + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets + permissible_values: + HETEROZYGOUS: + description: Different alleles at a locus + meaning: GENO:0000135 annotations: - fischer_projection: 'true' - optical_rotation: positive - L: - description: Levorotatory + symbol: het + HOMOZYGOUS: + description: Identical alleles at a locus + meaning: GENO:0000136 annotations: - fischer_projection: 'true' - optical_rotation: negative - RACEMIC: - description: Racemic mixture (50:50 of enantiomers) + symbol: hom + HEMIZYGOUS: + description: Only one allele present (e.g., X-linked in males) + meaning: GENO:0000134 annotations: - optical_rotation: zero - MESO: - description: Meso compound (achiral despite stereocenters) + symbol: hemi + note: Common for X-linked genes in males + COMPOUND_HETEROZYGOUS: + description: Two different heterozygous variants in same gene + meaning: GENO:0000402 annotations: - internal_symmetry: 'true' - E: - description: Entgegen (opposite) configuration + symbol: comp het + HOMOZYGOUS_REFERENCE: + description: Two reference/wild-type alleles + meaning: GENO:0000036 + title: reference allele annotations: - geometric_isomer: 'true' - Z: - description: Zusammen (together) configuration + symbol: hom ref + HOMOZYGOUS_ALTERNATE: + description: Two alternate/variant alleles + meaning: GENO:0000002 + title: variant allele annotations: - geometric_isomer: 'true' - is_a: ChemicalEntitiesSchemaEnum - annotations: - source_domain: chemistry - source_schema: chemical_entities - NanostructureMorphologyEnum: - description: Types of nanostructure morphologies + symbol: hom alt + is_a: PhenopacketsSchemaEnum + LateralityEnum: + title: Laterality + description: Laterality/sidedness of a finding or anatomical structure + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets permissible_values: - NANOTUBE: - description: Cylindrical nanostructure - meaning: CHEBI:50796 - annotations: - dimensions: 1D - examples: carbon nanotubes - NANOPARTICLE: - description: Particle with nanoscale dimensions - meaning: CHEBI:50803 - annotations: - dimensions: 0D - size_range: 1-100 nm - NANOROD: - description: Rod-shaped nanostructure - meaning: CHEBI:50805 + RIGHT: + description: Right side + meaning: HP:0012834 annotations: - dimensions: 1D - aspect_ratio: 3-20 - QUANTUM_DOT: - description: Semiconductor nanocrystal - meaning: CHEBI:50853 + anatomical_term: dexter + LEFT: + description: Left side + meaning: HP:0012835 annotations: - dimensions: 0D - property: quantum confinement - NANOWIRE: - description: Wire with nanoscale diameter + anatomical_term: sinister + BILATERAL: + description: Both sides + meaning: HP:0012832 annotations: - dimensions: 1D - diameter: <100 nm - NANOSHEET: - description: Two-dimensional nanostructure + note: Affecting both left and right + UNILATERAL: + description: One side (unspecified which) + meaning: HP:0012833 annotations: - dimensions: 2D - thickness: <100 nm - NANOFIBER: - description: Fiber with nanoscale diameter + note: Affecting only one side + MIDLINE: + description: In the midline/center annotations: - dimensions: 1D - diameter: <1000 nm - is_a: ChemicalEntitiesSchemaEnum - annotations: - source_domain: chemistry - source_schema: chemical_entities - ReactionDirectionalitySchemaEnum: - description: Schema-level enum for reaction_directionality in chemistry - is_a: ChemistryDomainEnum - abstract: true - annotations: - source_file: chemistry/reaction_directionality.yaml - ReactionDirectionality: - title: Reaction Directionality - description: The directionality of a chemical reaction or process - permissible_values: - LEFT_TO_RIGHT: - description: Reaction proceeds from left to right (forward direction) - aliases: - - LR - - forward - - --> - RIGHT_TO_LEFT: - description: Reaction proceeds from right to left (reverse direction) - aliases: - - RL - - reverse - - backward - - <-- - BIDIRECTIONAL: - description: Reaction can proceed in both directions - aliases: - - BIDI - - reversible - - <--> - exact_mappings: - - SBO:0000650 - AGNOSTIC: - description: Direction is unknown or not specified - aliases: - - unknown - - unspecified - IRREVERSIBLE_LEFT_TO_RIGHT: - description: Reaction proceeds only from left to right and cannot be reversed - aliases: - - irreversible forward - - ->> - exact_mappings: - - SBO:0000651 - IRREVERSIBLE_RIGHT_TO_LEFT: - description: Reaction proceeds only from right to left and cannot be reversed - aliases: - - irreversible reverse - - <<- - is_a: ReactionDirectionalitySchemaEnum - annotations: - source_domain: chemistry - source_schema: reaction_directionality - ReactionsSchemaEnum: - description: Schema-level enum for reactions in chemistry - is_a: ChemistryDomainEnum - abstract: true - annotations: - source_file: chemistry/reactions.yaml - ReactionTypeEnum: - description: Types of chemical reactions + note: Along the body's central axis + is_a: PhenopacketsSchemaEnum + OnsetTimingEnum: + title: Onset Timing + description: Timing of disease or phenotype onset relative to developmental stages + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets permissible_values: - SYNTHESIS: - description: Combination reaction (A + B → AB) + ANTENATAL_ONSET: + description: Before birth (prenatal) + meaning: HP:0030674 annotations: - aliases: combination, addition - pattern: A + B → AB - DECOMPOSITION: - description: Breakdown reaction (AB → A + B) + period: Before birth + EMBRYONAL_ONSET: + description: During embryonic period (0-8 weeks) + meaning: HP:0011460 annotations: - aliases: analysis - pattern: AB → A + B - SINGLE_DISPLACEMENT: - description: Single replacement reaction (A + BC → AC + B) + period: 0-8 weeks gestation + FETAL_ONSET: + description: During fetal period (8 weeks to birth) + meaning: HP:0011461 annotations: - aliases: single replacement - pattern: A + BC → AC + B - DOUBLE_DISPLACEMENT: - description: Double replacement reaction (AB + CD → AD + CB) + period: 8 weeks to birth + CONGENITAL_ONSET: + description: Present at birth + meaning: HP:0003577 annotations: - aliases: double replacement, metathesis - pattern: AB + CD → AD + CB - COMBUSTION: - description: Reaction with oxygen producing heat and light + period: At birth + NEONATAL_ONSET: + description: Within first 28 days of life + meaning: HP:0003623 annotations: - reactant: oxygen - products: usually CO2 and H2O - SUBSTITUTION: - title: substitution reaction - description: Replacement of one group by another - meaning: MOP:0000790 + period: 0-28 days + INFANTILE_ONSET: + description: Between 28 days and 1 year + meaning: HP:0003593 annotations: - subtypes: SN1, SN2, SNAr - ELIMINATION: - title: elimination reaction - description: Removal of atoms/groups forming double bond - meaning: MOP:0000656 + period: 28 days to 1 year + CHILDHOOD_ONSET: + description: Between 1 year and 16 years + meaning: HP:0011463 annotations: - subtypes: E1, E2, E1cB - ADDITION: - title: addition reaction - description: Addition to multiple bond - meaning: MOP:0000642 + period: 1-16 years + JUVENILE_ONSET: + description: Between 5 years and 16 years + meaning: HP:0003621 annotations: - subtypes: electrophilic, nucleophilic, radical - REARRANGEMENT: - description: Reorganization of molecular structure + period: 5-16 years + YOUNG_ADULT_ONSET: + description: Between 16 years and 40 years + meaning: HP:0011462 annotations: - examples: Claisen, Cope, Wagner-Meerwein - OXIDATION: - description: Loss of electrons or increase in oxidation state + period: 16-40 years + MIDDLE_AGE_ONSET: + description: Between 40 years and 60 years + meaning: HP:0003596 + annotations: + period: 40-60 years + LATE_ONSET: + description: After 60 years + meaning: HP:0003584 annotations: - electron_change: loss - REDUCTION: - description: Gain of electrons or decrease in oxidation state + period: '>60 years' + is_a: PhenopacketsSchemaEnum + ACMGPathogenicityEnum: + title: ACMG Pathogenicity + description: ACMG/AMP variant pathogenicity classification for clinical genetics + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets + permissible_values: + PATHOGENIC: + description: Pathogenic variant + meaning: NCIT:C168799 + title: Pathogenic Variant annotations: - electron_change: gain - DIELS_ALDER: - title: Diels-Alder reaction - description: '[4+2] cycloaddition reaction' - meaning: RXNO:0000006 + abbreviation: P + clinical_significance: Disease-causing + LIKELY_PATHOGENIC: + description: Likely pathogenic variant + meaning: NCIT:C168800 + title: Likely Pathogenic Variant annotations: - type: pericyclic - components: diene + dienophile - FRIEDEL_CRAFTS: - title: Friedel-Crafts reaction - description: Electrophilic aromatic substitution - meaning: RXNO:0000369 + abbreviation: LP + probability: '>90% certain' + UNCERTAIN_SIGNIFICANCE: + description: Variant of uncertain significance + meaning: NCIT:C94187 + title: Variant of Unknown Significance annotations: - subtypes: alkylation, acylation - GRIGNARD: - title: Grignard reaction - description: Organometallic addition reaction - meaning: RXNO:0000014 + abbreviation: VUS + note: Insufficient evidence + LIKELY_BENIGN: + description: Likely benign variant + meaning: NCIT:C168801 + title: Variant Likely Benign annotations: - reagent: RMgX - WITTIG: - title: Wittig reaction - description: Alkene formation from phosphonium ylide - meaning: RXNO:0000015 + abbreviation: LB + probability: '>90% certain benign' + BENIGN: + description: Benign variant + meaning: NCIT:C168802 + title: Variant Benign annotations: - product: alkene - ALDOL: - title: aldol condensation - description: Condensation forming β-hydroxy carbonyl - meaning: RXNO:0000017 + abbreviation: B + clinical_significance: Not disease-causing + is_a: PhenopacketsSchemaEnum + TherapeuticActionabilityEnum: + title: Therapeutic Actionability + description: Clinical actionability of a genetic finding for treatment decisions + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets + permissible_values: + ACTIONABLE: + description: Finding has direct therapeutic implications + meaning: NCIT:C206303 + title: Actionable Variation annotations: - mechanism: enolate addition - MICHAEL_ADDITION: - title: Michael addition - description: 1,4-addition to α,β-unsaturated carbonyl - meaning: RXNO:0000009 + note: Can guide treatment selection + NOT_ACTIONABLE: + description: No current therapeutic implications + meaning: NCIT:C206304 + title: Non-Actionable Variation annotations: - type: conjugate addition - is_a: ReactionsSchemaEnum - annotations: - source_domain: chemistry - source_schema: reactions - ReactionMechanismEnum: - description: Reaction mechanism types + note: No treatment changes indicated + UNKNOWN_ACTIONABILITY: + description: Therapeutic implications unclear + meaning: NCIT:C17998 + title: Unknown + is_a: PhenopacketsSchemaEnum + InterpretationProgressEnum: + title: Interpretation Progress + description: Progress status of clinical interpretation or diagnosis + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets permissible_values: - SN1: - description: Unimolecular nucleophilic substitution + SOLVED: + description: Diagnosis achieved/case solved + meaning: NCIT:C20826 + title: Molecular Diagnosis annotations: - rate_determining: carbocation formation - stereochemistry: racemization - SN2: - description: Bimolecular nucleophilic substitution + note: Molecular cause identified + UNSOLVED: + description: No diagnosis achieved + meaning: NCIT:C125009 + title: Clinical Interpretation annotations: - rate_determining: concerted - stereochemistry: inversion - E1: - description: Unimolecular elimination + note: Molecular cause not identified + IN_PROGRESS: + description: Analysis ongoing + meaning: NCIT:C25630 + title: Progress + COMPLETED: + description: Analysis completed + meaning: NCIT:C216251 + title: Procedure Completed annotations: - intermediate: carbocation - E2: - description: Bimolecular elimination + note: May be solved or unsolved + UNKNOWN_PROGRESS: + description: Progress status unknown + meaning: NCIT:C17998 + title: Unknown + is_a: PhenopacketsSchemaEnum + RegimenStatusEnum: + title: Regimen Status + description: Status of a therapeutic regimen or treatment protocol + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets + permissible_values: + NOT_STARTED: + description: Treatment not yet begun + meaning: NCIT:C53601 + title: Device Evaluation Anticipated But Not Yet Begun + STARTED: + description: Treatment initiated + meaning: NCIT:C165209 + title: Treatment Ongoing + COMPLETED: + description: Treatment finished as planned + meaning: NCIT:C105740 + title: Treatment Completed as Prescribed + DISCONTINUED_ADVERSE_EVENT: + description: Stopped due to adverse event + meaning: NCIT:C41331 + title: Adverse Event annotations: - requirement: antiperiplanar - E1CB: - description: Elimination via conjugate base + reason: Toxicity or side effects + DISCONTINUED_LACK_OF_EFFICACY: + description: Stopped due to lack of efficacy + meaning: NCIT:C49502 + title: Drug Withdrawn annotations: - intermediate: carbanion - RADICAL: - description: Free radical mechanism + reason: Treatment not effective + DISCONTINUED_PHYSICIAN_DECISION: + description: Stopped by physician decision + meaning: NCIT:C49502 + title: Drug Withdrawn + DISCONTINUED_PATIENT_DECISION: + description: Stopped by patient choice + meaning: NCIT:C48271 + title: Consent Withdrawn + UNKNOWN_STATUS: + description: Treatment status unknown + meaning: NCIT:C17998 + title: Unknown + is_a: PhenopacketsSchemaEnum + DrugResponseEnum: + title: Drug Response + description: Response categories for drug treatment outcomes + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org + source_domain: clinical + source_schema: phenopackets + permissible_values: + FAVORABLE: + description: Favorable response to treatment + meaning: NCIT:C123584 + title: Favorable Response annotations: - initiation: homolytic cleavage - PERICYCLIC: - description: Concerted cyclic electron reorganization + note: Better than expected response + UNFAVORABLE: + description: Unfavorable response to treatment + meaning: NCIT:C102561 annotations: - examples: Diels-Alder, Cope - ELECTROPHILIC_AROMATIC: - description: Electrophilic aromatic substitution + note: Worse than expected response + RESPONSIVE: + description: Responsive to treatment + meaning: NCIT:C165206 + title: Responsive Disease annotations: - intermediate: arenium ion - NUCLEOPHILIC_AROMATIC: - description: Nucleophilic aromatic substitution + note: Shows expected response + RESISTANT: + description: Resistant to treatment + meaning: NCIT:C16523 + title: Drug Resistance Process annotations: - requirement: electron-withdrawing groups - ADDITION_ELIMINATION: - description: Addition followed by elimination + note: No response to treatment + PARTIALLY_RESPONSIVE: + description: Partial response to treatment + meaning: NCIT:C18213 + title: Stable Disease annotations: - intermediate: tetrahedral - is_a: ReactionsSchemaEnum + note: Some but not complete response + UNKNOWN_RESPONSE: + description: Treatment response unknown + meaning: NCIT:C17998 + title: Unknown + is_a: PhenopacketsSchemaEnum + ProvenanceSchemaEnum: + description: Schema-level enum for provenance in clinical + is_a: ClinicalDomainEnum + abstract: true + annotations: + source_file: clinical/provenance.yaml + ConditionProvenanceEnum: + title: Condition Provenance + description: Sources of condition/diagnosis records indicating how the condition was documented or determined. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://github.com/RTIInternational/NHLBI-BDC-DMC-HM + - https://ohdsi.github.io/CommonDataModel/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + EHR_BILLING_DIAGNOSIS: + description: Diagnosis recorded for billing purposes in EHR + EHR_CHIEF_COMPLAINT: + description: Condition documented as chief complaint in EHR + EHR_ENCOUNTER_DIAGNOSIS: + description: Diagnosis recorded during healthcare encounter + EHR_EPISODE_ENTRY: + description: Condition recorded as part of care episode + EHR_PROBLEM_LIST_ENTRY: + description: Condition on patient problem list in EHR + FIRST_POSITION_CONDITION: + description: Primary diagnosis in first position on claim + NLP_DERIVED: + description: Condition derived through natural language processing + OBSERVATION_RECORDED_FROM_EHR: + description: Condition recorded as observation in EHR + PATIENT_SELF_REPORTED_CONDITION: + description: Condition reported by the patient + aliases: + - PATIENT_SELF-REPORTED_CONDITION + PRIMARY_CONDITION: + description: Primary condition for an encounter or episode + REFERRAL_RECORD: + description: Condition documented in referral record + SECONDARY_CONDITION: + description: Secondary or comorbid condition + TUMOR_REGISTRY: + description: Condition from tumor registry + WORKING_DIAGNOSIS: + description: Preliminary or working diagnosis + CLINICAL_DIAGNOSIS: + description: Clinically confirmed diagnosis + is_a: ProvenanceSchemaEnum + annotations: + source_domain: clinical + source_schema: provenance + VisitProvenanceEnum: + title: Visit Provenance + description: Sources of healthcare visit/encounter records indicating the origin of the visit documentation. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://github.com/RTIInternational/NHLBI-BDC-DMC-HM + - https://ohdsi.github.io/CommonDataModel/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CASE_REPORT_FORM: + description: Visit from clinical trial case report form + CLAIM: + description: Visit derived from insurance claim + EHR: + description: Visit from electronic health record + EHR_ENCOUNTER_RECORD: + description: Visit from EHR encounter documentation + EHR_ADMISSION_NOTE: + description: Visit from EHR admission note + EHR_DISCHARGE_RECORD: + description: Visit from EHR discharge documentation + EHR_EMERGENCY_ROOM_NOTE: + description: Visit from EHR emergency room note + EHR_INPATIENT_NOTE: + description: Visit from EHR inpatient note + EHR_OUTPATIENT_NOTE: + description: Visit from EHR outpatient note + INPATIENT_CLAIM: + description: Visit from inpatient insurance claim + OUTPATIENT_CLAIM: + description: Visit from outpatient insurance claim + FACILITY_CLAIM: + description: Visit from facility insurance claim + PROFESSIONAL_CLAIM: + description: Visit from professional services claim + PHARMACY_CLAIM: + description: Visit from pharmacy claim + LAB: + description: Visit from laboratory record + REGISTRY: + description: Visit from disease or patient registry + SURVEY: + description: Visit from patient survey + PATIENT_SELF_REPORT: + description: Visit reported by patient + aliases: + - PATIENT_SELF-REPORT + NLP: + description: Visit derived through natural language processing + HEALTH_INFORMATION_EXCHANGE_RECORD: + description: Visit from health information exchange + is_a: ProvenanceSchemaEnum + annotations: + source_domain: clinical + source_schema: provenance + DrugExposureProvenanceEnum: + title: Drug Exposure Provenance + description: Sources of drug exposure records indicating how the medication information was documented. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://github.com/RTIInternational/NHLBI-BDC-DMC-HM + - https://ohdsi.github.io/CommonDataModel/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + RANDOMIZED_DRUG: + description: Drug from clinical trial randomization + aliases: + - RANDOMIZED DRUG + PATIENT_SELF_REPORTED_MEDICATION: + description: Medication reported by patient + aliases: + - PATIENT SELF-REPORTED MEDICATION + NLP_DERIVED: + description: Drug exposure derived through NLP + aliases: + - NLP DERIVED + PRESCRIPTION_DISPENSED_IN_PHARMACY: + description: Prescription dispensed at pharmacy + aliases: + - PRESCRIPTION DISPENSED IN PHARMACY + PHYSICIAN_ADMINISTERED_DRUG_FROM_EHR_ORDER: + description: Drug administered by physician from EHR order + aliases: + - PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) + DISPENSED_IN_OUTPATIENT_OFFICE: + description: Drug dispensed in outpatient office + aliases: + - DISPENSED IN OUTPATIENT OFFICE + PRESCRIPTION_DISPENSED_THROUGH_MAIL_ORDER: + description: Prescription dispensed via mail order + aliases: + - PRESCRIPTION DISPENSED THROUGH MAIL ORDER + PRESCRIPTION_WRITTEN: + description: Prescription written by provider + aliases: + - PRESCRIPTION WRITTEN + MEDICATION_LIST_ENTRY: + description: Drug from medication list + aliases: + - MEDICATION LIST ENTRY + PHYSICIAN_ADMINISTERED_DRUG_AS_PROCEDURE: + description: Drug administered as procedure + aliases: + - PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) + INPATIENT_ADMINISTRATION: + description: Drug administered during inpatient stay + aliases: + - INPATIENT ADMINISTRATION + is_a: ProvenanceSchemaEnum + annotations: + source_domain: clinical + source_schema: provenance + StatusEnum: + title: Presence Status + description: Values indicating whether a condition or observation is present, absent, or of unknown status. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PRESENT: + description: Was present in the patient at observation time + ABSENT: + description: Was absent in the patient at observation time + UNKNOWN: + description: Status was unknown at observation time + is_a: ProvenanceSchemaEnum + annotations: + source_domain: clinical + source_schema: provenance + HistoricalStatusEnum: + title: Historical Status + description: Extended status values including historical presence of conditions or observations. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PRESENT: + description: Currently present in the patient + ABSENT: + description: Currently absent in the patient + UNKNOWN: + description: Current status is unknown + HISTORICAL: + description: Was present in the patient historically but not currently + is_a: ProvenanceSchemaEnum annotations: - source_domain: chemistry - source_schema: reactions - CatalystTypeEnum: - description: Types of catalysts + source_domain: clinical + source_schema: provenance + ResearchProjectTypeEnum: + title: Research Project Types + description: Types of research projects and studies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CONSORTIUM: + description: Multi-institutional research consortium + STUDY: + description: Individual research study + is_a: ProvenanceSchemaEnum + annotations: + source_domain: clinical + source_schema: provenance + ComputingDomainEnum: + description: Domain-level enum for computing value sets + is_a: ValueSetEnum + abstract: true + CroissantMlSchemaEnum: + description: Schema-level enum for croissant_ml in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/croissant_ml.yaml + MLDataType: + title: ML Data Type + description: 'Data types used in Croissant ML for describing field types in datasets. + + Based on XSD (XML Schema Definition) and schema.org vocabulary. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - HOMOGENEOUS: - description: Catalyst in same phase as reactants + TEXT: + description: Text or string data + meaning: xsd:string + mappings: + - schema:Text + - EDAM:3671 + INTEGER: + description: Integer numbers + meaning: xsd:integer + mappings: + - schema:Integer + - IAO:0000031 + FLOAT: + description: Floating point numbers + meaning: xsd:float + mappings: + - schema:Float + BOOLEAN: + description: Boolean values (true/false) + meaning: xsd:boolean + mappings: + - schema:Boolean + DATE: + description: Date values + meaning: xsd:date + mappings: + - schema:Date + TIME: + description: Time values + meaning: xsd:time + mappings: + - schema:Time + DATETIME: + description: Combined date and time values + meaning: xsd:dateTime + mappings: + - schema:DateTime + URL: + description: Uniform Resource Locators + meaning: xsd:anyURI + mappings: + - schema:URL + is_a: CroissantMlSchemaEnum + annotations: + source_domain: computing + source_schema: croissant_ml + DatasetEncodingFormat: + title: Dataset Encoding Format + description: 'Encoding formats (MIME types) commonly used for ML dataset files in Croissant. + + These specify how data is serialized and stored. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CSV: + description: Comma-separated values format for tabular data + meaning: EDAM:format_3752 annotations: - phase: same as reactants - examples: acid, base, metal complexes - HETEROGENEOUS: - description: Catalyst in different phase from reactants + mime_type: text/csv + JSON: + description: JavaScript Object Notation format for structured data + meaning: EDAM:format_3464 annotations: - phase: different from reactants - examples: Pt/Pd on carbon, zeolites - ENZYME: - title: cofactor - description: Biological catalyst - meaning: CHEBI:23357 + mime_type: application/json + JSONL: + description: JSON Lines format (newline-delimited JSON) annotations: - type: protein - specificity: high - ORGANOCATALYST: - description: Small organic molecule catalyst + mime_type: application/jsonl + alt_mime_type: application/x-ndjson + PARQUET: + description: Apache Parquet columnar storage format annotations: - metal_free: 'true' - examples: proline, thiourea - PHOTOCATALYST: - description: Light-activated catalyst + mime_type: application/parquet + PLAIN_TEXT: + description: Plain text files annotations: - activation: light - examples: TiO2, Ru complexes - PHASE_TRANSFER: - description: Catalyst facilitating reaction between phases + mime_type: text/plain + JPEG: + description: JPEG image format + meaning: EDAM:format_3579 + title: JPG annotations: - function: transfers reactant between phases - ACID: - description: Acid catalyst + mime_type: image/jpeg + PNG: + description: Portable Network Graphics image format + meaning: EDAM:format_3603 + title: PNG annotations: - mechanism: proton donation - BASE: - description: Base catalyst + mime_type: image/png + WAV: + description: Waveform Audio File Format annotations: - mechanism: proton abstraction - METAL: - description: Metal catalyst + mime_type: audio/wav + MP4: + description: MPEG-4 multimedia container format + meaning: EDAM:format_3997 + title: MPEG-4 annotations: - examples: Pd, Pt, Ni, Ru - BIFUNCTIONAL: - description: Catalyst with two active sites + mime_type: video/mp4 + ZIP: + description: ZIP archive format + meaning: EDAM:format_3987 + title: ZIP format annotations: - sites: multiple - is_a: ReactionsSchemaEnum - annotations: - source_domain: chemistry - source_schema: reactions - ReactionConditionEnum: - description: Reaction conditions - permissible_values: - ROOM_TEMPERATURE: - description: Standard room temperature (20-25°C) + mime_type: application/zip + TAR: + description: Tape Archive format + meaning: EDAM:format_3981 + title: TAR format annotations: - temperature: 20-25°C - REFLUX: - description: Boiling with condensation return + mime_type: application/x-tar + is_a: CroissantMlSchemaEnum + annotations: + source_domain: computing + source_schema: croissant_ml + DatasetSplitType: + title: Dataset Split Type + description: 'Standard dataset split types used in machine learning for training, + + validation, and testing. These splits are fundamental to ML model + + development and evaluation workflows. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TRAIN: + description: Training split used for model learning + annotations: + typical_size: 60-80% of data + purpose: model training + VALIDATION: + description: Validation split used for hyperparameter tuning and model selection annotations: - temperature: solvent boiling point - CRYOGENIC: - description: Very low temperature conditions + typical_size: 10-20% of data + purpose: model tuning + aliases: val, dev + TEST: + description: Test split used for final model evaluation annotations: - temperature: <-150°C - examples: liquid N2, liquid He - HIGH_PRESSURE: - description: Elevated pressure conditions + typical_size: 10-20% of data + purpose: model evaluation + ALL: + description: Complete dataset without splits + is_a: CroissantMlSchemaEnum + annotations: + source_domain: computing + source_schema: croissant_ml + MLLicenseType: + title: ML License Type + description: 'Common open source and Creative Commons licenses used for ML datasets. + + These licenses specify terms of use, redistribution, and modification. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CC_BY_4_0: + description: Creative Commons Attribution 4.0 International + title: CC-BY-4.0 + meaning: spdx:CC-BY-4.0 + see_also: + - https://creativecommons.org/licenses/by/4.0/ + annotations: + allows_commercial: true + requires_attribution: true + CC_BY_SA_4_0: + description: Creative Commons Attribution-ShareAlike 4.0 International + title: CC-BY-SA-4.0 + meaning: spdx:CC-BY-SA-4.0 + see_also: + - https://creativecommons.org/licenses/by-sa/4.0/ + annotations: + allows_commercial: true + requires_attribution: true + share_alike: true + CC0_1_0: + description: Creative Commons Zero 1.0 Universal (Public Domain Dedication) + title: CC0-1.0 + meaning: spdx:CC0-1.0 + see_also: + - https://creativecommons.org/publicdomain/zero/1.0/ annotations: - pressure: '>10 atm' - VACUUM: - description: Reduced pressure conditions + public_domain: true + MIT: + description: MIT License + meaning: spdx:MIT + see_also: + - https://opensource.org/licenses/MIT annotations: - pressure: <1 atm - INERT_ATMOSPHERE: - description: Non-reactive gas atmosphere + osi_approved: true + APACHE_2_0: + description: Apache License 2.0 + title: Apache-2.0 + meaning: spdx:Apache-2.0 + see_also: + - https://www.apache.org/licenses/LICENSE-2.0 annotations: - gases: N2, Ar - MICROWAVE: - description: Microwave heating + osi_approved: true + patent_grant: true + BSD_3_CLAUSE: + description: BSD 3-Clause "New" or "Revised" License + title: BSD-3-Clause + meaning: spdx:BSD-3-Clause + see_also: + - https://opensource.org/licenses/BSD-3-Clause annotations: - heating: microwave irradiation - ULTRASOUND: - description: Ultrasonic conditions + osi_approved: true + GPL_3_0: + description: GNU General Public License v3.0 + title: GPL-3.0 + meaning: spdx:GPL-3.0-only + see_also: + - https://www.gnu.org/licenses/gpl-3.0.html annotations: - activation: ultrasound - PHOTOCHEMICAL: - description: Light-induced conditions + osi_approved: true + copyleft: true + is_a: CroissantMlSchemaEnum + annotations: + source_domain: computing + source_schema: croissant_ml + MLFieldRole: + title: ML Field Role + description: 'Semantic roles that fields play in ML datasets. These roles help understand + + the purpose and usage of different data columns or attributes. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FEATURE: + description: Input features used for model prediction annotations: - activation: UV or visible light - ELECTROCHEMICAL: - description: Electrically driven conditions + also_known_as: input, predictor, independent variable + LABEL: + description: Target labels or outputs for supervised learning annotations: - activation: electric current - FLOW: - description: Continuous flow conditions + also_known_as: target, output, dependent variable, ground truth + METADATA: + description: Descriptive information about the dataset or records annotations: - type: continuous process - BATCH: - description: Batch reaction conditions + also_known_as: descriptive field, provenance + IDENTIFIER: + description: Unique identifiers for records or entities annotations: - type: batch process - is_a: ReactionsSchemaEnum + also_known_as: ID, key, primary key + is_a: CroissantMlSchemaEnum annotations: - source_domain: chemistry - source_schema: reactions - ReactionRateOrderEnum: - description: Reaction rate orders + source_domain: computing + source_schema: croissant_ml + CompressionFormat: + title: Compression Format + description: 'Compression and archive formats commonly used for ML dataset distribution. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ZERO_ORDER: - description: Rate independent of concentration - annotations: - rate_law: rate = k - integrated: '[A] = [A]₀ - kt' - FIRST_ORDER: - description: Rate proportional to concentration - annotations: - rate_law: rate = k[A] - integrated: ln[A] = ln[A]₀ - kt - SECOND_ORDER: - description: Rate proportional to concentration squared + ZIP: + description: ZIP archive format with lossless data compression + meaning: EDAM:format_3987 + title: ZIP format annotations: - rate_law: rate = k[A]² - integrated: 1/[A] = 1/[A]₀ + kt - PSEUDO_FIRST_ORDER: - description: Apparent first order (excess reagent) + mime_type: application/zip + typical_extension: .zip + TAR: + description: Tape Archive format (typically used with compression) + meaning: EDAM:format_3981 + title: TAR format annotations: - condition: one reagent in large excess - FRACTIONAL_ORDER: - description: Non-integer order + mime_type: application/x-tar + typical_extension: .tar + GZIP: + description: GNU zip compression format + meaning: EDAM:format_3989 + title: GZIP format annotations: - indicates: complex mechanism - MIXED_ORDER: - description: Different orders for different reactants + mime_type: application/gzip + typical_extension: .gz + TAR_GZ: + description: TAR archive compressed with GZIP annotations: - example: rate = k[A][B]² - is_a: ReactionsSchemaEnum + mime_type: application/gzip + typical_extension: .tar.gz + is_a: CroissantMlSchemaEnum annotations: - source_domain: chemistry - source_schema: reactions - EnzymeClassEnum: - description: EC enzyme classification + source_domain: computing + source_schema: croissant_ml + MLMediaType: + title: ML Media Type + description: 'Media types (MIME types) for different modalities of ML data including + + images, audio, video, and text. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - OXIDOREDUCTASE: - title: Oxidoreductases - description: Catalyzes oxidation-reduction reactions - meaning: EC:1 + IMAGE_JPEG: + description: JPEG image format + meaning: EDAM:format_3579 + title: JPG annotations: - EC_class: '1' - examples: dehydrogenases, oxidases - TRANSFERASE: - title: Transferases - description: Catalyzes group transfer reactions - meaning: EC:2 + mime_type: image/jpeg + modality: image + IMAGE_PNG: + description: PNG image format + meaning: EDAM:format_3603 + title: PNG annotations: - EC_class: '2' - examples: kinases, transaminases - HYDROLASE: - title: Hydrolases - description: Catalyzes hydrolysis reactions - meaning: EC:3 + mime_type: image/png + modality: image + IMAGE_GIF: + description: GIF image format annotations: - EC_class: '3' - examples: proteases, lipases - LYASE: - title: Lyases - description: Catalyzes non-hydrolytic additions/removals - meaning: EC:4 + mime_type: image/gif + modality: image + IMAGE_TIFF: + description: TIFF image format annotations: - EC_class: '4' - examples: decarboxylases, aldolases - ISOMERASE: - title: Isomerases - description: Catalyzes isomerization reactions - meaning: EC:5 + mime_type: image/tiff + modality: image + AUDIO_WAV: + description: Waveform Audio File Format + annotations: + mime_type: audio/wav + modality: audio + AUDIO_MP3: + description: MP3 audio format + annotations: + mime_type: audio/mpeg + modality: audio + AUDIO_FLAC: + description: FLAC lossless audio format + annotations: + mime_type: audio/flac + modality: audio + VIDEO_MP4: + description: MPEG-4 video format + meaning: EDAM:format_3997 + title: MPEG-4 annotations: - EC_class: '5' - examples: racemases, epimerases - LIGASE: - title: Ligases - description: Catalyzes formation of bonds with ATP - meaning: EC:6 + mime_type: video/mp4 + modality: video + VIDEO_AVI: + description: Audio Video Interleaved format + meaning: EDAM:format_3990 + title: AVI annotations: - EC_class: '6' - examples: synthetases, carboxylases - TRANSLOCASE: - title: Translocases - description: Catalyzes movement across membranes - meaning: EC:7 + mime_type: video/x-msvideo + modality: video + VIDEO_WEBM: + description: WebM video format annotations: - EC_class: '7' - examples: ATPases, ion pumps - is_a: ReactionsSchemaEnum + mime_type: video/webm + modality: video + TEXT_PLAIN: + description: Plain text format + annotations: + mime_type: text/plain + modality: text + TEXT_HTML: + description: HTML format + annotations: + mime_type: text/html + modality: text + is_a: CroissantMlSchemaEnum annotations: - source_domain: chemistry - source_schema: reactions - SolventClassEnum: - description: Classes of solvents + source_domain: computing + source_schema: croissant_ml + MLModalityType: + title: ML Modality Type + description: 'High-level data modalities used in machine learning. These represent + + the fundamental types of input data that ML models process. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - PROTIC: - description: Solvents with acidic hydrogen + TEXT: + description: Textual data (natural language, code, etc.) annotations: - H_bonding: donor - examples: water, alcohols, acids - APROTIC_POLAR: - description: Polar solvents without acidic H + examples: documents, sentences, tokens + IMAGE: + description: Visual image data + meaning: EDAM:data_2968 annotations: - H_bonding: acceptor only - examples: DMSO, DMF, acetone - APROTIC_NONPOLAR: - description: Nonpolar solvents + examples: photographs, diagrams, scans + AUDIO: + description: Audio/sound data annotations: - H_bonding: none - examples: hexane, benzene, CCl4 - IONIC_LIQUID: - description: Room temperature ionic liquids + examples: speech, music, sound effects + VIDEO: + description: Video data (sequences of images with optional audio) annotations: - state: liquid salt - examples: imidazolium salts - SUPERCRITICAL: - description: Supercritical fluids + examples: movies, recordings, animations + MULTIMODAL: + description: Data combining multiple modalities annotations: - state: supercritical - examples: scCO2, scH2O - AQUEOUS: - description: Water-based solvents + examples: image-text pairs, audio-visual data + TABULAR: + description: Structured tabular data annotations: - base: water - ORGANIC: - description: Organic solvents + examples: spreadsheets, databases, CSV files + TIME_SERIES: + description: Sequential temporal data annotations: - base: organic compounds - GREEN: - description: Environmentally friendly solvents + examples: sensor readings, stock prices, logs + GRAPH: + description: Graph-structured data with nodes and edges annotations: - property: low environmental impact - examples: water, ethanol, scCO2 - is_a: ReactionsSchemaEnum + examples: social networks, knowledge graphs, molecular structures + is_a: CroissantMlSchemaEnum annotations: - source_domain: chemistry - source_schema: reactions - ThermodynamicParameterEnum: - description: Thermodynamic parameters + source_domain: computing + source_schema: croissant_ml + DataCentersSchemaEnum: + description: Schema-level enum for data_centers in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/data_centers.yaml + DataCenterCoolingType: + title: Data Center Cooling Type + description: Types of cooling systems used in data center facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AIR_COOLING: + description: Traditional air-based cooling using computer room air conditioning (CRAC) or air handling units + close_mappings: + - brick:Computer_Room_Air_Conditioning + LIQUID_COOLING: + description: Cooling using liquid coolant circulated through heat exchangers near server components + IMMERSION_COOLING: + description: Cooling by submerging server hardware in a thermally conductive dielectric liquid + REAR_DOOR_HEAT_EXCHANGER: + description: Liquid-to-air heat exchanger mounted on the rear door of server racks + broad_mappings: + - brick:Heat_Exchanger + EVAPORATIVE_COOLING: + description: Cooling that uses water evaporation to reduce air temperature + related_mappings: + - brick:Cooling_Tower + GEOTHERMAL_COOLING: + description: Cooling that leverages underground temperature stability for heat dissipation + FREE_AIR_COOLING: + description: Cooling using outside ambient air when conditions permit, reducing mechanical cooling load + DIRECT_TO_CHIP_LIQUID_COOLING: + description: Liquid cooling with cold plates attached directly to processors and other heat-generating components + is_a: DataCentersSchemaEnum + annotations: + source_domain: computing + source_schema: data_centers + DataCenterTierLevel: + title: Data Center Tier Level + description: Uptime Institute data center tier classification levels defining infrastructure reliability + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TIER_I: + description: Basic capacity - single non-redundant distribution path with no redundancy + annotations: + uptime_guarantee: 99.671% + classification: Basic + TIER_II: + description: Redundant capacity components - single non-redundant distribution path with redundant components + annotations: + uptime_guarantee: 99.741% + classification: Redundant Components + TIER_III: + description: Concurrently maintainable - multiple independent distribution paths with redundant components + annotations: + uptime_guarantee: 99.982% + classification: Concurrently Maintainable + TIER_IV: + description: Fault tolerant - multiple independent distribution paths with redundant components, fault tolerant + annotations: + uptime_guarantee: 99.995% + classification: Fault Tolerant + is_a: DataCentersSchemaEnum + annotations: + source_domain: computing + source_schema: data_centers + FileFormatsSchemaEnum: + description: Schema-level enum for file_formats in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/file_formats.yaml + ImageFileFormatEnum: + title: Image File Format + description: Common image file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ENTHALPY: - description: Heat content (ΔH) + JPEG: + description: Joint Photographic Experts Group + title: JPEG + meaning: EDAM:format_3579 + aliases: + - JPG annotations: - symbol: ΔH - units: kJ/mol - ENTROPY: - description: Disorder (ΔS) + extension: .jpg, .jpeg + mime_type: image/jpeg + compression: lossy + PNG: + description: Portable Network Graphics + meaning: EDAM:format_3603 annotations: - symbol: ΔS - units: J/mol·K - GIBBS_ENERGY: - description: Free energy (ΔG) + extension: .png + mime_type: image/png + compression: lossless + GIF: + description: Graphics Interchange Format + meaning: EDAM:format_3467 annotations: - symbol: ΔG - units: kJ/mol - ACTIVATION_ENERGY: - description: Energy barrier (Ea) + extension: .gif + mime_type: image/gif + features: animation support + BMP: + description: Bitmap Image File + meaning: EDAM:format_3592 annotations: - symbol: Ea - units: kJ/mol - HEAT_CAPACITY: - description: Heat capacity (Cp) + extension: .bmp + mime_type: image/bmp + compression: uncompressed + TIFF: + description: Tagged Image File Format + meaning: EDAM:format_3591 annotations: - symbol: Cp - units: J/mol·K - INTERNAL_ENERGY: - description: Internal energy (ΔU) + extension: .tif, .tiff + mime_type: image/tiff + use: professional photography, scanning + SVG: + description: Scalable Vector Graphics + meaning: EDAM:format_3604 annotations: - symbol: ΔU - units: kJ/mol - is_a: ReactionsSchemaEnum - annotations: - source_domain: chemistry - source_schema: reactions - ClinicalDomainEnum: - description: Domain-level enum for clinical value sets - is_a: ValueSetEnum - abstract: true - NihDemographicsSchemaEnum: - description: Schema-level enum for nih_demographics in clinical - is_a: ClinicalDomainEnum - abstract: true + extension: .svg + mime_type: image/svg+xml + type: vector + WEBP: + description: WebP image format + annotations: + extension: .webp + mime_type: image/webp + compression: lossy and lossless + HEIC: + description: High Efficiency Image Container + annotations: + extension: .heic, .heif + mime_type: image/heic + use: Apple devices + RAW: + description: Raw image format + annotations: + extension: .raw, .cr2, .nef, .arw + type: unprocessed sensor data + ICO: + description: Icon file format + annotations: + extension: .ico + mime_type: image/x-icon + use: favicons, app icons + is_a: FileFormatsSchemaEnum annotations: - source_file: clinical/nih_demographics.yaml - RaceOMB1997Enum: - description: 'Race categories following OMB 1997 standards used by NIH and federal agencies. - - Respondents may select multiple races.' + source_domain: computing + source_schema: file_formats + DocumentFormatEnum: + title: Document Format + description: Document and text file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - AMERICAN_INDIAN_OR_ALASKA_NATIVE: - description: A person having origins in any of the original peoples of North and South America (including Central - America), and who maintains tribal affiliation or community attachment - meaning: NCIT:C41259 + PDF: + description: Portable Document Format + meaning: EDAM:format_3508 annotations: - omb_code: 1002-5 - ASIAN: - description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian - subcontinent - meaning: NCIT:C41260 + extension: .pdf + mime_type: application/pdf + creator: Adobe + DOCX: + description: Microsoft Word Open XML annotations: - omb_code: 2028-9 - includes: Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, Philippine Islands, Thailand, Vietnam - BLACK_OR_AFRICAN_AMERICAN: - description: A person having origins in any of the black racial groups of Africa - meaning: NCIT:C16352 + extension: .docx + mime_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document + application: Microsoft Word + DOC: + description: Microsoft Word legacy format annotations: - omb_code: 2054-5 - NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER: - description: A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands - meaning: NCIT:C41219 + extension: .doc + mime_type: application/msword + application: Microsoft Word (legacy) + TXT: + description: Plain text file + title: TXT + meaning: EDAM:format_1964 + aliases: + - plain text format (unformatted) annotations: - omb_code: 2076-8 - WHITE: - description: A person having origins in any of the original peoples of Europe, the Middle East, or North Africa - meaning: NCIT:C41261 + extension: .txt + mime_type: text/plain + encoding: UTF-8, ASCII + RTF: + description: Rich Text Format annotations: - omb_code: 2106-3 - MORE_THAN_ONE_RACE: - description: Person identifies with more than one race category - meaning: NCIT:C67109 - title: Multiracial + extension: .rtf + mime_type: application/rtf + ODT: + description: OpenDocument Text annotations: - note: Added after 1997 revision to allow multiple race reporting - UNKNOWN_OR_NOT_REPORTED: - description: Race not known, not reported, or declined to answer - meaning: NCIT:C17998 - title: Unknown + extension: .odt + mime_type: application/vnd.oasis.opendocument.text + application: LibreOffice, OpenOffice + LATEX: + description: LaTeX document + title: LATEX + meaning: EDAM:format_3817 + aliases: + - latex + - LaTeX annotations: - aliases: Unknown, Not Reported, Prefer not to answer - is_a: NihDemographicsSchemaEnum - annotations: - source_domain: clinical - source_schema: nih_demographics - EthnicityOMB1997Enum: - description: Ethnicity categories following OMB 1997 standards used by NIH and federal agencies - permissible_values: - HISPANIC_OR_LATINO: - description: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, - regardless of race - meaning: NCIT:C17459 + extension: .tex + mime_type: application/x-latex + use: scientific documents + MARKDOWN: + description: Markdown formatted text annotations: - omb_code: 2135-2 - NOT_HISPANIC_OR_LATINO: - description: A person not of Hispanic or Latino origin - meaning: NCIT:C41222 + extension: .md, .markdown + mime_type: text/markdown + HTML: + description: HyperText Markup Language + meaning: EDAM:format_2331 annotations: - omb_code: 2186-5 - UNKNOWN_OR_NOT_REPORTED: - description: Ethnicity not known, not reported, or declined to answer - meaning: NCIT:C17998 - title: Unknown + extension: .html, .htm + mime_type: text/html + XML: + description: Extensible Markup Language + meaning: EDAM:format_2332 annotations: - aliases: Unknown, Not Reported, Prefer not to answer - is_a: NihDemographicsSchemaEnum - annotations: - source_domain: clinical - source_schema: nih_demographics - BiologicalSexEnum: - description: 'Biological sex assigned at birth based on anatomical and physiological traits. - - Required by NIH as a biological variable in research.' - permissible_values: - MALE: - description: Male sex assigned at birth - meaning: PATO:0000384 - exact_mappings: - - NCIT:C20197 - - GSSO:000371 - FEMALE: - description: Female sex assigned at birth - meaning: PATO:0000383 - exact_mappings: - - NCIT:C16576 - - GSSO:000369 - INTERSEX: - description: Born with reproductive or sexual anatomy that doesn't fit typical definitions of male or female - meaning: NCIT:C45908 + extension: .xml + mime_type: application/xml + EPUB: + description: Electronic Publication annotations: - prevalence: 0.018% to 1.7% - note: May be assigned male or female at birth - UNKNOWN_OR_NOT_REPORTED: - description: Sex not known, not reported, or declined to answer - meaning: NCIT:C17998 - title: Unknown - is_a: NihDemographicsSchemaEnum + extension: .epub + mime_type: application/epub+zip + use: e-books + is_a: FileFormatsSchemaEnum annotations: - source_domain: clinical - source_schema: nih_demographics - AgeGroupEnum: - description: Standard age groups used in NIH clinical research, particularly NINDS CDEs + source_domain: computing + source_schema: file_formats + DataFormatEnum: + title: Data Format + description: Structured data file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - NEONATE: - description: Birth to 28 days - meaning: NCIT:C16731 - title: Newborn - annotations: - max_age_days: 28 - INFANT: - description: 29 days to less than 1 year - meaning: NCIT:C27956 + JSON: + description: JavaScript Object Notation + meaning: EDAM:format_3464 annotations: - min_age_days: 29 - max_age_years: 1 - YOUNG_PEDIATRIC: - description: 0 to 5 years (NINDS CDE definition) - meaning: NCIT:C39299 - title: Pediatric + extension: .json + mime_type: application/json + type: text-based + CSV: + description: Comma-Separated Values + title: CSV + meaning: EDAM:format_3752 annotations: - min_age_years: 0 - max_age_years: 5 - ninds_category: true - PEDIATRIC: - description: 6 to 12 years (NINDS CDE definition) - meaning: NCIT:C16423 - title: Child + extension: .csv + mime_type: text/csv + delimiter: comma + TSV: + description: Tab-Separated Values + meaning: EDAM:format_3475 annotations: - min_age_years: 6 - max_age_years: 12 - ninds_category: true - ADOLESCENT: - description: 13 to 17 years - meaning: NCIT:C27954 + extension: .tsv, .tab + mime_type: text/tab-separated-values + delimiter: tab + YAML: + description: YAML Ain't Markup Language + meaning: EDAM:format_3750 annotations: - min_age_years: 13 - max_age_years: 17 - YOUNG_ADULT: - description: 18 to 24 years - meaning: NCIT:C91107 + extension: .yaml, .yml + mime_type: application/x-yaml + TOML: + description: Tom's Obvious Minimal Language annotations: - min_age_years: 18 - max_age_years: 24 - ADULT: - description: 25 to 64 years - meaning: NCIT:C17600 + extension: .toml + mime_type: application/toml + use: configuration files + XLSX: + description: Microsoft Excel Open XML annotations: - min_age_years: 25 - max_age_years: 64 - OLDER_ADULT: - description: 65 years and older - meaning: NCIT:C16268 - title: Elderly + extension: .xlsx + mime_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet + XLS: + description: Microsoft Excel legacy format annotations: - min_age_years: 65 - aliases: Geriatric, Elderly, Senior - is_a: NihDemographicsSchemaEnum - annotations: - source_domain: clinical - source_schema: nih_demographics - ParticipantVitalStatusEnum: - description: Vital status of a research participant in clinical studies - permissible_values: - ALIVE: - description: Participant is living - meaning: NCIT:C37987 - exact_mappings: - - PATO:0001421 - DECEASED: - title: Dead - description: Participant is deceased - meaning: NCIT:C28554 - exact_mappings: - - PATO:0001422 - UNKNOWN: - description: Vital status unknown or lost to follow-up - meaning: NCIT:C17998 - is_a: NihDemographicsSchemaEnum - annotations: - source_domain: clinical - source_schema: nih_demographics - RecruitmentStatusEnum: - description: Clinical trial or study recruitment status per NIH/ClinicalTrials.gov - permissible_values: - NOT_YET_RECRUITING: - description: Study has not started recruiting participants - meaning: NCIT:C211610 - title: Not Yet Enrolling - RECRUITING: - description: Currently recruiting participants - meaning: NCIT:C142621 - title: Open To Enrollment - ENROLLING_BY_INVITATION: - description: Enrolling participants by invitation only - meaning: NCIT:C211611 - ACTIVE_NOT_RECRUITING: - description: Study ongoing but not recruiting new participants - meaning: NCIT:C211612 - title: Study Active, Not Enrolling - SUSPENDED: - description: Study temporarily stopped - meaning: NCIT:C211613 - title: Study Enrollment Suspended - TERMINATED: - description: Study stopped early and will not resume - meaning: NCIT:C70757 - title: Study Terminated - COMPLETED: - description: Study has ended normally - meaning: NCIT:C70756 - title: Completed Clinical Study - WITHDRAWN: - description: Study withdrawn before enrollment - meaning: NCIT:C70758 - title: Study Withdrawn - is_a: NihDemographicsSchemaEnum - annotations: - source_domain: clinical - source_schema: nih_demographics - StudyPhaseEnum: - description: Clinical trial phases per FDA and NIH definitions - permissible_values: - EARLY_PHASE_1: - description: Exploratory trials before traditional Phase 1 - meaning: NCIT:C54721 - title: Phase 0 Trial + extension: .xls + mime_type: application/vnd.ms-excel + ODS: + description: OpenDocument Spreadsheet annotations: - aliases: Phase 0 - PHASE_1: - title: Phase I Trial - description: Initial safety and dosage studies - meaning: NCIT:C15600 + extension: .ods + mime_type: application/vnd.oasis.opendocument.spreadsheet + PARQUET: + description: Apache Parquet columnar format annotations: - participants: 20-100 - PHASE_1_2: - title: Phase II/III Trial - description: Combined Phase 1 and Phase 2 trial - meaning: NCIT:C15694 - PHASE_2: - title: Phase II Trial - description: Efficacy and side effects studies - meaning: NCIT:C15601 + extension: .parquet + mime_type: application/parquet + type: columnar storage + AVRO: + description: Apache Avro data serialization annotations: - participants: 100-300 - PHASE_2_3: - title: Phase IIa Trial - description: Combined Phase 2 and Phase 3 trial - meaning: NCIT:C49686 - PHASE_3: - title: Phase III Trial - description: Efficacy comparison with standard treatment - meaning: NCIT:C15602 + extension: .avro + mime_type: application/avro + features: schema evolution + HDF5: + description: Hierarchical Data Format version 5 + meaning: EDAM:format_3590 annotations: - participants: 300-3000 - PHASE_4: - title: Phase IV Trial - description: Post-marketing surveillance - meaning: NCIT:C15603 + extension: .h5, .hdf5 + mime_type: application/x-hdf + use: scientific data + NETCDF: + description: Network Common Data Form + meaning: EDAM:format_3650 annotations: - note: After FDA approval - NOT_APPLICABLE: - description: Not a phased clinical trial - meaning: NCIT:C48660 + extension: .nc, .nc4 + mime_type: application/x-netcdf + use: array-oriented scientific data + SQLITE: + description: SQLite database annotations: - note: For observational studies, device trials, etc. - is_a: NihDemographicsSchemaEnum - annotations: - source_domain: clinical - source_schema: nih_demographics - PhenopacketsSchemaEnum: - description: Schema-level enum for phenopackets in clinical - is_a: ClinicalDomainEnum - abstract: true + extension: .db, .sqlite, .sqlite3 + mime_type: application/x-sqlite3 + type: embedded database + is_a: FileFormatsSchemaEnum annotations: - source_file: clinical/phenopackets.yaml - KaryotypicSexEnum: - description: Karyotypic sex of an individual based on chromosome composition + source_domain: computing + source_schema: file_formats + ArchiveFormatEnum: + title: Archive Format + description: Archive and compression formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - XX: - description: Female karyotype (46,XX) - meaning: NCIT:C45976 - title: XX Genotype + ZIP: + description: ZIP archive annotations: - chromosome_count: 46 - typical_phenotypic_sex: female - XY: - description: Male karyotype (46,XY) - meaning: NCIT:C45977 - title: XY Genotype + extension: .zip + mime_type: application/zip + compression: DEFLATE + TAR: + description: Tape Archive annotations: - chromosome_count: 46 - typical_phenotypic_sex: male - XO: - description: Turner syndrome karyotype (45,X) - meaning: NCIT:C176780 - title: 45,XO Karyotype + extension: .tar + mime_type: application/x-tar + compression: none (archive only) + GZIP: + description: GNU zip annotations: - chromosome_count: 45 - condition: Turner syndrome - XXY: - description: Klinefelter syndrome karyotype (47,XXY) - meaning: NCIT:C176784 - title: 47,XXY Karyotype + extension: .gz + mime_type: application/gzip + compression: DEFLATE + TAR_GZ: + description: Gzipped tar archive annotations: - chromosome_count: 47 - condition: Klinefelter syndrome - XXX: - description: Triple X syndrome karyotype (47,XXX) - meaning: NCIT:C176785 - title: 47,XXX Karyotype + extension: .tar.gz, .tgz + mime_type: application/x-gtar + compression: tar + gzip + BZIP2: + description: Bzip2 compression annotations: - chromosome_count: 47 - condition: Triple X syndrome - XXXY: - description: XXXY syndrome karyotype (48,XXXY) - meaning: NCIT:C176786 - title: 48,XXXY Karyotype + extension: .bz2 + mime_type: application/x-bzip2 + compression: Burrows-Wheeler + TAR_BZ2: + description: Bzip2 compressed tar archive annotations: - chromosome_count: 48 - condition: XXXY syndrome - XXXX: - description: Tetrasomy X karyotype (48,XXXX) - meaning: NCIT:C176787 - title: 48,XXXX Karyotype + extension: .tar.bz2, .tbz2 + mime_type: application/x-bzip2 + XZ: + description: XZ compression annotations: - chromosome_count: 48 - condition: Tetrasomy X - XXYY: - description: XXYY syndrome karyotype (48,XXYY) - meaning: NCIT:C89801 - title: XXYY Syndrome + extension: .xz + mime_type: application/x-xz + compression: LZMA2 + TAR_XZ: + description: XZ compressed tar archive annotations: - chromosome_count: 48 - condition: XXYY syndrome - XYY: - description: Jacob's syndrome karyotype (47,XYY) - meaning: NCIT:C176782 - title: 47,XYY Karyotype + extension: .tar.xz, .txz + mime_type: application/x-xz + SEVEN_ZIP: + description: 7-Zip archive annotations: - chromosome_count: 47 - condition: Jacob's syndrome - OTHER_KARYOTYPE: - description: Other karyotypic sex not listed + extension: .7z + mime_type: application/x-7z-compressed + compression: LZMA + RAR: + description: RAR archive annotations: - note: May include complex chromosomal arrangements - UNKNOWN_KARYOTYPE: - description: Karyotype not determined or unknown - meaning: NCIT:C17998 - title: Unknown - is_a: PhenopacketsSchemaEnum + extension: .rar + mime_type: application/vnd.rar + proprietary: 'true' + is_a: FileFormatsSchemaEnum annotations: - source_domain: clinical - source_schema: phenopackets - PhenotypicSexEnum: - description: 'Phenotypic sex of an individual based on observable characteristics. - - FHIR mapping: AdministrativeGender' + source_domain: computing + source_schema: file_formats + VideoFormatEnum: + title: Video Format + description: Video file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - MALE: - description: Male phenotypic sex - meaning: PATO:0000384 - exact_mappings: - - NCIT:C20197 - FEMALE: - description: Female phenotypic sex - meaning: PATO:0000383 - exact_mappings: - - NCIT:C16576 - OTHER_SEX: - description: Sex characteristics not clearly male or female - meaning: NCIT:C45908 - title: Intersex + MP4: + description: MPEG-4 Part 14 + annotations: + extension: .mp4 + mime_type: video/mp4 + codec: H.264, H.265 + AVI: + description: Audio Video Interleave + annotations: + extension: .avi + mime_type: video/x-msvideo + creator: Microsoft + MOV: + description: QuickTime Movie + annotations: + extension: .mov + mime_type: video/quicktime + creator: Apple + MKV: + description: Matroska Video + annotations: + extension: .mkv + mime_type: video/x-matroska + features: multiple tracks + WEBM: + description: WebM video + annotations: + extension: .webm + mime_type: video/webm + codec: VP8, VP9 + FLV: + description: Flash Video + annotations: + extension: .flv + mime_type: video/x-flv + status: legacy + WMV: + description: Windows Media Video + annotations: + extension: .wmv + mime_type: video/x-ms-wmv + creator: Microsoft + MPEG: + description: Moving Picture Experts Group annotations: - note: Includes differences of sex development (DSD) - UNKNOWN_SEX: - description: Sex not assessed or not available - meaning: NCIT:C17998 - title: Unknown - is_a: PhenopacketsSchemaEnum + extension: .mpeg, .mpg + mime_type: video/mpeg + is_a: FileFormatsSchemaEnum annotations: - source_domain: clinical - source_schema: phenopackets - AllelicStateEnum: - description: Allelic state/zygosity of a variant or genetic feature + source_domain: computing + source_schema: file_formats + AudioFormatEnum: + title: Audio Format + description: Audio file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - HETEROZYGOUS: - description: Different alleles at a locus - meaning: GENO:0000135 - annotations: - symbol: het - HOMOZYGOUS: - description: Identical alleles at a locus - meaning: GENO:0000136 - annotations: - symbol: hom - HEMIZYGOUS: - description: Only one allele present (e.g., X-linked in males) - meaning: GENO:0000134 + MP3: + description: MPEG Audio Layer 3 annotations: - symbol: hemi - note: Common for X-linked genes in males - COMPOUND_HETEROZYGOUS: - description: Two different heterozygous variants in same gene - meaning: GENO:0000402 + extension: .mp3 + mime_type: audio/mpeg + compression: lossy + WAV: + description: Waveform Audio File Format annotations: - symbol: comp het - HOMOZYGOUS_REFERENCE: - description: Two reference/wild-type alleles - meaning: GENO:0000036 - title: reference allele + extension: .wav + mime_type: audio/wav + compression: uncompressed + FLAC: + description: Free Lossless Audio Codec annotations: - symbol: hom ref - HOMOZYGOUS_ALTERNATE: - description: Two alternate/variant alleles - meaning: GENO:0000002 - title: variant allele + extension: .flac + mime_type: audio/flac + compression: lossless + AAC: + description: Advanced Audio Coding annotations: - symbol: hom alt - is_a: PhenopacketsSchemaEnum - annotations: - source_domain: clinical - source_schema: phenopackets - LateralityEnum: - description: Laterality/sidedness of a finding or anatomical structure - permissible_values: - RIGHT: - description: Right side - meaning: HP:0012834 + extension: .aac + mime_type: audio/aac + compression: lossy + OGG: + description: Ogg Vorbis annotations: - anatomical_term: dexter - LEFT: - description: Left side - meaning: HP:0012835 + extension: .ogg + mime_type: audio/ogg + compression: lossy + M4A: + description: MPEG-4 Audio annotations: - anatomical_term: sinister - BILATERAL: - description: Both sides - meaning: HP:0012832 + extension: .m4a + mime_type: audio/mp4 + compression: lossy or lossless + WMA: + description: Windows Media Audio annotations: - note: Affecting both left and right - UNILATERAL: - description: One side (unspecified which) - meaning: HP:0012833 + extension: .wma + mime_type: audio/x-ms-wma + creator: Microsoft + OPUS: + description: Opus Interactive Audio Codec annotations: - note: Affecting only one side - MIDLINE: - description: In the midline/center + extension: .opus + mime_type: audio/opus + use: streaming, VoIP + AIFF: + description: Audio Interchange File Format annotations: - note: Along the body's central axis - is_a: PhenopacketsSchemaEnum + extension: .aiff, .aif + mime_type: audio/aiff + creator: Apple + is_a: FileFormatsSchemaEnum annotations: - source_domain: clinical - source_schema: phenopackets - OnsetTimingEnum: - description: Timing of disease or phenotype onset relative to developmental stages + source_domain: computing + source_schema: file_formats + ProgrammingLanguageFileEnum: + title: Programming Language File + description: Programming language source file extensions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ANTENATAL_ONSET: - description: Before birth (prenatal) - meaning: HP:0030674 + PYTHON: + description: Python source file annotations: - period: Before birth - EMBRYONAL_ONSET: - description: During embryonic period (0-8 weeks) - meaning: HP:0011460 + extension: .py + mime_type: text/x-python + JAVASCRIPT: + description: JavaScript source file annotations: - period: 0-8 weeks gestation - FETAL_ONSET: - description: During fetal period (8 weeks to birth) - meaning: HP:0011461 + extension: .js + mime_type: text/javascript + TYPESCRIPT: + description: TypeScript source file annotations: - period: 8 weeks to birth - CONGENITAL_ONSET: - description: Present at birth - meaning: HP:0003577 + extension: .ts + mime_type: text/typescript + JAVA: + description: Java source file annotations: - period: At birth - NEONATAL_ONSET: - description: Within first 28 days of life - meaning: HP:0003623 + extension: .java + mime_type: text/x-java-source + C: + description: C source file annotations: - period: 0-28 days - INFANTILE_ONSET: - description: Between 28 days and 1 year - meaning: HP:0003593 + extension: .c + mime_type: text/x-c + CPP: + description: C++ source file annotations: - period: 28 days to 1 year - CHILDHOOD_ONSET: - description: Between 1 year and 16 years - meaning: HP:0011463 + extension: .cpp, .cc, .cxx + mime_type: text/x-c++ + C_SHARP: + description: C# source file annotations: - period: 1-16 years - JUVENILE_ONSET: - description: Between 5 years and 16 years - meaning: HP:0003621 + extension: .cs + mime_type: text/x-csharp + GO: + description: Go source file annotations: - period: 5-16 years - YOUNG_ADULT_ONSET: - description: Between 16 years and 40 years - meaning: HP:0011462 + extension: .go + mime_type: text/x-go + RUST: + description: Rust source file annotations: - period: 16-40 years - MIDDLE_AGE_ONSET: - description: Between 40 years and 60 years - meaning: HP:0003596 + extension: .rs + mime_type: text/x-rust + RUBY: + description: Ruby source file annotations: - period: 40-60 years - LATE_ONSET: - description: After 60 years - meaning: HP:0003584 + extension: .rb + mime_type: text/x-ruby + PHP: + description: PHP source file annotations: - period: '>60 years' - is_a: PhenopacketsSchemaEnum - annotations: - source_domain: clinical - source_schema: phenopackets - ACMGPathogenicityEnum: - description: ACMG/AMP variant pathogenicity classification for clinical genetics - permissible_values: - PATHOGENIC: - description: Pathogenic variant - meaning: NCIT:C168799 - title: Pathogenic Variant + extension: .php + mime_type: text/x-php + SWIFT: + description: Swift source file annotations: - abbreviation: P - clinical_significance: Disease-causing - LIKELY_PATHOGENIC: - description: Likely pathogenic variant - meaning: NCIT:C168800 - title: Likely Pathogenic Variant + extension: .swift + mime_type: text/x-swift + KOTLIN: + description: Kotlin source file annotations: - abbreviation: LP - probability: '>90% certain' - UNCERTAIN_SIGNIFICANCE: - description: Variant of uncertain significance - meaning: NCIT:C94187 - title: Variant of Unknown Significance + extension: .kt + mime_type: text/x-kotlin + R: + description: R source file annotations: - abbreviation: VUS - note: Insufficient evidence - LIKELY_BENIGN: - description: Likely benign variant - meaning: NCIT:C168801 - title: Variant Likely Benign + extension: .r, .R + mime_type: text/x-r + MATLAB: + description: MATLAB source file annotations: - abbreviation: LB - probability: '>90% certain benign' - BENIGN: - description: Benign variant - meaning: NCIT:C168802 - title: Variant Benign + extension: .m + mime_type: text/x-matlab + JULIA: + description: Julia source file annotations: - abbreviation: B - clinical_significance: Not disease-causing - is_a: PhenopacketsSchemaEnum + extension: .jl + mime_type: text/x-julia + SHELL: + description: Shell script + annotations: + extension: .sh, .bash + mime_type: text/x-shellscript + is_a: FileFormatsSchemaEnum annotations: - source_domain: clinical - source_schema: phenopackets - TherapeuticActionabilityEnum: - description: Clinical actionability of a genetic finding for treatment decisions + source_domain: computing + source_schema: file_formats + NetworkProtocolEnum: + title: Network Protocol + description: Network communication protocols + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ACTIONABLE: - description: Finding has direct therapeutic implications - meaning: NCIT:C206303 - title: Actionable Variation + HTTP: + description: Hypertext Transfer Protocol annotations: - note: Can guide treatment selection - NOT_ACTIONABLE: - description: No current therapeutic implications - meaning: NCIT:C206304 - title: Non-Actionable Variation + port: '80' + layer: application + version: 1.0, 1.1, 2, 3 + HTTPS: + description: HTTP Secure annotations: - note: No treatment changes indicated - UNKNOWN_ACTIONABILITY: - description: Therapeutic implications unclear - meaning: NCIT:C17998 - title: Unknown - is_a: PhenopacketsSchemaEnum - annotations: - source_domain: clinical - source_schema: phenopackets - InterpretationProgressEnum: - description: Progress status of clinical interpretation or diagnosis - permissible_values: - SOLVED: - description: Diagnosis achieved/case solved - meaning: NCIT:C20826 - title: Molecular Diagnosis + port: '443' + layer: application + encryption: TLS/SSL + FTP: + description: File Transfer Protocol annotations: - note: Molecular cause identified - UNSOLVED: - description: No diagnosis achieved - meaning: NCIT:C125009 - title: Clinical Interpretation + port: '21' + layer: application + use: file transfer + SFTP: + description: SSH File Transfer Protocol annotations: - note: Molecular cause not identified - IN_PROGRESS: - description: Analysis ongoing - meaning: NCIT:C25630 - title: Progress - COMPLETED: - description: Analysis completed - meaning: NCIT:C216251 - title: Procedure Completed + port: '22' + layer: application + encryption: SSH + SSH: + description: Secure Shell annotations: - note: May be solved or unsolved - UNKNOWN_PROGRESS: - description: Progress status unknown - meaning: NCIT:C17998 - title: Unknown - is_a: PhenopacketsSchemaEnum - annotations: - source_domain: clinical - source_schema: phenopackets - RegimenStatusEnum: - description: Status of a therapeutic regimen or treatment protocol - permissible_values: - NOT_STARTED: - description: Treatment not yet begun - meaning: NCIT:C53601 - title: Device Evaluation Anticipated But Not Yet Begun - STARTED: - description: Treatment initiated - meaning: NCIT:C165209 - title: Treatment Ongoing - COMPLETED: - description: Treatment finished as planned - meaning: NCIT:C105740 - title: Treatment Completed as Prescribed - DISCONTINUED_ADVERSE_EVENT: - description: Stopped due to adverse event - meaning: NCIT:C41331 - title: Adverse Event + port: '22' + layer: application + use: secure remote access + TELNET: + description: Telnet protocol annotations: - reason: Toxicity or side effects - DISCONTINUED_LACK_OF_EFFICACY: - description: Stopped due to lack of efficacy - meaning: NCIT:C49502 - title: Drug Withdrawn + port: '23' + layer: application + security: unencrypted + SMTP: + description: Simple Mail Transfer Protocol annotations: - reason: Treatment not effective - DISCONTINUED_PHYSICIAN_DECISION: - description: Stopped by physician decision - meaning: NCIT:C49502 - title: Drug Withdrawn - DISCONTINUED_PATIENT_DECISION: - description: Stopped by patient choice - meaning: NCIT:C48271 - title: Consent Withdrawn - UNKNOWN_STATUS: - description: Treatment status unknown - meaning: NCIT:C17998 - title: Unknown - is_a: PhenopacketsSchemaEnum - annotations: - source_domain: clinical - source_schema: phenopackets - DrugResponseEnum: - description: Response categories for drug treatment outcomes - permissible_values: - FAVORABLE: - description: Favorable response to treatment - meaning: NCIT:C123584 - title: Favorable Response + port: 25, 587 + layer: application + use: email sending + POP3: + description: Post Office Protocol version 3 annotations: - note: Better than expected response - UNFAVORABLE: - description: Unfavorable response to treatment - meaning: NCIT:C102561 + port: 110, 995 + layer: application + use: email retrieval + IMAP: + description: Internet Message Access Protocol annotations: - note: Worse than expected response - RESPONSIVE: - description: Responsive to treatment - meaning: NCIT:C165206 - title: Responsive Disease + port: 143, 993 + layer: application + use: email access + DNS: + description: Domain Name System annotations: - note: Shows expected response - RESISTANT: - description: Resistant to treatment - meaning: NCIT:C16523 - title: Drug Resistance Process + port: '53' + layer: application + use: name resolution + DHCP: + description: Dynamic Host Configuration Protocol annotations: - note: No response to treatment - PARTIALLY_RESPONSIVE: - description: Partial response to treatment - meaning: NCIT:C18213 - title: Stable Disease + port: 67, 68 + layer: application + use: IP assignment + TCP: + description: Transmission Control Protocol annotations: - note: Some but not complete response - UNKNOWN_RESPONSE: - description: Treatment response unknown - meaning: NCIT:C17998 - title: Unknown - is_a: PhenopacketsSchemaEnum - annotations: - source_domain: clinical - source_schema: phenopackets - ComputingDomainEnum: - description: Domain-level enum for computing value sets - is_a: ValueSetEnum - abstract: true - FileFormatsSchemaEnum: - description: Schema-level enum for file_formats in computing - is_a: ComputingDomainEnum - abstract: true - annotations: - source_file: computing/file_formats.yaml - ImageFileFormatEnum: - description: Common image file formats - permissible_values: - JPEG: - description: Joint Photographic Experts Group - title: JPEG - meaning: EDAM:format_3579 - aliases: - - JPG + layer: transport + type: connection-oriented + UDP: + description: User Datagram Protocol annotations: - extension: .jpg, .jpeg - mime_type: image/jpeg - compression: lossy - PNG: - description: Portable Network Graphics - meaning: EDAM:format_3603 + layer: transport + type: connectionless + WEBSOCKET: + description: WebSocket protocol annotations: - extension: .png - mime_type: image/png - compression: lossless - GIF: - description: Graphics Interchange Format - meaning: EDAM:format_3467 + port: 80, 443 + layer: application + use: bidirectional communication + MQTT: + description: Message Queuing Telemetry Transport annotations: - extension: .gif - mime_type: image/gif - features: animation support - BMP: - description: Bitmap Image File - meaning: EDAM:format_3592 + port: 1883, 8883 + layer: application + use: IoT messaging + AMQP: + description: Advanced Message Queuing Protocol annotations: - extension: .bmp - mime_type: image/bmp - compression: uncompressed - TIFF: - description: Tagged Image File Format - meaning: EDAM:format_3591 + port: '5672' + layer: application + use: message queuing + GRPC: + description: gRPC Remote Procedure Call + annotations: + transport: HTTP/2 + use: RPC framework + is_a: FileFormatsSchemaEnum + annotations: + source_domain: computing + source_schema: file_formats + GeospatialFormatsSchemaEnum: + description: Schema-level enum for geospatial_formats in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/geospatial_formats.yaml + GeospatialRasterFormat: + title: Geospatial Raster Format + description: File formats for raster (gridded) geospatial data including satellite imagery, digital elevation models, + and environmental model outputs. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GEOTIFF: + title: GeoTIFF + description: TIFF image format with embedded georeferencing information. Standard format for satellite imagery and + raster GIS data. annotations: extension: .tif, .tiff mime_type: image/tiff - use: professional photography, scanning - SVG: - description: Scalable Vector Graphics - meaning: EDAM:format_3604 + georeferencing: embedded + organization: OGC + COG: + title: Cloud Optimized GeoTIFF + description: GeoTIFF optimized for cloud storage with internal tiling and overviews for efficient partial reads over + HTTP. + annotations: + extension: .tif + mime_type: image/tiff + georeferencing: embedded + features: cloud-optimized, COG + NETCDF: + title: NetCDF + description: Network Common Data Form. Self-describing array-oriented scientific data format widely used for climate + and environmental data. + meaning: EDAM:format_3650 annotations: - extension: .svg - mime_type: image/svg+xml - type: vector - WEBP: - description: WebP image format + extension: .nc, .nc4 + mime_type: application/x-netcdf + organization: Unidata + conventions: CF (Climate and Forecast) + HDF5: + title: HDF5 + description: Hierarchical Data Format version 5. High-performance format for large scientific datasets including satellite + data. + meaning: EDAM:format_3590 annotations: - extension: .webp - mime_type: image/webp - compression: lossy and lossless - HEIC: - description: High Efficiency Image Container + extension: .h5, .hdf5, .he5 + mime_type: application/x-hdf + organization: HDF Group + HDF_EOS: + title: HDF-EOS + description: HDF format extended for NASA Earth Observing System data. Used for MODIS, ASTER, and other NASA satellite + products. + annotations: + extension: .hdf + organization: NASA + variants: HDF-EOS2, HDF-EOS5 + GRIB: + title: GRIB + description: GRIdded Binary format. Standard WMO format for meteorological data exchange. + annotations: + extension: .grib, .grb, .grib2 + organization: WMO + versions: GRIB1, GRIB2 + JPEG2000: + title: JPEG 2000 + description: Wavelet-based image compression format with georeferencing capability. Used for satellite imagery distribution. + annotations: + extension: .jp2, .j2k + mime_type: image/jp2 + features: lossy/lossless compression + MRF: + title: Meta Raster Format + description: NASA format optimized for cloud storage and fast random access to large imagery datasets. + annotations: + extension: .mrf + organization: NASA + features: cloud-optimized + ZARR: + title: Zarr + description: Chunked, compressed, N-dimensional array format designed for cloud storage. Growing adoption for climate + data. + annotations: + extension: .zarr (directory) + features: cloud-native, chunked + python: zarr library + ENVI: + title: ENVI + description: Format used by ENVI remote sensing software. Binary raster with separate header file. + annotations: + extension: .dat, .bsq, .bil, .bip + header: .hdr + ERDAS_IMAGINE: + title: ERDAS IMAGINE + description: Proprietary format for ERDAS IMAGINE software. Commonly used for satellite imagery processing. + annotations: + extension: .img + organization: Hexagon Geospatial + ASCII_GRID: + title: Esri ASCII Grid + description: Simple text-based raster format. Header followed by space-delimited cell values. + annotations: + extension: .asc + format: text + organization: Esri + is_a: GeospatialFormatsSchemaEnum + annotations: + source_domain: computing + source_schema: geospatial_formats + GeospatialVectorFormat: + title: Geospatial Vector Format + description: File formats for vector (point, line, polygon) geospatial data including geographic boundaries, infrastructure, + and sampling locations. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SHAPEFILE: + title: Esri Shapefile + description: Widely used vector format consisting of multiple files (.shp, .shx, .dbf). De facto standard despite + limitations. + annotations: + extension: .shp (+ .shx, .dbf, .prj) + organization: Esri + limitations: 2GB size limit, 10-char field names + GEOJSON: + title: GeoJSON + description: JSON-based format for encoding geographic data structures. Web-friendly and human-readable. + annotations: + extension: .geojson, .json + mime_type: application/geo+json + organization: IETF (RFC 7946) + crs: WGS84 only + GEOPACKAGE: + title: GeoPackage + description: OGC standard SQLite-based format for vector and raster data. Modern replacement for Shapefile. + annotations: + extension: .gpkg + organization: OGC + features: single file, no size limit, transactions + KML: + title: KML + description: Keyhole Markup Language. XML-based format for Google Earth and other applications. + annotations: + extension: .kml + mime_type: application/vnd.google-earth.kml+xml + organization: OGC (originally Google) + KMZ: + title: KMZ + description: Compressed KML file (ZIP archive containing KML and supporting files). + annotations: + extension: .kmz + mime_type: application/vnd.google-earth.kmz + compression: ZIP + GML: + title: GML + description: Geography Markup Language. OGC XML-based format for geographic features. + annotations: + extension: .gml + mime_type: application/gml+xml + organization: OGC + TOPOJSON: + title: TopoJSON + description: Extension of GeoJSON that encodes topology. Smaller file sizes through shared arc representation. + annotations: + extension: .topojson, .json + features: topology encoding, smaller files + FLATGEOBUF: + title: FlatGeobuf + description: Binary format optimized for fast streaming and random access. Cloud-native alternative to Shapefile. + annotations: + extension: .fgb + features: streaming, spatial index + GEOPARQUET: + title: GeoParquet + description: Apache Parquet with geospatial extensions. Columnar format optimized for analytics on large vector datasets. annotations: - extension: .heic, .heif - mime_type: image/heic - use: Apple devices + extension: .parquet + features: columnar, cloud-optimized + GEODATABASE: + title: Esri File Geodatabase + description: Esri proprietary format for storing multiple feature classes and tables in a folder structure. + annotations: + extension: .gdb (folder) + organization: Esri + features: multiple layers, domains, relationships + GPKG_VECTOR: + title: GeoPackage (Vector) + description: Vector data stored in GeoPackage format. Can coexist with raster data in same file. + annotations: + extension: .gpkg + organization: OGC + WKT: + title: Well-Known Text + description: Text markup language for representing vector geometry objects. + annotations: + format: text + organization: OGC + use: geometry representation + WKB: + title: Well-Known Binary + description: Binary equivalent of WKT for efficient storage and transfer. + annotations: + format: binary + organization: OGC + is_a: GeospatialFormatsSchemaEnum + annotations: + source_domain: computing + source_schema: geospatial_formats + MaturityLevelsSchemaEnum: + description: Schema-level enum for maturity_levels in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/maturity_levels.yaml + TechnologyReadinessLevel: + title: Technology Readiness Level (TRL) + description: NASA's Technology Readiness Level scale for assessing the maturity of technologies from basic research through + operational deployment + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + source: https://www.nasa.gov/directorates/heo/scan/engineering/technology/technology_readiness_level + conforms_to: ISO-16290:2013 + permissible_values: + TRL_1: + description: Basic principles observed and reported + title: TRL 1 - Basic Principles + TRL_2: + description: Technology concept and/or application formulated + title: TRL 2 - Technology Concept + TRL_3: + description: Analytical and experimental critical function and/or characteristic proof of concept + title: TRL 3 - Experimental Proof of Concept + TRL_4: + description: Component and/or breadboard validation in laboratory environment + title: TRL 4 - Lab Validation + TRL_5: + description: Component and/or breadboard validation in relevant environment + title: TRL 5 - Relevant Environment Validation + TRL_6: + description: System/subsystem model or prototype demonstration in a relevant environment + title: TRL 6 - Prototype Demonstration + TRL_7: + description: System prototype demonstration in an operational environment + title: TRL 7 - Operational Prototype + TRL_8: + description: Actual system completed and qualified through test and demonstration + title: TRL 8 - System Complete + TRL_9: + description: Actual system proven through successful mission operations + title: TRL 9 - Mission Proven + is_a: MaturityLevelsSchemaEnum + annotations: + source_domain: computing + source_schema: maturity_levels + SoftwareMaturityLevel: + title: Software Maturity Level + description: General software maturity assessment levels + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + permissible_values: + ALPHA: + description: Early development stage with basic functionality, may be unstable + title: Alpha + BETA: + description: Feature-complete but may contain bugs, ready for testing + title: Beta + RELEASE_CANDIDATE: + description: Stable version ready for final testing before release + title: Release Candidate + STABLE: + description: Production-ready with proven stability and reliability + title: Stable + MATURE: + description: Well-established with extensive usage and proven track record + title: Mature + LEGACY: + description: Older version still in use but no longer actively developed + title: Legacy + DEPRECATED: + description: No longer recommended for use, superseded by newer versions + title: Deprecated + OBSOLETE: + description: No longer supported or maintained + title: Obsolete + is_a: MaturityLevelsSchemaEnum + annotations: + source_domain: computing + source_schema: maturity_levels + CapabilityMaturityLevel: + title: Capability Maturity Model Integration (CMMI) Level + description: CMMI levels for assessing organizational process maturity in software development + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + source: https://cmmiinstitute.com/ + conforms_to: CMMI Version 2.0 + permissible_values: + LEVEL_1: + description: Initial - Processes are unpredictable, poorly controlled, and reactive + title: Level 1 - Initial + LEVEL_2: + description: Managed - Processes are characterized for projects and reactive + title: Level 2 - Managed + LEVEL_3: + description: Defined - Processes are characterized for the organization and proactive + title: Level 3 - Defined + LEVEL_4: + description: Quantitatively Managed - Processes are measured and controlled + title: Level 4 - Quantitatively Managed + LEVEL_5: + description: Optimizing - Focus on continuous process improvement + title: Level 5 - Optimizing + is_a: MaturityLevelsSchemaEnum + annotations: + source_domain: computing + source_schema: maturity_levels + StandardsMaturityLevel: + title: Standards Development Maturity Level + description: Maturity levels for standards and specifications + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + permissible_values: + DRAFT: + description: Initial draft under development + title: Draft + WORKING_DRAFT: + description: Work in progress by working group + title: Working Draft + COMMITTEE_DRAFT: + description: Draft reviewed by committee + title: Committee Draft + CANDIDATE_RECOMMENDATION: + description: Mature draft ready for implementation testing + title: Candidate Recommendation + PROPOSED_STANDARD: + description: Stable specification ready for adoption + title: Proposed Standard + STANDARD: + description: Approved and published standard + title: Standard + MATURE_STANDARD: + description: Well-established standard with wide adoption + title: Mature Standard + SUPERSEDED: + description: Replaced by a newer version + title: Superseded + WITHDRAWN: + description: No longer valid or recommended + title: Withdrawn + is_a: MaturityLevelsSchemaEnum + annotations: + source_domain: computing + source_schema: maturity_levels + ProjectMaturityLevel: + title: Project Maturity Level + description: General project development maturity assessment + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + permissible_values: + CONCEPT: + description: Initial idea or concept stage + title: Concept + PLANNING: + description: Project planning and design phase + title: Planning + DEVELOPMENT: + description: Active development in progress + title: Development + TESTING: + description: Testing and quality assurance phase + title: Testing + PILOT: + description: Limited deployment or pilot testing + title: Pilot + PRODUCTION: + description: Full production deployment + title: Production + MAINTENANCE: + description: Maintenance and support mode + title: Maintenance + END_OF_LIFE: + description: Project reaching end of lifecycle + title: End of Life + is_a: MaturityLevelsSchemaEnum + annotations: + source_domain: computing + source_schema: maturity_levels + DataMaturityLevel: + title: Data Maturity Level + description: Levels of data quality, governance, and organizational maturity + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + permissible_values: RAW: - description: Raw image format - annotations: - extension: .raw, .cr2, .nef, .arw - type: unprocessed sensor data - ICO: - description: Icon file format - annotations: - extension: .ico - mime_type: image/x-icon - use: favicons, app icons - is_a: FileFormatsSchemaEnum + description: Unprocessed, uncleaned data + title: Raw Data + CLEANED: + description: Basic cleaning and validation applied + title: Cleaned Data + STANDARDIZED: + description: Conforms to defined standards and formats + title: Standardized Data + INTEGRATED: + description: Combined with other data sources + title: Integrated Data + CURATED: + description: Expert-reviewed and validated + title: Curated Data + PUBLISHED: + description: Publicly available with proper metadata + title: Published Data + ARCHIVED: + description: Long-term preservation with access controls + title: Archived Data + is_a: MaturityLevelsSchemaEnum annotations: source_domain: computing - source_schema: file_formats - DocumentFormatEnum: - description: Document and text file formats + source_schema: maturity_levels + OpenSourceMaturityLevel: + title: Open Source Project Maturity + description: Maturity assessment for open source projects + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition permissible_values: - PDF: - description: Portable Document Format - meaning: EDAM:format_3508 - annotations: - extension: .pdf - mime_type: application/pdf - creator: Adobe - DOCX: - description: Microsoft Word Open XML - annotations: - extension: .docx - mime_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document - application: Microsoft Word - DOC: - description: Microsoft Word legacy format - annotations: - extension: .doc - mime_type: application/msword - application: Microsoft Word (legacy) - TXT: - description: Plain text file - title: TXT - meaning: EDAM:format_1964 - aliases: - - plain text format (unformatted) - annotations: - extension: .txt - mime_type: text/plain - encoding: UTF-8, ASCII - RTF: - description: Rich Text Format - annotations: - extension: .rtf - mime_type: application/rtf - ODT: - description: OpenDocument Text - annotations: - extension: .odt - mime_type: application/vnd.oasis.opendocument.text - application: LibreOffice, OpenOffice - LATEX: - description: LaTeX document - title: LATEX - meaning: EDAM:format_3817 - aliases: - - latex - - LaTeX - annotations: - extension: .tex - mime_type: application/x-latex - use: scientific documents - MARKDOWN: - description: Markdown formatted text - annotations: - extension: .md, .markdown - mime_type: text/markdown - HTML: - description: HyperText Markup Language - meaning: EDAM:format_2331 - annotations: - extension: .html, .htm - mime_type: text/html - XML: - description: Extensible Markup Language - meaning: EDAM:format_2332 - annotations: - extension: .xml - mime_type: application/xml - EPUB: - description: Electronic Publication - annotations: - extension: .epub - mime_type: application/epub+zip - use: e-books - is_a: FileFormatsSchemaEnum + EXPERIMENTAL: + description: Early experimental project + title: Experimental + EMERGING: + description: Gaining traction and contributors + title: Emerging + ESTABLISHED: + description: Stable with active community + title: Established + MATURE: + description: Well-established with proven governance + title: Mature + DECLINING: + description: Decreasing activity and maintenance + title: Declining + ARCHIVED: + description: No longer actively maintained + title: Archived + is_a: MaturityLevelsSchemaEnum + annotations: + source_domain: computing + source_schema: maturity_levels + MicroelectronicsSchemaEnum: + description: Schema-level enum for microelectronics in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/microelectronics.yaml + SemiconductorMaterialType: + title: Semiconductor Material Type + description: Types of semiconductor materials used in microelectronics fabrication + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SILICON: + description: Elemental silicon, the most widely used semiconductor material + title: silicon atom + meaning: CHEBI:27573 + GALLIUM_ARSENIDE: + description: Gallium arsenide (GaAs) compound semiconductor for high-frequency applications + SILICON_CARBIDE: + description: Silicon carbide (SiC) wide-bandgap semiconductor for high-power applications + title: silicon carbide + meaning: CHEBI:29390 + GALLIUM_NITRIDE: + description: Gallium nitride (GaN) wide-bandgap semiconductor for power electronics and LEDs + INDIUM_PHOSPHIDE: + description: Indium phosphide (InP) compound semiconductor for optoelectronics and fiber communications + title: Indium phosphide + meaning: CHEBI:82281 + GERMANIUM: + description: Elemental germanium semiconductor used in high-speed transistors and detectors + title: germanium atom + meaning: CHEBI:30441 + SILICON_GERMANIUM: + description: Silicon-germanium (SiGe) alloy semiconductor for heterojunction bipolar transistors + DIAMOND: + description: Diamond as an ultra-wide-bandgap semiconductor for extreme environment electronics + title: diamond + meaning: CHEBI:33417 + is_a: MicroelectronicsSchemaEnum + annotations: + source_domain: computing + source_schema: microelectronics + ChipFabricationNodeType: + title: Chip Fabrication Node Type + description: Semiconductor fabrication process node sizes defining transistor feature dimensions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NODE_3NM: + description: 3 nanometer process node + annotations: + feature_size: 3nm + NODE_5NM: + description: 5 nanometer process node + annotations: + feature_size: 5nm + NODE_7NM: + description: 7 nanometer process node + annotations: + feature_size: 7nm + NODE_10NM: + description: 10 nanometer process node + annotations: + feature_size: 10nm + NODE_14NM: + description: 14 nanometer process node + annotations: + feature_size: 14nm + NODE_22NM: + description: 22 nanometer process node + annotations: + feature_size: 22nm + NODE_28NM: + description: 28 nanometer process node + annotations: + feature_size: 28nm + NODE_45NM: + description: 45 nanometer process node + annotations: + feature_size: 45nm + MATURE_NODE: + description: Mature fabrication node (65nm and larger) for legacy and specialty applications + annotations: + feature_size: 65nm+ + is_a: MicroelectronicsSchemaEnum + annotations: + source_domain: computing + source_schema: microelectronics + MimeTypesSchemaEnum: + description: Schema-level enum for mime_types in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/mime_types.yaml + MimeType: + title: Mime Type + description: Common MIME types for various file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + APPLICATION_JSON: + description: JSON format + meaning: iana:application/json + APPLICATION_XML: + description: XML format + meaning: iana:application/xml + APPLICATION_PDF: + description: Adobe Portable Document Format + meaning: iana:application/pdf + APPLICATION_ZIP: + description: ZIP archive + meaning: iana:application/zip + APPLICATION_GZIP: + description: GZIP compressed archive + meaning: iana:application/gzip + APPLICATION_OCTET_STREAM: + description: Binary data + meaning: iana:application/octet-stream + APPLICATION_X_WWW_FORM_URLENCODED: + description: Form data encoded + meaning: iana:application/x-www-form-urlencoded + APPLICATION_VND_MS_EXCEL: + description: Microsoft Excel + meaning: iana:application/vnd.ms-excel + APPLICATION_VND_OPENXMLFORMATS_SPREADSHEET: + description: Microsoft Excel (OpenXML) + meaning: iana:application/vnd.openxmlformats-officedocument.spreadsheetml.sheet + APPLICATION_VND_MS_POWERPOINT: + description: Microsoft PowerPoint + meaning: iana:application/vnd.ms-powerpoint + APPLICATION_MSWORD: + description: Microsoft Word + meaning: iana:application/msword + APPLICATION_VND_OPENXMLFORMATS_DOCUMENT: + description: Microsoft Word (OpenXML) + meaning: iana:application/vnd.openxmlformats-officedocument.wordprocessingml.document + APPLICATION_JAVASCRIPT: + description: JavaScript + meaning: iana:application/javascript + APPLICATION_TYPESCRIPT: + description: TypeScript source code + meaning: iana:application/typescript + APPLICATION_SQL: + description: SQL database format + meaning: iana:application/sql + APPLICATION_GRAPHQL: + description: GraphQL query language + meaning: iana:application/graphql + APPLICATION_LD_JSON: + description: JSON-LD format + meaning: iana:application/ld+json + APPLICATION_N_QUADS: + description: N-Quads RDF serialization format + meaning: iana:application/n-quads + APPLICATION_N_TRIPLES: + description: N-Triples RDF serialization format + meaning: iana:application/n-triples + APPLICATION_RDF_XML: + description: RDF/XML serialization format + meaning: iana:application/rdf+xml + APPLICATION_SPARQL_RESULTS_JSON: + description: SPARQL 1.1 Query Results JSON format + meaning: iana:application/sparql-results+json + APPLICATION_SPARQL_RESULTS_XML: + description: SPARQL 1.1 Query Results XML format + meaning: iana:application/sparql-results+xml + APPLICATION_TRIG: + description: TriG RDF serialization format + meaning: iana:application/trig + APPLICATION_WASM: + description: WebAssembly binary format + meaning: iana:application/wasm + TEXT_PLAIN: + description: Plain text + meaning: iana:text/plain + TEXT_HTML: + description: HTML document + meaning: iana:text/html + TEXT_CSS: + description: Cascading Style Sheets + meaning: iana:text/css + TEXT_CSV: + description: Comma-separated values + meaning: iana:text/csv + TEXT_MARKDOWN: + description: Markdown format + meaning: iana:text/markdown + TEXT_YAML: + description: YAML format + meaning: iana:text/yaml + TEXT_X_PYTHON: + description: Python source code + meaning: iana:text/x-python + TEXT_X_JAVA: + description: Java source code + meaning: iana:text/x-java-source + TEXT_X_C: + description: C source code + meaning: iana:text/x-c + TEXT_X_CPP: + description: C++ source code + meaning: iana:text/x-c++ + TEXT_X_CSHARP: + description: C# source code + meaning: iana:text/x-csharp + TEXT_X_GO: + description: Go source code + meaning: iana:text/x-go + TEXT_X_RUST: + description: Rust source code + meaning: iana:text/x-rust + TEXT_X_RUBY: + description: Ruby source code + meaning: iana:text/x-ruby + TEXT_X_SHELLSCRIPT: + description: Shell script + meaning: iana:text/x-shellscript + IMAGE_JPEG: + description: JPEG image + meaning: iana:image/jpeg + IMAGE_PNG: + description: PNG image + meaning: iana:image/png + IMAGE_GIF: + description: GIF image + meaning: iana:image/gif + IMAGE_SVG_XML: + description: SVG vector image + meaning: iana:image/svg+xml + IMAGE_WEBP: + description: WebP image + meaning: iana:image/webp + IMAGE_BMP: + description: Bitmap image + meaning: iana:image/bmp + IMAGE_ICO: + description: Icon format + meaning: iana:image/vnd.microsoft.icon + IMAGE_TIFF: + description: TIFF image + meaning: iana:image/tiff + IMAGE_AVIF: + description: AVIF image format + meaning: iana:image/avif + AUDIO_MPEG: + description: MP3 audio + meaning: iana:audio/mpeg + AUDIO_WAV: + description: WAV audio + meaning: iana:audio/wav + AUDIO_OGG: + description: OGG audio + meaning: iana:audio/ogg + AUDIO_WEBM: + description: WebM audio + meaning: iana:audio/webm + AUDIO_AAC: + description: AAC audio + meaning: iana:audio/aac + VIDEO_MP4: + description: MP4 video + meaning: iana:video/mp4 + VIDEO_MPEG: + description: MPEG video + meaning: iana:video/mpeg + VIDEO_WEBM: + description: WebM video + meaning: iana:video/webm + VIDEO_OGG: + description: OGG video + meaning: iana:video/ogg + VIDEO_QUICKTIME: + description: QuickTime video + meaning: iana:video/quicktime + VIDEO_AVI: + description: AVI video + meaning: iana:video/x-msvideo + FONT_WOFF: + description: Web Open Font Format + meaning: iana:font/woff + FONT_WOFF2: + description: Web Open Font Format 2 + meaning: iana:font/woff2 + FONT_TTF: + description: TrueType Font + meaning: iana:font/ttf + FONT_OTF: + description: OpenType Font + meaning: iana:font/otf + MULTIPART_FORM_DATA: + description: Form data with file upload + meaning: iana:multipart/form-data + MULTIPART_MIXED: + description: Mixed multipart message + meaning: iana:multipart/mixed + is_a: MimeTypesSchemaEnum annotations: source_domain: computing - source_schema: file_formats - DataFormatEnum: - description: Structured data file formats + source_schema: mime_types + MimeTypeCategory: + title: Mime Type Category + description: Categories of MIME types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - JSON: - description: JavaScript Object Notation - meaning: EDAM:format_3464 - annotations: - extension: .json - mime_type: application/json - type: text-based - CSV: - description: Comma-Separated Values - title: CSV - meaning: EDAM:format_3752 - annotations: - extension: .csv - mime_type: text/csv - delimiter: comma - TSV: - description: Tab-Separated Values - meaning: EDAM:format_3475 - annotations: - extension: .tsv, .tab - mime_type: text/tab-separated-values - delimiter: tab - YAML: - description: YAML Ain't Markup Language - meaning: EDAM:format_3750 - annotations: - extension: .yaml, .yml - mime_type: application/x-yaml - TOML: - description: Tom's Obvious Minimal Language - annotations: - extension: .toml - mime_type: application/toml - use: configuration files - XLSX: - description: Microsoft Excel Open XML - annotations: - extension: .xlsx - mime_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet - XLS: - description: Microsoft Excel legacy format - annotations: - extension: .xls - mime_type: application/vnd.ms-excel - ODS: - description: OpenDocument Spreadsheet - annotations: - extension: .ods - mime_type: application/vnd.oasis.opendocument.spreadsheet - PARQUET: - description: Apache Parquet columnar format - annotations: - extension: .parquet - mime_type: application/parquet - type: columnar storage - AVRO: - description: Apache Avro data serialization - annotations: - extension: .avro - mime_type: application/avro - features: schema evolution - HDF5: - description: Hierarchical Data Format version 5 - meaning: EDAM:format_3590 - annotations: - extension: .h5, .hdf5 - mime_type: application/x-hdf - use: scientific data - NETCDF: - description: Network Common Data Form - meaning: EDAM:format_3650 - annotations: - extension: .nc, .nc4 - mime_type: application/x-netcdf - use: array-oriented scientific data - SQLITE: - description: SQLite database - annotations: - extension: .db, .sqlite, .sqlite3 - mime_type: application/x-sqlite3 - type: embedded database - is_a: FileFormatsSchemaEnum + APPLICATION: + description: Application data + TEXT: + description: Text documents + IMAGE: + description: Image files + AUDIO: + description: Audio files + VIDEO: + description: Video files + FONT: + description: Font files + MULTIPART: + description: Multipart messages + MESSAGE: + description: Message formats + MODEL: + description: 3D models and similar + is_a: MimeTypesSchemaEnum annotations: source_domain: computing - source_schema: file_formats - ArchiveFormatEnum: - description: Archive and compression formats + source_schema: mime_types + TextCharset: + title: Text Charset + description: Character encodings for text content + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ZIP: - description: ZIP archive - annotations: - extension: .zip - mime_type: application/zip - compression: DEFLATE - TAR: - description: Tape Archive - annotations: - extension: .tar - mime_type: application/x-tar - compression: none (archive only) - GZIP: - description: GNU zip - annotations: - extension: .gz - mime_type: application/gzip - compression: DEFLATE - TAR_GZ: - description: Gzipped tar archive - annotations: - extension: .tar.gz, .tgz - mime_type: application/x-gtar - compression: tar + gzip - BZIP2: - description: Bzip2 compression - annotations: - extension: .bz2 - mime_type: application/x-bzip2 - compression: Burrows-Wheeler - TAR_BZ2: - description: Bzip2 compressed tar archive - annotations: - extension: .tar.bz2, .tbz2 - mime_type: application/x-bzip2 - XZ: - description: XZ compression - annotations: - extension: .xz - mime_type: application/x-xz - compression: LZMA2 - TAR_XZ: - description: XZ compressed tar archive - annotations: - extension: .tar.xz, .txz - mime_type: application/x-xz - SEVEN_ZIP: - description: 7-Zip archive - annotations: - extension: .7z - mime_type: application/x-7z-compressed - compression: LZMA - RAR: - description: RAR archive - annotations: - extension: .rar - mime_type: application/vnd.rar - proprietary: 'true' - is_a: FileFormatsSchemaEnum + UTF_8: + description: UTF-8 Unicode encoding + UTF_16: + description: UTF-16 Unicode encoding + UTF_32: + description: UTF-32 Unicode encoding + ASCII: + description: ASCII encoding + ISO_8859_1: + description: ISO-8859-1 (Latin-1) encoding + ISO_8859_2: + description: ISO-8859-2 (Latin-2) encoding + WINDOWS_1252: + description: Windows-1252 encoding + GB2312: + description: Simplified Chinese encoding + SHIFT_JIS: + description: Japanese encoding + EUC_KR: + description: Korean encoding + BIG5: + description: Traditional Chinese encoding + is_a: MimeTypesSchemaEnum + annotations: + source_domain: computing + source_schema: mime_types + CompressionType: + title: Compression Type + description: Compression types used with Content-Encoding + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GZIP: + description: GZIP compression + DEFLATE: + description: DEFLATE compression + BR: + description: Brotli compression + COMPRESS: + description: Unix compress + IDENTITY: + description: No compression + is_a: MimeTypesSchemaEnum annotations: source_domain: computing - source_schema: file_formats - VideoFormatEnum: - description: Video file formats + source_schema: mime_types + OntologiesSchemaEnum: + description: Schema-level enum for ontologies in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/ontologies.yaml + OWLProfileEnum: + title: OWL Profile + description: OWL 2 profiles that provide different tradeoffs between expressiveness and computational complexity + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + OWL_2_EL: + description: OWL 2 EL (Existential Language) - optimized for applications using very large ontologies with basic relationships. + Provides polynomial time reasoning. + title: OWL 2 EL + see_also: + - https://www.w3.org/TR/owl2-profiles/#OWL_2_EL + annotations: + complexity: polynomial time + use_case: large biomedical ontologies, SNOMED CT + OWL_2_QL: + description: OWL 2 QL (Query Language) - optimized for query answering over large data repositories. Based on DL-Lite + family. + title: OWL 2 QL + see_also: + - https://www.w3.org/TR/owl2-profiles/#OWL_2_QL + annotations: + complexity: LogSpace data complexity + use_case: ontology-based data access, database integration + OWL_2_RL: + description: OWL 2 RL (Rule Language) - optimized for rule-based reasoning and can be implemented using rule engines. + Compatible with RDF Schema. + title: OWL 2 RL + see_also: + - https://www.w3.org/TR/owl2-profiles/#OWL_2_RL + annotations: + complexity: polynomial time + use_case: business rules, policy systems + OWL_2_DL: + description: OWL 2 DL (Description Logic) - full expressiveness while maintaining computational completeness and decidability. + Maximum expressiveness without sacrificing decidability. + title: OWL 2 DL + see_also: + - https://www.w3.org/TR/owl2-syntax/ + annotations: + complexity: NExpTime + use_case: general purpose ontologies requiring high expressiveness + OWL_2_FULL: + description: OWL 2 Full - maximum expressiveness with no restrictions, but reasoning is undecidable. Allows full RDF + capabilities. + title: OWL 2 Full + see_also: + - https://www.w3.org/TR/owl2-syntax/ + annotations: + complexity: undecidable + use_case: maximum flexibility, no guaranteed reasoning + is_a: OntologiesSchemaEnum + annotations: + source_domain: computing + source_schema: ontologies + QuantumSchemaEnum: + description: Schema-level enum for quantum in computing + is_a: ComputingDomainEnum + abstract: true + annotations: + source_file: computing/quantum.yaml + QubitType: + title: Qubit Type + description: Types of physical qubit implementations used in quantum computing hardware + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - MP4: - description: MPEG-4 Part 14 - annotations: - extension: .mp4 - mime_type: video/mp4 - codec: H.264, H.265 - AVI: - description: Audio Video Interleave - annotations: - extension: .avi - mime_type: video/x-msvideo - creator: Microsoft - MOV: - description: QuickTime Movie - annotations: - extension: .mov - mime_type: video/quicktime - creator: Apple - MKV: - description: Matroska Video - annotations: - extension: .mkv - mime_type: video/x-matroska - features: multiple tracks - WEBM: - description: WebM video - annotations: - extension: .webm - mime_type: video/webm - codec: VP8, VP9 - FLV: - description: Flash Video - annotations: - extension: .flv - mime_type: video/x-flv - status: legacy - WMV: - description: Windows Media Video - annotations: - extension: .wmv - mime_type: video/x-ms-wmv - creator: Microsoft - MPEG: - description: Moving Picture Experts Group - annotations: - extension: .mpeg, .mpg - mime_type: video/mpeg - is_a: FileFormatsSchemaEnum + SUPERCONDUCTING: + description: Superconducting qubit using Josephson junctions cooled to millikelvin temperatures + TRAPPED_ION: + description: Qubit encoded in electronic states of trapped atomic ions + PHOTONIC: + description: Qubit encoded in quantum states of photons + title: photon + meaning: CHEBI:30212 + TOPOLOGICAL: + description: Qubit based on topological states of matter resistant to local perturbations + NEUTRAL_ATOM: + description: Qubit encoded in energy levels of electrically neutral atoms held in optical traps + QUANTUM_DOT: + description: Qubit using semiconductor quantum dot nanostructures + title: Quantum Dot + meaning: NCIT:C62378 + NITROGEN_VACANCY_CENTER: + description: Qubit based on nitrogen-vacancy defect centers in diamond lattice + SPIN_QUBIT: + description: Qubit encoded in the spin state of an electron or nucleus in a semiconductor + is_a: QuantumSchemaEnum annotations: source_domain: computing - source_schema: file_formats - AudioFormatEnum: - description: Audio file formats + source_schema: quantum + QuantumAlgorithmCategoryType: + title: Quantum Algorithm Category Type + description: Categories of quantum algorithms by their primary application domain + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + OPTIMIZATION: + description: Quantum algorithms for combinatorial and continuous optimization problems + SIMULATION: + description: Quantum algorithms for simulating physical and chemical systems + MACHINE_LEARNING: + description: Quantum algorithms for machine learning and pattern recognition tasks + CRYPTOGRAPHY: + description: Quantum algorithms for cryptographic applications including key distribution and code breaking + LINEAR_ALGEBRA: + description: Quantum algorithms for linear algebra problems such as solving linear systems + SEARCH: + description: Quantum search algorithms for unstructured database search + ERROR_CORRECTION: + description: Quantum error correction codes and fault-tolerant computation protocols + VARIATIONAL: + description: Hybrid quantum-classical variational algorithms for near-term quantum devices + is_a: QuantumSchemaEnum + annotations: + source_domain: computing + source_schema: quantum + DataDomainEnum: + description: Domain-level enum for data value sets + is_a: ValueSetEnum + abstract: true + DataAbsentReasonSchemaEnum: + description: Schema-level enum for data_absent_reason in data + is_a: DataDomainEnum + abstract: true + annotations: + source_file: data/data_absent_reason.yaml + DataAbsentEnum: + title: Data Absent + description: Used to specify why the normally expected content of the data element is missing. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - MP3: - description: MPEG Audio Layer 3 + unknown: + description: The value is expected to exist but is not known. + meaning: fhir_data_absent_reason:unknown + title: Unknown + asked-unknown: + description: The source was asked but does not know the value. + meaning: fhir_data_absent_reason:asked-unknown + is_a: unknown + title: Asked But Unknown + temp-unknown: + description: There is reason to expect (from the workflow) that the value may become known. + meaning: fhir_data_absent_reason:temp-unknown + is_a: unknown + title: Temporarily Unknown + not-asked: + description: The workflow didn't lead to this value being known. + meaning: fhir_data_absent_reason:not-asked + is_a: unknown + title: Not Asked + asked-declined: + description: The source was asked but declined to answer. + meaning: fhir_data_absent_reason:asked-declined + is_a: unknown + title: Asked But Declined + masked: + description: The information is not available due to security, privacy or related reasons. + meaning: fhir_data_absent_reason:masked + title: Masked + not-applicable: + description: There is no proper value for this element (e.g. last menstrual period for a male). + meaning: fhir_data_absent_reason:not-applicable + title: Not Applicable + unsupported: + description: The source system wasn't capable of supporting this element. + meaning: fhir_data_absent_reason:unsupported + title: Unsupported + as-text: + description: The content of the data is represented in the resource narrative. + meaning: fhir_data_absent_reason:as-text + title: As Text + error: + description: Some system or workflow process error means that the information is not available. + meaning: fhir_data_absent_reason:error + title: Error + not-a-number: + description: The numeric value is undefined or unrepresentable due to a floating point processing error. + meaning: fhir_data_absent_reason:not-a-number + is_a: error + title: Not a Number (NaN) + negative-infinity: + description: The numeric value is excessively low and unrepresentable due to a floating point processing error. + meaning: fhir_data_absent_reason:negative-infinity + is_a: error + title: Negative Infinity (NINF) + positive-infinity: + description: The numeric value is excessively high and unrepresentable due to a floating point processing error. + meaning: fhir_data_absent_reason:positive-infinity + is_a: error + title: Positive Infinity (PINF) + not-performed: + description: The value is not available because the observation procedure (test, etc.) was not performed. + meaning: fhir_data_absent_reason:not-performed + title: Not Performed + not-permitted: + description: The value is not permitted in this context (e.g. due to profiles, or the base data types). + meaning: fhir_data_absent_reason:not-permitted + title: Not Permitted + is_a: DataAbsentReasonSchemaEnum + annotations: + source_domain: data + source_schema: data_absent_reason + DataUseSchemaEnum: + description: Schema-level enum for data_use in data + is_a: DataDomainEnum + abstract: true + annotations: + source_file: data/data_use.yaml + DataUsePermissionEnum: + title: Data Use Permissions + description: Primary data use permissions from the GA4GH Data Use Ontology (DUO) indicating what research purposes data + can be used for. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://github.com/EBISPOT/DUO + - https://www.ga4gh.org/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GRU: + description: General research use - allowed for any research purpose including health/medical/biomedical, fundamental + biology, population origins, statistical methods development, and social-sciences research. + meaning: DUO:0000042 + aliases: + - general research use + HMB: + description: Health/medical/biomedical research only - does not include study of population origins or ancestry. + meaning: DUO:0000006 + aliases: + - health or medical or biomedical research + DS: + description: Disease-specific research - use allowed only for research related to specified disease(s). Should be + coupled with disease ontology term. + meaning: DUO:0000007 + aliases: + - disease specific research + NO_RESTRICTION: + description: No restriction on use of the data. + meaning: DUO:0000004 + aliases: + - no restriction + is_a: DataUseSchemaEnum + annotations: + source_domain: data + source_schema: data_use + DataUseModifierEnum: + title: Data Use Modifiers + description: Additional conditions and modifiers for data use from the GA4GH Data Use Ontology (DUO). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://github.com/EBISPOT/DUO + - https://www.ga4gh.org/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NPUNCU: + description: Not-for-profit use only - use limited to not-for-profit organizations and non-commercial use. + meaning: DUO:0000018 + aliases: + - not for profit, non commercial use only + NPO: + description: Use limited to not-for-profit organizations only. + meaning: DUO:0000045 + aliases: + - not for profit organisation use only + NCU: + description: Non-commercial use only - data can be used by commercial organizations for research but not commercial + purposes. + meaning: DUO:0000046 + aliases: + - non-commercial use only + IRB: + description: Ethics approval required - requestor must provide documentation of local IRB/ERB approval. + meaning: DUO:0000021 + aliases: + - ethics approval required + NRES: + description: No restriction on data use. + meaning: DUO:0000004 + aliases: + - no restriction + NMDS: + description: No general methods research - does not allow methods development. + meaning: DUO:0000015 + aliases: + - no general methods research + RS: + description: Research-specific restrictions apply. + meaning: DUO:0000012 + aliases: + - research specific restrictions + is_a: DataUseSchemaEnum + annotations: + source_domain: data + source_schema: data_use + DataCatalogDomainEnum: + description: Domain-level enum for data_catalog value sets + is_a: ValueSetEnum + abstract: true + AccessSchemaEnum: + description: Schema-level enum for access in data_catalog + is_a: DataCatalogDomainEnum + abstract: true + annotations: + source_file: data_catalog/access.yaml + AccessRights: + title: Access Rights + description: 'Information about who can access the resource or an indication of + + its security status. Based on EU Vocabularies Access Rights authority list + + and DCAT recommendations. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/access-right + - https://www.w3.org/TR/vocab-dcat-3/#Property:resource_access_rights + permissible_values: + PUBLIC: + description: 'The resource is publicly accessible to everyone without + + restrictions. + + ' + meaning: euvoc:access-right/PUBLIC + aliases: + - Open + - Unrestricted annotations: - extension: .mp3 - mime_type: audio/mpeg - compression: lossy - WAV: - description: Waveform Audio File Format + dcat_mapping: http://publications.europa.eu/resource/authority/access-right/PUBLIC + RESTRICTED: + description: 'The resource is available under certain conditions or to + + authorized users only. Access may require authentication, + + payment, or agreement to terms. + + ' + meaning: euvoc:access-right/RESTRICTED + aliases: + - Limited Access annotations: - extension: .wav - mime_type: audio/wav - compression: uncompressed - FLAC: - description: Free Lossless Audio Codec + dcat_mapping: http://publications.europa.eu/resource/authority/access-right/RESTRICTED + NON_PUBLIC: + title: Non-Public + description: 'The resource is not publicly accessible. May include confidential, + + sensitive, or internal-use-only resources. + + ' + meaning: euvoc:access-right/NON_PUBLIC + aliases: + - Closed + - Private annotations: - extension: .flac - mime_type: audio/flac - compression: lossless - AAC: - description: Advanced Audio Coding + dcat_mapping: http://publications.europa.eu/resource/authority/access-right/NON_PUBLIC + EMBARGOED: + description: 'The resource is temporarily restricted and will become publicly + + available after a specific date or event. + + ' annotations: - extension: .aac - mime_type: audio/aac - compression: lossy - OGG: - description: Ogg Vorbis + common_in: academic publishing, research data + SENSITIVE: + description: 'The resource contains sensitive information requiring special + + handling or access controls. + + ' annotations: - extension: .ogg - mime_type: audio/ogg - compression: lossy - M4A: - description: MPEG-4 Audio + examples: PII, health data, classified information + is_a: AccessSchemaEnum + annotations: + source_domain: data_catalog + source_schema: access + DatasetStatus: + title: Dataset Status + description: 'The status of a dataset in its lifecycle. Based on ADMS (Asset + + Description Metadata Schema) status vocabulary. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.w3.org/TR/vocab-adms/ + - https://joinup.ec.europa.eu/collection/semantic-interoperability-community-semic/solution/asset-description-metadata-schema-adms + permissible_values: + COMPLETED: + description: 'The dataset is complete and no further updates are planned. + + The data is in its final form. + + ' + meaning: adms:Completed + aliases: + - Final + - Finished + DEPRECATED: + description: 'The dataset has been superseded by a newer version or is + + no longer recommended for use. + + ' + meaning: adms:Deprecated + aliases: + - Superseded + - Legacy + UNDER_DEVELOPMENT: + title: Under Development + description: 'The dataset is still being created, collected, or processed. + + Not yet ready for production use. + + ' + meaning: adms:UnderDevelopment + aliases: + - In Progress + - Draft + - Work in Progress + WITHDRAWN: + description: 'The dataset has been removed from availability, either + + temporarily or permanently. + + ' + meaning: adms:Withdrawn + aliases: + - Retracted + - Removed + is_a: AccessSchemaEnum + annotations: + source_domain: data_catalog + source_schema: access + UpdateFrequency: + title: Update Frequency + description: 'The frequency at which a dataset is updated with new data. + + Based on Dublin Core Collection Description Frequency Vocabulary. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - http://purl.org/cld/freq/ + - https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_frequency + permissible_values: + CONTINUOUS: + description: Data is updated continuously or in real-time. + meaning: dcterms:Frequency + annotations: + iso_duration: PT0S + DAILY: + description: Data is updated once per day. annotations: - extension: .m4a - mime_type: audio/mp4 - compression: lossy or lossless - WMA: - description: Windows Media Audio + iso_duration: P1D + TWICE_WEEKLY: + title: Twice Weekly + description: Data is updated twice per week. annotations: - extension: .wma - mime_type: audio/x-ms-wma - creator: Microsoft - OPUS: - description: Opus Interactive Audio Codec + iso_duration: P3D + WEEKLY: + description: Data is updated once per week. annotations: - extension: .opus - mime_type: audio/opus - use: streaming, VoIP - AIFF: - description: Audio Interchange File Format + iso_duration: P1W + BIWEEKLY: + description: Data is updated every two weeks. + aliases: + - Fortnightly annotations: - extension: .aiff, .aif - mime_type: audio/aiff - creator: Apple - is_a: FileFormatsSchemaEnum - annotations: - source_domain: computing - source_schema: file_formats - ProgrammingLanguageFileEnum: - description: Programming language source file extensions - permissible_values: - PYTHON: - description: Python source file + iso_duration: P2W + MONTHLY: + description: Data is updated once per month. annotations: - extension: .py - mime_type: text/x-python - JAVASCRIPT: - description: JavaScript source file + iso_duration: P1M + BIMONTHLY: + description: Data is updated every two months. annotations: - extension: .js - mime_type: text/javascript - TYPESCRIPT: - description: TypeScript source file + iso_duration: P2M + QUARTERLY: + description: Data is updated once per quarter (every three months). annotations: - extension: .ts - mime_type: text/typescript - JAVA: - description: Java source file + iso_duration: P3M + SEMIANNUAL: + description: Data is updated twice per year. + aliases: + - Biannual annotations: - extension: .java - mime_type: text/x-java-source - C: - description: C source file + iso_duration: P6M + ANNUAL: + description: Data is updated once per year. + aliases: + - Yearly annotations: - extension: .c - mime_type: text/x-c - CPP: - description: C++ source file + iso_duration: P1Y + BIENNIAL: + description: Data is updated every two years. annotations: - extension: .cpp, .cc, .cxx - mime_type: text/x-c++ - C_SHARP: - description: C# source file + iso_duration: P2Y + TRIENNIAL: + description: Data is updated every three years. annotations: - extension: .cs - mime_type: text/x-csharp - GO: - description: Go source file + iso_duration: P3Y + IRREGULAR: + description: Data is updated at irregular intervals. + aliases: + - As Needed + - Ad Hoc + NEVER: + description: 'Data is not updated after initial publication. + + Historical or archival datasets. + + ' + aliases: + - Static + - One-time + UNKNOWN: + description: The update frequency is not known. + is_a: AccessSchemaEnum + annotations: + source_domain: data_catalog + source_schema: access + DataServiceType: + title: Data Service Type + description: 'The type of data service provided. Based on INSPIRE spatial data + + service types and common data access patterns. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://inspire.ec.europa.eu/metadata-codelist/SpatialDataServiceType + - https://www.w3.org/TR/vocab-dcat-3/#Class:Data_Service + permissible_values: + DISCOVERY: + description: 'Service enabling search and discovery of datasets and services. + + ' + aliases: + - Catalog Service + - Search Service annotations: - extension: .go - mime_type: text/x-go - RUST: - description: Rust source file + inspire_type: discovery + VIEW: + description: 'Service enabling viewing or visualization of data without + + full download. + + ' + aliases: + - Visualization Service + - Display Service annotations: - extension: .rs - mime_type: text/x-rust - RUBY: - description: Ruby source file + inspire_type: view + DOWNLOAD: + description: 'Service enabling bulk download of datasets or portions thereof. + + ' + aliases: + - Access Service + - Retrieval Service annotations: - extension: .rb - mime_type: text/x-ruby - PHP: - description: PHP source file + inspire_type: download + TRANSFORMATION: + description: 'Service enabling transformation of data, such as format + + conversion or coordinate transformation. + + ' + aliases: + - Processing Service + - Conversion Service annotations: - extension: .php - mime_type: text/x-php - SWIFT: - description: Swift source file + inspire_type: transformation + INVOKE: + description: 'Service enabling invocation of operations on data, typically + + through an API. + + ' + aliases: + - API Service + - Web Service annotations: - extension: .swift - mime_type: text/x-swift - KOTLIN: - description: Kotlin source file + inspire_type: invoke + SUBSCRIPTION: + description: 'Service enabling subscription to data updates or notifications. + + ' + aliases: + - Notification Service + - Event Service + QUERY: + description: 'Service enabling query-based access to data, returning + + filtered or aggregated results. + + ' + aliases: + - SPARQL Endpoint + - Query Service + is_a: AccessSchemaEnum + annotations: + source_domain: data_catalog + source_schema: access + ContributorRolesSchemaEnum: + description: Schema-level enum for contributor_roles in data_catalog + is_a: DataCatalogDomainEnum + abstract: true + annotations: + source_file: data_catalog/contributor_roles.yaml + DataCiteContributorType: + title: DataCite Contributor Type + description: 'Types of contributors to research resources from DataCite 4.6. + + These describe organizational and functional roles rather than + + specific contribution activities (see CRediT/ResearchRole for those). + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://datacite-metadata-schema.readthedocs.io/en/4.6/appendices/appendix-1/contributorType/ + - https://credit.niso.org/ + permissible_values: + CONTACT_PERSON: + title: Contact Person + description: 'Person with knowledge of how to access, troubleshoot, or + + otherwise field issues related to the resource. + + ' + meaning: DataCite:ContactPerson annotations: - extension: .kt - mime_type: text/x-kotlin - R: - description: R source file + category: support + DATA_COLLECTOR: + title: Data Collector + description: 'Person or institution responsible for finding, gathering, or + + collecting data under the guidelines of the author(s) or + + Principal Investigator (PI). + + ' + meaning: DataCite:DataCollector + close_mappings: + - CRediT:investigation annotations: - extension: .r, .R - mime_type: text/x-r - MATLAB: - description: MATLAB source file + category: data_work + DATA_CURATOR: + title: Data Curator + description: 'Person tasked with reviewing, enhancing, cleaning, or standardizing + + metadata and the associated data submitted for storage, use, and + + maintenance within a repository. + + ' + meaning: DataCite:DataCurator + close_mappings: + - CRediT:data-curation annotations: - extension: .m - mime_type: text/x-matlab - JULIA: - description: Julia source file + category: data_work + DATA_MANAGER: + title: Data Manager + description: 'Person or organization responsible for maintaining the finished + + resource, including data quality, access permissions, and + + long-term availability. + + ' + meaning: DataCite:DataManager + close_mappings: + - CRediT:data-curation annotations: - extension: .jl - mime_type: text/x-julia - SHELL: - description: Shell script + category: data_work + DISTRIBUTOR: + description: 'Institution tasked with responsibility to generate or disseminate + + copies of the resource in either electronic or print form. + + ' + meaning: DataCite:Distributor + exact_mappings: + - marcrel:dst annotations: - extension: .sh, .bash - mime_type: text/x-shellscript - is_a: FileFormatsSchemaEnum - annotations: - source_domain: computing - source_schema: file_formats - NetworkProtocolEnum: - description: Network communication protocols - permissible_values: - HTTP: - description: Hypertext Transfer Protocol + category: dissemination + EDITOR: + description: 'A person who oversees the details related to the publication + + format of the resource. + + ' + meaning: DataCite:Editor + exact_mappings: + - marcrel:edt + close_mappings: + - CRediT:writing-review-editing annotations: - port: '80' - layer: application - version: 1.0, 1.1, 2, 3 - HTTPS: - description: HTTP Secure + category: editorial + HOSTING_INSTITUTION: + title: Hosting Institution + description: 'Typically, the organization allowing the resource to be available + + on the internet through the provision of its hardware, software, + + or operating support. + + ' + meaning: DataCite:HostingInstitution annotations: - port: '443' - layer: application - encryption: TLS/SSL - FTP: - description: File Transfer Protocol + category: infrastructure + PRODUCER: + description: 'Person or organization responsible for the artistic and technical + + aspects of a resource, typically in audiovisual or media contexts. + + ' + meaning: DataCite:Producer + exact_mappings: + - marcrel:pro annotations: - port: '21' - layer: application - use: file transfer - SFTP: - description: SSH File Transfer Protocol + category: production + PROJECT_LEADER: + title: Project Leader + description: 'Person officially designated as head of a project team or + + sub-project team instrumental in the work necessary to the + + development of the resource. + + ' + meaning: DataCite:ProjectLeader + exact_mappings: + - NCIT:C19924 + close_mappings: + - CRediT:project-administration + aliases: + - Principal Investigator + - PI annotations: - port: '22' - layer: application - encryption: SSH - SSH: - description: Secure Shell + category: leadership + PROJECT_MANAGER: + title: Project Manager + description: 'Person officially designated as manager of a project, responsible + + for day-to-day management activities. + + ' + meaning: DataCite:ProjectManager + close_mappings: + - CRediT:project-administration annotations: - port: '22' - layer: application - use: secure remote access - TELNET: - description: Telnet protocol + category: leadership + PROJECT_MEMBER: + title: Project Member + description: 'Person on the membership list of a designated project or + + project team. + + ' + meaning: DataCite:ProjectMember annotations: - port: '23' - layer: application - security: unencrypted - SMTP: - description: Simple Mail Transfer Protocol + category: team + REGISTRATION_AGENCY: + title: Registration Agency + description: 'Institution or organization officially appointed by a Registration + + Authority to handle specific tasks within a defined area of + + responsibility. + + ' + meaning: DataCite:RegistrationAgency annotations: - port: 25, 587 - layer: application - use: email sending - POP3: - description: Post Office Protocol version 3 + category: governance + examples: DataCite member organizations + REGISTRATION_AUTHORITY: + title: Registration Authority + description: 'A standards-setting body from which Registration Agencies obtain + + their official recognition and guidance. + + ' + meaning: DataCite:RegistrationAuthority annotations: - port: 110, 995 - layer: application - use: email retrieval - IMAP: - description: Internet Message Access Protocol + category: governance + examples: International DOI Foundation + RELATED_PERSON: + title: Related Person + description: 'A person without a specifically defined role in the development + + of the resource, but who is someone the author wishes to recognize. + + ' + meaning: DataCite:RelatedPerson annotations: - port: 143, 993 - layer: application - use: email access - DNS: - description: Domain Name System + category: acknowledgment + RESEARCHER: + description: 'A person involved in analyzing data or the results of an + + experiment or formal study. + + ' + meaning: DataCite:Researcher + exact_mappings: + - NCIT:C25741 + close_mappings: + - CRediT:formal-analysis + - CRediT:investigation annotations: - port: '53' - layer: application - use: name resolution - DHCP: - description: Dynamic Host Configuration Protocol + category: research + RESEARCH_GROUP: + title: Research Group + description: 'A group of individuals with a common research focus, typically + + within a lab, department, or division. + + ' + meaning: DataCite:ResearchGroup annotations: - port: 67, 68 - layer: application - use: IP assignment - TCP: - description: Transmission Control Protocol + category: team + RIGHTS_HOLDER: + title: Rights Holder + description: 'Person or institution owning or managing property rights, + + including intellectual property rights, over the resource. + + ' + meaning: DataCite:RightsHolder + exact_mappings: + - marcrel:own + - NCIT:C54131 annotations: - layer: transport - type: connection-oriented - UDP: - description: User Datagram Protocol + category: legal + SPONSOR: + description: 'Person or organization that issued a contract or under the + + auspices of which a work has been written, printed, published, + + developed, etc. + + ' + meaning: DataCite:Sponsor + exact_mappings: + - marcrel:spn + close_mappings: + - CRediT:funding-acquisition annotations: - layer: transport - type: connectionless - WEBSOCKET: - description: WebSocket protocol + category: funding + SUPERVISOR: + description: 'Designated administrator overseeing one or more groups or teams + + working to produce the resource. + + ' + meaning: DataCite:Supervisor + exact_mappings: + - marcrel:ths + close_mappings: + - CRediT:supervision annotations: - port: 80, 443 - layer: application - use: bidirectional communication - MQTT: - description: Message Queuing Telemetry Transport + category: leadership + TRANSLATOR: + description: 'Person, organization, or automated system responsible for + + rendering the content of a resource from one language into + + another. + + ' + meaning: DataCite:Translator + exact_mappings: + - marcrel:trl annotations: - port: 1883, 8883 - layer: application - use: IoT messaging - AMQP: - description: Advanced Message Queuing Protocol + category: translation + added_version: '4.6' + WORK_PACKAGE_LEADER: + title: Work Package Leader + description: 'A Work Package is a recognized data product, and the Work Package + + Leader ensures the comprehensive contents, availability, and + + quality of the work package. + + ' + meaning: DataCite:WorkPackageLeader annotations: - port: '5672' - layer: application - use: message queuing - GRPC: - description: gRPC Remote Procedure Call + category: leadership + OTHER: + description: 'Any person or institution making a significant contribution not + + covered by other contributor type values. + + ' + meaning: DataCite:Other annotations: - transport: HTTP/2 - use: RPC framework - is_a: FileFormatsSchemaEnum + note: Should be accompanied by free-text description + is_a: ContributorRolesSchemaEnum annotations: - source_domain: computing - source_schema: file_formats - MaturityLevelsSchemaEnum: - description: Schema-level enum for maturity_levels in computing - is_a: ComputingDomainEnum + source_domain: data_catalog + source_schema: contributor_roles + RelationsSchemaEnum: + description: Schema-level enum for relations in data_catalog + is_a: DataCatalogDomainEnum abstract: true annotations: - source_file: computing/maturity_levels.yaml - TechnologyReadinessLevel: - title: Technology Readiness Level (TRL) - description: NASA's Technology Readiness Level scale for assessing the maturity of technologies from basic research through - operational deployment - source: https://www.nasa.gov/directorates/heo/scan/engineering/technology/technology_readiness_level - conforms_to: ISO-16290:2013 - permissible_values: - TRL_1: - description: Basic principles observed and reported - title: TRL 1 - Basic Principles - TRL_2: - description: Technology concept and/or application formulated - title: TRL 2 - Technology Concept - TRL_3: - description: Analytical and experimental critical function and/or characteristic proof of concept - title: TRL 3 - Experimental Proof of Concept - TRL_4: - description: Component and/or breadboard validation in laboratory environment - title: TRL 4 - Lab Validation - TRL_5: - description: Component and/or breadboard validation in relevant environment - title: TRL 5 - Relevant Environment Validation - TRL_6: - description: System/subsystem model or prototype demonstration in a relevant environment - title: TRL 6 - Prototype Demonstration - TRL_7: - description: System prototype demonstration in an operational environment - title: TRL 7 - Operational Prototype - TRL_8: - description: Actual system completed and qualified through test and demonstration - title: TRL 8 - System Complete - TRL_9: - description: Actual system proven through successful mission operations - title: TRL 9 - Mission Proven - is_a: MaturityLevelsSchemaEnum - annotations: - source_domain: computing - source_schema: maturity_levels - SoftwareMaturityLevel: - title: Software Maturity Level - description: General software maturity assessment levels - permissible_values: - ALPHA: - description: Early development stage with basic functionality, may be unstable - title: Alpha - BETA: - description: Feature-complete but may contain bugs, ready for testing - title: Beta - RELEASE_CANDIDATE: - description: Stable version ready for final testing before release - title: Release Candidate - STABLE: - description: Production-ready with proven stability and reliability - title: Stable - MATURE: - description: Well-established with extensive usage and proven track record - title: Mature - LEGACY: - description: Older version still in use but no longer actively developed - title: Legacy - DEPRECATED: - description: No longer recommended for use, superseded by newer versions - title: Deprecated - OBSOLETE: - description: No longer supported or maintained - title: Obsolete - is_a: MaturityLevelsSchemaEnum - annotations: - source_domain: computing - source_schema: maturity_levels - CapabilityMaturityLevel: - title: Capability Maturity Model Integration (CMMI) Level - description: CMMI levels for assessing organizational process maturity in software development - source: https://cmmiinstitute.com/ - conforms_to: CMMI Version 2.0 - permissible_values: - LEVEL_1: - description: Initial - Processes are unpredictable, poorly controlled, and reactive - title: Level 1 - Initial - LEVEL_2: - description: Managed - Processes are characterized for projects and reactive - title: Level 2 - Managed - LEVEL_3: - description: Defined - Processes are characterized for the organization and proactive - title: Level 3 - Defined - LEVEL_4: - description: Quantitatively Managed - Processes are measured and controlled - title: Level 4 - Quantitatively Managed - LEVEL_5: - description: Optimizing - Focus on continuous process improvement - title: Level 5 - Optimizing - is_a: MaturityLevelsSchemaEnum + source_file: data_catalog/relations.yaml + DataCiteRelationType: + title: DataCite Relation Type + description: 'Types of relationships between research resources from DataCite 4.6. + + Relations are expressed from the perspective of the resource being + + described (A) in relation to another resource (B). + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://datacite-metadata-schema.readthedocs.io/en/4.6/appendices/appendix-1/relationType/ + - http://purl.org/spar/cito/ + permissible_values: + IS_CITED_BY: + title: Is Cited By + description: Indicates that B includes A in a citation. + meaning: DataCite:IsCitedBy + exact_mappings: + - cito:isCitedBy + annotations: + inverse: CITES + category: citation + CITES: + description: Indicates that A includes B in a citation. + meaning: DataCite:Cites + exact_mappings: + - cito:cites + - dcterms:references + annotations: + inverse: IS_CITED_BY + category: citation + IS_SUPPLEMENT_TO: + title: Is Supplement To + description: Indicates that A is a supplement to B. + meaning: DataCite:IsSupplementTo + annotations: + inverse: IS_SUPPLEMENTED_BY + category: supplementary + IS_SUPPLEMENTED_BY: + title: Is Supplemented By + description: Indicates that B is a supplement to A. + meaning: DataCite:IsSupplementedBy + annotations: + inverse: IS_SUPPLEMENT_TO + category: supplementary + IS_CONTINUED_BY: + title: Is Continued By + description: Indicates that A is continued by the work B. + meaning: DataCite:IsContinuedBy + annotations: + inverse: CONTINUES + category: continuation + CONTINUES: + description: Indicates that A is a continuation of the work B. + meaning: DataCite:Continues + annotations: + inverse: IS_CONTINUED_BY + category: continuation + DESCRIBES: + description: Indicates that A describes B. + meaning: DataCite:Describes + annotations: + inverse: IS_DESCRIBED_BY + category: description + IS_DESCRIBED_BY: + title: Is Described By + description: Indicates that A is described by B. + meaning: DataCite:IsDescribedBy + annotations: + inverse: DESCRIBES + category: description + HAS_METADATA: + title: Has Metadata + description: Indicates that resource A has additional metadata B. + meaning: DataCite:HasMetadata + annotations: + inverse: IS_METADATA_FOR + category: metadata + IS_METADATA_FOR: + title: Is Metadata For + description: Indicates that additional metadata A describes resource B. + meaning: DataCite:IsMetadataFor + annotations: + inverse: HAS_METADATA + category: metadata + HAS_VERSION: + title: Has Version + description: Indicates that A has a version B. + meaning: DataCite:HasVersion + annotations: + inverse: IS_VERSION_OF + category: versioning + IS_VERSION_OF: + title: Is Version Of + description: Indicates that A is a version of B. + meaning: DataCite:IsVersionOf + annotations: + inverse: HAS_VERSION + category: versioning + IS_NEW_VERSION_OF: + title: Is New Version Of + description: 'Indicates that A is a new edition of B, where the new edition + + has been modified or updated. + + ' + meaning: DataCite:IsNewVersionOf + annotations: + inverse: IS_PREVIOUS_VERSION_OF + category: versioning + IS_PREVIOUS_VERSION_OF: + title: Is Previous Version Of + description: Indicates that A is a previous edition of B. + meaning: DataCite:IsPreviousVersionOf + annotations: + inverse: IS_NEW_VERSION_OF + category: versioning + IS_PART_OF: + title: Is Part Of + description: 'Indicates that A is a portion of B. May be used for elements + + of a series. + + ' + meaning: DataCite:IsPartOf + exact_mappings: + - dcterms:isPartOf + annotations: + inverse: HAS_PART + category: partonomy + HAS_PART: + title: Has Part + description: Indicates that A includes the part B. + meaning: DataCite:HasPart + exact_mappings: + - dcterms:hasPart + annotations: + inverse: IS_PART_OF + category: partonomy + IS_PUBLISHED_IN: + title: Is Published In + description: 'Indicates that A is published inside B, but is independent of + + other things published inside of B. + + ' + meaning: DataCite:IsPublishedIn + annotations: + category: publication + IS_REFERENCED_BY: + title: Is Referenced By + description: Indicates that A is used as a source of information by B. + meaning: DataCite:IsReferencedBy + exact_mappings: + - dcterms:isReferencedBy + annotations: + inverse: REFERENCES + category: reference + REFERENCES: + description: Indicates that B is used as a source of information for A. + meaning: DataCite:References + exact_mappings: + - dcterms:references + annotations: + inverse: IS_REFERENCED_BY + category: reference + IS_DOCUMENTED_BY: + title: Is Documented By + description: Indicates that B is documentation about/explaining A. + meaning: DataCite:IsDocumentedBy + annotations: + inverse: DOCUMENTS + category: documentation + DOCUMENTS: + description: Indicates that A is documentation about/explaining B. + meaning: DataCite:Documents + annotations: + inverse: IS_DOCUMENTED_BY + category: documentation + IS_COMPILED_BY: + title: Is Compiled By + description: Indicates that B is used to compile or create A. + meaning: DataCite:IsCompiledBy + annotations: + inverse: COMPILES + category: derivation + COMPILES: + description: Indicates that B is the result of a compile or creation event using A. + meaning: DataCite:Compiles + annotations: + inverse: IS_COMPILED_BY + category: derivation + IS_VARIANT_FORM_OF: + title: Is Variant Form Of + description: Indicates that A is a variant or different form of B. + meaning: DataCite:IsVariantFormOf + annotations: + inverse: IS_ORIGINAL_FORM_OF + category: form + IS_ORIGINAL_FORM_OF: + title: Is Original Form Of + description: Indicates that A is the original form of B. + meaning: DataCite:IsOriginalFormOf + annotations: + inverse: IS_VARIANT_FORM_OF + category: form + IS_IDENTICAL_TO: + title: Is Identical To + description: 'Indicates that A is identical to B, for use when there is a need + + to register two separate instances of the same resource. + + ' + meaning: DataCite:IsIdenticalTo + annotations: + category: identity + IS_REVIEWED_BY: + title: Is Reviewed By + description: Indicates that A is reviewed by B. + meaning: DataCite:IsReviewedBy + exact_mappings: + - cito:hasReview + annotations: + inverse: REVIEWS + category: review + REVIEWS: + description: Indicates that A is a review of B. + meaning: DataCite:Reviews + exact_mappings: + - cito:reviews + annotations: + inverse: IS_REVIEWED_BY + category: review + IS_DERIVED_FROM: + title: Is Derived From + description: Indicates that B is a source upon which A is based. + meaning: DataCite:IsDerivedFrom + exact_mappings: + - prov:wasDerivedFrom + annotations: + inverse: IS_SOURCE_OF + category: derivation + IS_SOURCE_OF: + title: Is Source Of + description: Indicates that A is a source upon which B is based. + meaning: DataCite:IsSourceOf + annotations: + inverse: IS_DERIVED_FROM + category: derivation + IS_REQUIRED_BY: + title: Is Required By + description: Indicates that A is required by B. + meaning: DataCite:IsRequiredBy + exact_mappings: + - dcterms:isRequiredBy + annotations: + inverse: REQUIRES + category: dependency + REQUIRES: + description: Indicates that A requires B. + meaning: DataCite:Requires + exact_mappings: + - dcterms:requires + annotations: + inverse: IS_REQUIRED_BY + category: dependency + OBSOLETES: + description: Indicates that A replaces B. + meaning: DataCite:Obsoletes + exact_mappings: + - dcterms:replaces + annotations: + inverse: IS_OBSOLETED_BY + category: obsolescence + IS_OBSOLETED_BY: + title: Is Obsoleted By + description: Indicates that A is replaced by B. + meaning: DataCite:IsObsoletedBy + exact_mappings: + - dcterms:isReplacedBy + annotations: + inverse: OBSOLETES + category: obsolescence + IS_COLLECTED_BY: + title: Is Collected By + description: Indicates that A is collected by B. + meaning: DataCite:IsCollectedBy + annotations: + inverse: COLLECTS + category: collection + COLLECTS: + description: Indicates that A collects B. + meaning: DataCite:Collects + annotations: + inverse: IS_COLLECTED_BY + category: collection + IS_TRANSLATION_OF: + title: Is Translation Of + description: Indicates that A is a translation of B. + meaning: DataCite:IsTranslationOf + annotations: + inverse: HAS_TRANSLATION + category: translation + added_version: '4.6' + HAS_TRANSLATION: + title: Has Translation + description: Indicates that A has a translation B. + meaning: DataCite:HasTranslation + annotations: + inverse: IS_TRANSLATION_OF + category: translation + added_version: '4.6' + is_a: RelationsSchemaEnum + annotations: + source_domain: data_catalog + source_schema: relations + ResourceTypesSchemaEnum: + description: Schema-level enum for resource_types in data_catalog + is_a: DataCatalogDomainEnum + abstract: true annotations: - source_domain: computing - source_schema: maturity_levels - StandardsMaturityLevel: - title: Standards Development Maturity Level - description: Maturity levels for standards and specifications - permissible_values: - DRAFT: - description: Initial draft under development - title: Draft - WORKING_DRAFT: - description: Work in progress by working group - title: Working Draft - COMMITTEE_DRAFT: - description: Draft reviewed by committee - title: Committee Draft - CANDIDATE_RECOMMENDATION: - description: Mature draft ready for implementation testing - title: Candidate Recommendation - PROPOSED_STANDARD: - description: Stable specification ready for adoption - title: Proposed Standard + source_file: data_catalog/resource_types.yaml + DataCiteResourceType: + title: DataCite Resource Type + description: 'General resource type classifications from DataCite 4.6. + + Used for categorizing research outputs in data repositories. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://datacite-metadata-schema.readthedocs.io/en/4.6/appendices/appendix-1/resourceTypeGeneral/ + permissible_values: + AUDIOVISUAL: + description: 'A series of visual representations imparting an impression of motion + + when shown in succession. May include sound. + + ' + meaning: DataCite:Audiovisual + exact_mappings: + - DCMITYPE:MovingImage + annotations: + examples: video, film, animation + AWARD: + description: 'Funding or support provided to an individual or organization + + for research, academic work, or professional development. + + ' + meaning: DataCite:Award + annotations: + added_version: '4.6' + examples: grant award, fellowship, scholarship + BOOK: + description: 'A medium for recording information in the form of writing or images, + + typically composed of many pages bound together. + + ' + meaning: DataCite:Book + exact_mappings: + - FABIO:Book + - DCMITYPE:Text + BOOK_CHAPTER: + title: Book Chapter + description: One of the main divisions of a book. + meaning: DataCite:BookChapter + exact_mappings: + - FABIO:BookChapter + COLLECTION: + description: 'An aggregation of resources, which may encompass collections of + + one resource type as well as those of mixed types. + + ' + meaning: DataCite:Collection + exact_mappings: + - DCMITYPE:Collection + COMPUTATIONAL_NOTEBOOK: + title: Computational Notebook + description: 'A virtual notebook environment used for literate programming, + + combining code, documentation, and visualizations. + + ' + meaning: DataCite:ComputationalNotebook + annotations: + examples: Jupyter notebook, R Markdown, Observable + CONFERENCE_PAPER: + title: Conference Paper + description: 'Article written with the goal of being accepted to a conference. + + ' + meaning: DataCite:ConferencePaper + exact_mappings: + - FABIO:ConferencePaper + CONFERENCE_PROCEEDING: + title: Conference Proceeding + description: 'Collection of academic papers published in the context of + + an academic conference. + + ' + meaning: DataCite:ConferenceProceeding + exact_mappings: + - FABIO:ConferenceProceedings + DATA_PAPER: + title: Data Paper + description: 'A scholarly publication describing a dataset, intended to + + facilitate its discovery, interpretation, and reuse. + + ' + meaning: DataCite:DataPaper + exact_mappings: + - FABIO:DataPaper + DATASET: + description: 'Data encoded in a defined structure. May include tables, + + databases, or other structured data. + + ' + meaning: DataCite:Dataset + exact_mappings: + - DCMITYPE:Dataset + DISSERTATION: + description: 'A written essay, treatise, or thesis, especially one written + + by a candidate for a doctoral degree. + + ' + meaning: DataCite:Dissertation + exact_mappings: + - FABIO:DoctoralThesis + EVENT: + description: 'A non-persistent, time-based occurrence. May be planned or + + unplanned. + + ' + meaning: DataCite:Event + exact_mappings: + - DCMITYPE:Event + annotations: + examples: conference, workshop, exhibition + IMAGE: + description: 'A visual representation other than text, including photographs, + + diagrams, illustrations, and other static visual works. + + ' + meaning: DataCite:Image + exact_mappings: + - DCMITYPE:Image + - DCMITYPE:StillImage + INSTRUMENT: + description: 'A device, tool, or apparatus used to obtain, measure, and/or + + analyze data. + + ' + meaning: DataCite:Instrument + annotations: + examples: microscope, telescope, sensor, spectrometer + INTERACTIVE_RESOURCE: + title: Interactive Resource + description: 'A resource requiring interaction from the user to be understood, + + executed, or experienced. + + ' + meaning: DataCite:InteractiveResource + exact_mappings: + - DCMITYPE:InteractiveResource + annotations: + examples: web application, game, simulation + JOURNAL: + description: 'A scholarly publication consisting of articles that is published + + regularly throughout the year. + + ' + meaning: DataCite:Journal + exact_mappings: + - FABIO:Journal + JOURNAL_ARTICLE: + title: Journal Article + description: 'A written composition on a topic of interest, which forms a + + separate part of a journal. + + ' + meaning: DataCite:JournalArticle + exact_mappings: + - FABIO:JournalArticle + - IAO:0000013 + MODEL: + description: 'An abstract, conceptual, graphical, mathematical, or visualization + + model that represents empirical objects, phenomena, or processes. + + ' + meaning: DataCite:Model + annotations: + examples: 3D model, statistical model, simulation model + OUTPUT_MANAGEMENT_PLAN: + title: Output Management Plan + description: 'A formal document that outlines how research outputs are to be + + handled during and after a research project. + + ' + meaning: DataCite:OutputManagementPlan + aliases: + - Data Management Plan + - DMP + PEER_REVIEW: + title: Peer Review + description: 'Evaluation of scientific, academic, or professional work by + + others working in the same field. + + ' + meaning: DataCite:PeerReview + PHYSICAL_OBJECT: + title: Physical Object + description: 'A physical object or substance, including artifacts, specimens, + + samples, and material objects. + + ' + meaning: DataCite:PhysicalObject + exact_mappings: + - DCMITYPE:PhysicalObject + annotations: + examples: fossil, artifact, tissue sample, mineral specimen + PREPRINT: + description: 'A version of a scholarly or scientific paper that precedes + + formal peer review and publication in a journal. + + ' + meaning: DataCite:Preprint + exact_mappings: + - FABIO:Preprint + PROJECT: + description: 'A planned endeavor or activity, frequently collaborative, + + intended to achieve a particular aim. + + ' + meaning: DataCite:Project + annotations: + added_version: '4.6' + REPORT: + description: 'A document that presents information in an organized format + + for a specific audience and purpose. + + ' + meaning: DataCite:Report + exact_mappings: + - FABIO:TechnicalReport + - IAO:0000088 + SERVICE: + description: 'An organized system of apparatus, appliances, staff, etc., + + for supplying some function required by end users. + + ' + meaning: DataCite:Service + exact_mappings: + - DCMITYPE:Service + annotations: + examples: API, web service, data service + SOFTWARE: + description: 'A computer program other than a computational notebook, + + in either source code (text) or compiled form. + + ' + meaning: DataCite:Software + exact_mappings: + - DCMITYPE:Software + SOUND: + description: 'A resource primarily intended to be heard, including music, + + speech, and other audio recordings. + + ' + meaning: DataCite:Sound + exact_mappings: + - DCMITYPE:Sound STANDARD: - description: Approved and published standard - title: Standard - MATURE_STANDARD: - description: Well-established standard with wide adoption - title: Mature Standard - SUPERSEDED: - description: Replaced by a newer version - title: Superseded - WITHDRAWN: - description: No longer valid or recommended - title: Withdrawn - is_a: MaturityLevelsSchemaEnum + description: 'Something established by authority, custom, or general consent + + as a model, example, or point of reference. + + ' + meaning: DataCite:Standard + exact_mappings: + - FABIO:Standard + annotations: + examples: ISO standard, data format specification + STUDY_REGISTRATION: + title: Study Registration + description: 'A detailed, time-stamped description of a research plan, + + often openly shared in a registry or repository. + + ' + meaning: DataCite:StudyRegistration + annotations: + examples: clinical trial registration, pre-registration + TEXT: + description: 'A resource consisting primarily of words for reading that is + + not covered by any other textual resource type. + + ' + meaning: DataCite:Text + exact_mappings: + - DCMITYPE:Text + WORKFLOW: + description: 'A structured series of steps which can be executed to produce + + a final outcome, often automated. + + ' + meaning: DataCite:Workflow + annotations: + examples: bioinformatics pipeline, ETL workflow, analysis script + OTHER: + description: 'Use when the resource type does not fit any other category. + + Should be accompanied by a free-text description. + + ' + meaning: DataCite:Other + is_a: ResourceTypesSchemaEnum annotations: - source_domain: computing - source_schema: maturity_levels - ProjectMaturityLevel: - title: Project Maturity Level - description: General project development maturity assessment - permissible_values: - CONCEPT: - description: Initial idea or concept stage - title: Concept - PLANNING: - description: Project planning and design phase - title: Planning - DEVELOPMENT: - description: Active development in progress - title: Development - TESTING: - description: Testing and quality assurance phase - title: Testing - PILOT: - description: Limited deployment or pilot testing - title: Pilot - PRODUCTION: - description: Full production deployment - title: Production - MAINTENANCE: - description: Maintenance and support mode - title: Maintenance - END_OF_LIFE: - description: Project reaching end of lifecycle - title: End of Life - is_a: MaturityLevelsSchemaEnum + source_domain: data_catalog + source_schema: resource_types + DataScienceDomainEnum: + description: Domain-level enum for data_science value sets + is_a: ValueSetEnum + abstract: true + BinaryClassificationSchemaEnum: + description: Schema-level enum for binary_classification in data_science + is_a: DataScienceDomainEnum + abstract: true annotations: - source_domain: computing - source_schema: maturity_levels - DataMaturityLevel: - title: Data Maturity Level - description: Levels of data quality, governance, and organizational maturity + source_file: data_science/binary_classification.yaml + BinaryClassificationEnum: + title: Binary Classification + description: Generic binary classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - RAW: - description: Unprocessed, uncleaned data - title: Raw Data - CLEANED: - description: Basic cleaning and validation applied - title: Cleaned Data - STANDARDIZED: - description: Conforms to defined standards and formats - title: Standardized Data - INTEGRATED: - description: Combined with other data sources - title: Integrated Data - CURATED: - description: Expert-reviewed and validated - title: Curated Data - PUBLISHED: - description: Publicly available with proper metadata - title: Published Data - ARCHIVED: - description: Long-term preservation with access controls - title: Archived Data - is_a: MaturityLevelsSchemaEnum + POSITIVE: + description: Positive class + title: Positive Finding + meaning: NCIT:C38758 + aliases: + - '1' + - 'true' + - 'yes' + - T + NEGATIVE: + description: Negative class + title: Negative Test Result + meaning: NCIT:C35681 + aliases: + - '0' + - 'false' + - 'no' + - F + is_a: BinaryClassificationSchemaEnum annotations: - source_domain: computing - source_schema: maturity_levels - OpenSourceMaturityLevel: - title: Open Source Project Maturity - description: Maturity assessment for open source projects + source_domain: data_science + source_schema: binary_classification + SpamClassificationEnum: + title: Spam Classification + description: Standard labels for spam/ham email classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - EXPERIMENTAL: - description: Early experimental project - title: Experimental - EMERGING: - description: Gaining traction and contributors - title: Emerging - ESTABLISHED: - description: Stable with active community - title: Established - MATURE: - description: Well-established with proven governance - title: Mature - DECLINING: - description: Decreasing activity and maintenance - title: Declining - ARCHIVED: - description: No longer actively maintained - title: Archived - is_a: MaturityLevelsSchemaEnum - annotations: - source_domain: computing - source_schema: maturity_levels - MimeTypesSchemaEnum: - description: Schema-level enum for mime_types in computing - is_a: ComputingDomainEnum - abstract: true + SPAM: + description: Unwanted or unsolicited message + annotations: + note: No appropriate ontology term found for spam concept + aliases: + - junk + - '1' + HAM: + description: Legitimate, wanted message + annotations: + note: No appropriate ontology term found for ham concept + aliases: + - not_spam + - legitimate + - '0' + is_a: BinaryClassificationSchemaEnum annotations: - source_file: computing/mime_types.yaml - MimeType: - description: Common MIME types for various file formats + source_domain: data_science + source_schema: binary_classification + AnomalyDetectionEnum: + title: Anomaly Detection + description: Labels for anomaly detection tasks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - APPLICATION_JSON: - description: JSON format - meaning: iana:application/json - APPLICATION_XML: - description: XML format - meaning: iana:application/xml - APPLICATION_PDF: - description: Adobe Portable Document Format - meaning: iana:application/pdf - APPLICATION_ZIP: - description: ZIP archive - meaning: iana:application/zip - APPLICATION_GZIP: - description: GZIP compressed archive - meaning: iana:application/gzip - APPLICATION_OCTET_STREAM: - description: Binary data - meaning: iana:application/octet-stream - APPLICATION_X_WWW_FORM_URLENCODED: - description: Form data encoded - meaning: iana:application/x-www-form-urlencoded - APPLICATION_VND_MS_EXCEL: - description: Microsoft Excel - meaning: iana:application/vnd.ms-excel - APPLICATION_VND_OPENXMLFORMATS_SPREADSHEET: - description: Microsoft Excel (OpenXML) - meaning: iana:application/vnd.openxmlformats-officedocument.spreadsheetml.sheet - APPLICATION_VND_MS_POWERPOINT: - description: Microsoft PowerPoint - meaning: iana:application/vnd.ms-powerpoint - APPLICATION_MSWORD: - description: Microsoft Word - meaning: iana:application/msword - APPLICATION_VND_OPENXMLFORMATS_DOCUMENT: - description: Microsoft Word (OpenXML) - meaning: iana:application/vnd.openxmlformats-officedocument.wordprocessingml.document - APPLICATION_JAVASCRIPT: - description: JavaScript - meaning: iana:application/javascript - APPLICATION_TYPESCRIPT: - description: TypeScript source code - meaning: iana:application/typescript - APPLICATION_SQL: - description: SQL database format - meaning: iana:application/sql - APPLICATION_GRAPHQL: - description: GraphQL query language - meaning: iana:application/graphql - APPLICATION_LD_JSON: - description: JSON-LD format - meaning: iana:application/ld+json - APPLICATION_WASM: - description: WebAssembly binary format - meaning: iana:application/wasm - TEXT_PLAIN: - description: Plain text - meaning: iana:text/plain - TEXT_HTML: - description: HTML document - meaning: iana:text/html - TEXT_CSS: - description: Cascading Style Sheets - meaning: iana:text/css - TEXT_CSV: - description: Comma-separated values - meaning: iana:text/csv - TEXT_MARKDOWN: - description: Markdown format - meaning: iana:text/markdown - TEXT_YAML: - description: YAML format - meaning: iana:text/yaml - TEXT_X_PYTHON: - description: Python source code - meaning: iana:text/x-python - TEXT_X_JAVA: - description: Java source code - meaning: iana:text/x-java-source - TEXT_X_C: - description: C source code - meaning: iana:text/x-c - TEXT_X_CPP: - description: C++ source code - meaning: iana:text/x-c++ - TEXT_X_CSHARP: - description: C# source code - meaning: iana:text/x-csharp - TEXT_X_GO: - description: Go source code - meaning: iana:text/x-go - TEXT_X_RUST: - description: Rust source code - meaning: iana:text/x-rust - TEXT_X_RUBY: - description: Ruby source code - meaning: iana:text/x-ruby - TEXT_X_SHELLSCRIPT: - description: Shell script - meaning: iana:text/x-shellscript - IMAGE_JPEG: - description: JPEG image - meaning: iana:image/jpeg - IMAGE_PNG: - description: PNG image - meaning: iana:image/png - IMAGE_GIF: - description: GIF image - meaning: iana:image/gif - IMAGE_SVG_XML: - description: SVG vector image - meaning: iana:image/svg+xml - IMAGE_WEBP: - description: WebP image - meaning: iana:image/webp - IMAGE_BMP: - description: Bitmap image - meaning: iana:image/bmp - IMAGE_ICO: - description: Icon format - meaning: iana:image/vnd.microsoft.icon - IMAGE_TIFF: - description: TIFF image - meaning: iana:image/tiff - IMAGE_AVIF: - description: AVIF image format - meaning: iana:image/avif - AUDIO_MPEG: - description: MP3 audio - meaning: iana:audio/mpeg - AUDIO_WAV: - description: WAV audio - meaning: iana:audio/wav - AUDIO_OGG: - description: OGG audio - meaning: iana:audio/ogg - AUDIO_WEBM: - description: WebM audio - meaning: iana:audio/webm - AUDIO_AAC: - description: AAC audio - meaning: iana:audio/aac - VIDEO_MP4: - description: MP4 video - meaning: iana:video/mp4 - VIDEO_MPEG: - description: MPEG video - meaning: iana:video/mpeg - VIDEO_WEBM: - description: WebM video - meaning: iana:video/webm - VIDEO_OGG: - description: OGG video - meaning: iana:video/ogg - VIDEO_QUICKTIME: - description: QuickTime video - meaning: iana:video/quicktime - VIDEO_AVI: - description: AVI video - meaning: iana:video/x-msvideo - FONT_WOFF: - description: Web Open Font Format - meaning: iana:font/woff - FONT_WOFF2: - description: Web Open Font Format 2 - meaning: iana:font/woff2 - FONT_TTF: - description: TrueType Font - meaning: iana:font/ttf - FONT_OTF: - description: OpenType Font - meaning: iana:font/otf - MULTIPART_FORM_DATA: - description: Form data with file upload - meaning: iana:multipart/form-data - MULTIPART_MIXED: - description: Mixed multipart message - meaning: iana:multipart/mixed - is_a: MimeTypesSchemaEnum + NORMAL: + description: Normal, expected behavior or pattern + title: Normal + meaning: NCIT:C14165 + aliases: + - inlier + - regular + - '0' + ANOMALY: + description: Abnormal, unexpected behavior or pattern + title: Anomaly + meaning: STATO:0000036 + aliases: + - outlier + - abnormal + - irregular + - '1' + is_a: BinaryClassificationSchemaEnum annotations: - source_domain: computing - source_schema: mime_types - MimeTypeCategory: - description: Categories of MIME types + source_domain: data_science + source_schema: binary_classification + ChurnClassificationEnum: + title: Churn Classification + description: Customer churn prediction labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - APPLICATION: - description: Application data - TEXT: - description: Text documents - IMAGE: - description: Image files - AUDIO: - description: Audio files - VIDEO: - description: Video files - FONT: - description: Font files - MULTIPART: - description: Multipart messages - MESSAGE: - description: Message formats - MODEL: - description: 3D models and similar - is_a: MimeTypesSchemaEnum + RETAINED: + description: Customer continues using the service + annotations: + note: No appropriate ontology term found for customer retention + aliases: + - active + - staying + - '0' + CHURNED: + description: Customer stopped using the service + annotations: + note: No appropriate ontology term found for customer churn + aliases: + - lost + - inactive + - attrited + - '1' + is_a: BinaryClassificationSchemaEnum + annotations: + source_domain: data_science + source_schema: binary_classification + FraudDetectionEnum: + title: Fraud Detection + description: Fraud detection classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LEGITIMATE: + description: Legitimate, non-fraudulent transaction or activity + title: Normal + meaning: NCIT:C14165 + aliases: + - genuine + - valid + - '0' + FRAUDULENT: + description: Fraudulent transaction or activity + title: Fraudulently Obtained Product + meaning: NCIT:C121839 + aliases: + - fraud + - invalid + - '1' + is_a: BinaryClassificationSchemaEnum annotations: - source_domain: computing - source_schema: mime_types - TextCharset: - description: Character encodings for text content + source_domain: data_science + source_schema: binary_classification + EmotionClassificationSchemaEnum: + description: Schema-level enum for emotion_classification in data_science + is_a: DataScienceDomainEnum + abstract: true + annotations: + source_file: data_science/emotion_classification.yaml + BasicEmotionEnum: + title: Basic Emotion + description: Ekman's six basic emotions commonly used in emotion recognition + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + conforms_to: https://en.wikipedia.org/wiki/Basic_emotions permissible_values: - UTF_8: - description: UTF-8 Unicode encoding - UTF_16: - description: UTF-16 Unicode encoding - UTF_32: - description: UTF-32 Unicode encoding - ASCII: - description: ASCII encoding - ISO_8859_1: - description: ISO-8859-1 (Latin-1) encoding - ISO_8859_2: - description: ISO-8859-2 (Latin-2) encoding - WINDOWS_1252: - description: Windows-1252 encoding - GB2312: - description: Simplified Chinese encoding - SHIFT_JIS: - description: Japanese encoding - EUC_KR: - description: Korean encoding - BIG5: - description: Traditional Chinese encoding - is_a: MimeTypesSchemaEnum + ANGER: + description: Feeling of displeasure or hostility + title: Anger + meaning: MFOEM:000009 + aliases: + - angry + - mad + DISGUST: + description: Feeling of revulsion or strong disapproval + title: Disgust + meaning: MFOEM:000019 + aliases: + - disgusted + - repulsed + FEAR: + description: Feeling of anxiety or apprehension + title: Fear + meaning: MFOEM:000026 + aliases: + - afraid + - scared + HAPPINESS: + description: Feeling of pleasure or contentment + title: Happiness + meaning: MFOEM:000042 + aliases: + - happy + - joy + - joyful + SADNESS: + description: Feeling of sorrow or unhappiness + title: Sadness + meaning: MFOEM:000056 + aliases: + - sad + - sorrow + SURPRISE: + description: Feeling of mild astonishment or shock + title: Surprise + meaning: MFOEM:000032 + aliases: + - surprised + - shocked + is_a: EmotionClassificationSchemaEnum annotations: - source_domain: computing - source_schema: mime_types - CompressionType: - description: Compression types used with Content-Encoding + source_domain: data_science + source_schema: emotion_classification + ExtendedEmotionEnum: + title: Extended Emotion + description: Extended emotion set including complex emotions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + conforms_to: https://en.wikipedia.org/wiki/Emotion_classification permissible_values: - GZIP: - description: GZIP compression - DEFLATE: - description: DEFLATE compression - BR: - description: Brotli compression - COMPRESS: - description: Unix compress - IDENTITY: - description: No compression - is_a: MimeTypesSchemaEnum + ANGER: + description: Feeling of displeasure or hostility + title: Anger + meaning: MFOEM:000009 + DISGUST: + description: Feeling of revulsion + title: Disgust + meaning: MFOEM:000019 + FEAR: + description: Feeling of anxiety + title: Fear + meaning: MFOEM:000026 + HAPPINESS: + description: Feeling of pleasure + title: Happiness + meaning: MFOEM:000042 + SADNESS: + description: Feeling of sorrow + title: Sadness + meaning: MFOEM:000056 + SURPRISE: + description: Feeling of astonishment + title: Surprise + meaning: MFOEM:000032 + CONTEMPT: + description: Feeling that something is worthless + title: Contempt + meaning: MFOEM:000018 + ANTICIPATION: + description: Feeling of excitement about something that will happen + title: Erwartung + meaning: MFOEM:000175 + aliases: + - expectation + - expectant + TRUST: + description: Feeling of confidence in someone or something + title: Trust + meaning: MFOEM:000224 + LOVE: + description: Feeling of deep affection + title: Love + meaning: MFOEM:000048 + is_a: EmotionClassificationSchemaEnum annotations: - source_domain: computing - source_schema: mime_types - DataDomainEnum: - description: Domain-level enum for data value sets - is_a: ValueSetEnum - abstract: true - DataAbsentReasonSchemaEnum: - description: Schema-level enum for data_absent_reason in data - is_a: DataDomainEnum + source_domain: data_science + source_schema: emotion_classification + PrioritySeveritySchemaEnum: + description: Schema-level enum for priority_severity in data_science + is_a: DataScienceDomainEnum abstract: true annotations: - source_file: data/data_absent_reason.yaml - DataAbsentEnum: - description: Used to specify why the normally expected content of the data element is missing. + source_file: data_science/priority_severity.yaml + PriorityLevelEnum: + title: Priority Level + description: Standard priority levels for task/issue classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - unknown: - description: The value is expected to exist but is not known. - meaning: fhir_data_absent_reason:unknown - title: Unknown - asked-unknown: - description: The source was asked but does not know the value. - meaning: fhir_data_absent_reason:asked-unknown - is_a: unknown - title: Asked But Unknown - temp-unknown: - description: There is reason to expect (from the workflow) that the value may become known. - meaning: fhir_data_absent_reason:temp-unknown - is_a: unknown - title: Temporarily Unknown - not-asked: - description: The workflow didn't lead to this value being known. - meaning: fhir_data_absent_reason:not-asked - is_a: unknown - title: Not Asked - asked-declined: - description: The source was asked but declined to answer. - meaning: fhir_data_absent_reason:asked-declined - is_a: unknown - title: Asked But Declined - masked: - description: The information is not available due to security, privacy or related reasons. - meaning: fhir_data_absent_reason:masked - title: Masked - not-applicable: - description: There is no proper value for this element (e.g. last menstrual period for a male). - meaning: fhir_data_absent_reason:not-applicable - title: Not Applicable - unsupported: - description: The source system wasn't capable of supporting this element. - meaning: fhir_data_absent_reason:unsupported - title: Unsupported - as-text: - description: The content of the data is represented in the resource narrative. - meaning: fhir_data_absent_reason:as-text - title: As Text - error: - description: Some system or workflow process error means that the information is not available. - meaning: fhir_data_absent_reason:error - title: Error - not-a-number: - description: The numeric value is undefined or unrepresentable due to a floating point processing error. - meaning: fhir_data_absent_reason:not-a-number - is_a: error - title: Not a Number (NaN) - negative-infinity: - description: The numeric value is excessively low and unrepresentable due to a floating point processing error. - meaning: fhir_data_absent_reason:negative-infinity - is_a: error - title: Negative Infinity (NINF) - positive-infinity: - description: The numeric value is excessively high and unrepresentable due to a floating point processing error. - meaning: fhir_data_absent_reason:positive-infinity - is_a: error - title: Positive Infinity (PINF) - not-performed: - description: The value is not available because the observation procedure (test, etc.) was not performed. - meaning: fhir_data_absent_reason:not-performed - title: Not Performed - not-permitted: - description: The value is not permitted in this context (e.g. due to profiles, or the base data types). - meaning: fhir_data_absent_reason:not-permitted - title: Not Permitted - is_a: DataAbsentReasonSchemaEnum + CRITICAL: + description: Highest priority, requires immediate attention + title: Critical + aliases: + - P0 + - urgent + - blocker + - '1' + HIGH: + description: High priority, should be addressed soon + title: High + aliases: + - P1 + - important + - '2' + MEDIUM: + description: Medium priority, normal workflow + title: Medium + aliases: + - P2 + - normal + - '3' + LOW: + description: Low priority, can be deferred + title: Low + aliases: + - P3 + - minor + - '4' + TRIVIAL: + description: Lowest priority, nice to have + title: Trivial + aliases: + - P4 + - cosmetic + - '5' + is_a: PrioritySeveritySchemaEnum annotations: - source_domain: data - source_schema: data_absent_reason - DataScienceDomainEnum: - description: Domain-level enum for data_science value sets - is_a: ValueSetEnum - abstract: true - BinaryClassificationSchemaEnum: - description: Schema-level enum for binary_classification in data_science - is_a: DataScienceDomainEnum - abstract: true + source_domain: data_science + source_schema: priority_severity + SeverityLevelEnum: + title: Severity Level + description: Severity levels for incident/bug classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CRITICAL: + description: System is unusable, data loss possible + title: Critical + aliases: + - S1 + - blocker + - showstopper + MAJOR: + description: Major functionality impaired + title: Major + aliases: + - S2 + - severe + - high + MINOR: + description: Minor functionality impaired + title: Minor + aliases: + - S3 + - moderate + - medium + TRIVIAL: + description: Cosmetic issue, minimal impact + title: Trivial + aliases: + - S4 + - cosmetic + - low + is_a: PrioritySeveritySchemaEnum annotations: - source_file: data_science/binary_classification.yaml - BinaryClassificationEnum: - description: Generic binary classification labels + source_domain: data_science + source_schema: priority_severity + ConfidenceLevelEnum: + title: Confidence Level + description: Confidence levels for predictions and classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - POSITIVE: - description: Positive class - title: Positive Finding - meaning: NCIT:C38758 + VERY_HIGH: + description: Very high confidence (>95%) + title: Very High aliases: - - '1' - - 'true' - - 'yes' - - T - NEGATIVE: - description: Negative class - title: Negative Test Result - meaning: NCIT:C35681 + - certain + - '5' + HIGH: + description: High confidence (80-95%) + title: High aliases: - - '0' - - 'false' - - 'no' - - F - is_a: BinaryClassificationSchemaEnum + - confident + - '4' + MEDIUM: + description: Medium confidence (60-80%) + title: Medium + aliases: + - moderate + - '3' + LOW: + description: Low confidence (40-60%) + title: Low + aliases: + - uncertain + - '2' + VERY_LOW: + description: Very low confidence (<40%) + title: Very Low + aliases: + - guess + - '1' + is_a: PrioritySeveritySchemaEnum annotations: source_domain: data_science - source_schema: binary_classification - SpamClassificationEnum: - description: Standard labels for spam/ham email classification + source_schema: priority_severity + QualityControlSchemaEnum: + description: Schema-level enum for quality_control in data_science + is_a: DataScienceDomainEnum + abstract: true + annotations: + source_file: data_science/quality_control.yaml + QualityControlEnum: + title: Quality Control + description: Quality control classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - SPAM: - description: Unwanted or unsolicited message - annotations: - note: No appropriate ontology term found for spam concept + PASS: + description: Item meets quality standards + title: Pass + meaning: NCIT:C81275 aliases: - - junk + - passed + - acceptable + - ok - '1' - HAM: - description: Legitimate, wanted message - annotations: - note: No appropriate ontology term found for ham concept + FAIL: + description: Item does not meet quality standards + title: Fail + meaning: NCIT:C44281 aliases: - - not_spam - - legitimate + - failed + - reject + - defective - '0' - is_a: BinaryClassificationSchemaEnum + is_a: QualityControlSchemaEnum annotations: source_domain: data_science - source_schema: binary_classification - AnomalyDetectionEnum: - description: Labels for anomaly detection tasks + source_schema: quality_control + DefectClassificationEnum: + title: Defect Classification + description: Manufacturing defect classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - NORMAL: - description: Normal, expected behavior or pattern - title: Normal + NO_DEFECT: + description: No defect detected + title: No Defect meaning: NCIT:C14165 aliases: - - inlier - - regular + - good + - normal - '0' - ANOMALY: - description: Abnormal, unexpected behavior or pattern - title: Anomaly - meaning: STATO:0000036 + MINOR_DEFECT: + description: Minor defect that doesn't affect functionality + title: Minor Defect aliases: - - outlier - - abnormal - - irregular + - minor + - cosmetic - '1' - is_a: BinaryClassificationSchemaEnum + MAJOR_DEFECT: + description: Major defect affecting functionality + title: Major Defect + aliases: + - major + - functional + - '2' + CRITICAL_DEFECT: + description: Critical defect rendering item unusable or unsafe + title: Critical Defect + aliases: + - critical + - severe + - '3' + is_a: QualityControlSchemaEnum annotations: source_domain: data_science - source_schema: binary_classification - ChurnClassificationEnum: - description: Customer churn prediction labels + source_schema: quality_control + SentimentAnalysisSchemaEnum: + description: Schema-level enum for sentiment_analysis in data_science + is_a: DataScienceDomainEnum + abstract: true + annotations: + source_file: data_science/sentiment_analysis.yaml + SentimentClassificationEnum: + title: Sentiment Classification + description: Standard labels for sentiment analysis classification tasks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - RETAINED: - description: Customer continues using the service - annotations: - note: No appropriate ontology term found for customer retention + POSITIVE: + description: Positive sentiment or opinion + title: Positive Finding + meaning: NCIT:C38758 aliases: - - active - - staying + - pos + - '1' + - + + NEGATIVE: + description: Negative sentiment or opinion + title: Negative Test Result + meaning: NCIT:C35681 + aliases: + - neg - '0' - CHURNED: - description: Customer stopped using the service - annotations: - note: No appropriate ontology term found for customer churn + - '-' + NEUTRAL: + description: Neutral sentiment, neither positive nor negative + title: Normal + meaning: NCIT:C14165 aliases: - - lost - - inactive - - attrited - - '1' - is_a: BinaryClassificationSchemaEnum + - neu + - '2' + is_a: SentimentAnalysisSchemaEnum annotations: source_domain: data_science - source_schema: binary_classification - FraudDetectionEnum: - description: Fraud detection classification labels + source_schema: sentiment_analysis + FineSentimentClassificationEnum: + title: Fine Sentiment Classification + description: Fine-grained sentiment analysis labels with intensity levels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - LEGITIMATE: - description: Legitimate, non-fraudulent transaction or activity + VERY_POSITIVE: + description: Strongly positive sentiment + title: Positive Finding + is_a: POSITIVE + meaning: NCIT:C38758 + aliases: + - '5' + - ++ + POSITIVE: + description: Positive sentiment + title: Positive Finding + meaning: NCIT:C38758 + aliases: + - '4' + - + + NEUTRAL: + description: Neutral sentiment title: Normal meaning: NCIT:C14165 aliases: - - genuine - - valid + - '3' - '0' - FRAUDULENT: - description: Fraudulent transaction or activity - title: Fraudulently Obtained Product - meaning: NCIT:C121839 + NEGATIVE: + description: Negative sentiment + title: Negative Test Result + meaning: NCIT:C35681 + aliases: + - '2' + - '-' + VERY_NEGATIVE: + description: Strongly negative sentiment + title: Negative Test Result + is_a: NEGATIVE + meaning: NCIT:C35681 aliases: - - fraud - - invalid - '1' - is_a: BinaryClassificationSchemaEnum + - -- + is_a: SentimentAnalysisSchemaEnum annotations: source_domain: data_science - source_schema: binary_classification - EmotionClassificationSchemaEnum: - description: Schema-level enum for emotion_classification in data_science + source_schema: sentiment_analysis + TextClassificationSchemaEnum: + description: Schema-level enum for text_classification in data_science is_a: DataScienceDomainEnum abstract: true annotations: - source_file: data_science/emotion_classification.yaml - BasicEmotionEnum: - description: Ekman's six basic emotions commonly used in emotion recognition - conforms_to: https://en.wikipedia.org/wiki/Basic_emotions + source_file: data_science/text_classification.yaml + NewsTopicCategoryEnum: + title: News Topic Category + description: Common news article topic categories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ANGER: - description: Feeling of displeasure or hostility - title: Anger - meaning: MFOEM:000009 + POLITICS: + description: Political news and government affairs + title: Politics + BUSINESS: + description: Business, finance, and economic news + title: Business aliases: - - angry - - mad - DISGUST: - description: Feeling of revulsion or strong disapproval - title: Disgust - meaning: MFOEM:000019 + - finance + - economy + TECHNOLOGY: + description: Technology and computing news + title: Technology aliases: - - disgusted - - repulsed - FEAR: - description: Feeling of anxiety or apprehension - title: Fear - meaning: MFOEM:000026 + - tech + - IT + SPORTS: + description: Sports news and events + title: Sports + ENTERTAINMENT: + description: Entertainment and celebrity news + title: Entertainment aliases: - - afraid - - scared - HAPPINESS: - description: Feeling of pleasure or contentment - title: Happiness - meaning: MFOEM:000042 + - showbiz + SCIENCE: + description: Scientific discoveries and research + title: Science + HEALTH: + description: Health, medicine, and wellness news + title: Health aliases: - - happy - - joy - - joyful - SADNESS: - description: Feeling of sorrow or unhappiness - title: Sadness - meaning: MFOEM:000056 + - medical + WORLD: + description: International news and events + title: World aliases: - - sad - - sorrow - SURPRISE: - description: Feeling of mild astonishment or shock - title: Surprise - meaning: MFOEM:000032 + - international + - global + LOCAL: + description: Local and regional news + title: Local aliases: - - surprised - - shocked - is_a: EmotionClassificationSchemaEnum + - regional + is_a: TextClassificationSchemaEnum + annotations: + source_domain: data_science + source_schema: text_classification + ToxicityClassificationEnum: + title: Toxicity Classification + description: Text toxicity classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NON_TOXIC: + description: Text is appropriate and non-harmful + title: Non-Toxic + meaning: SIO:001010 + aliases: + - safe + - clean + - '0' + TOXIC: + description: Text contains harmful or inappropriate content + title: Toxic + aliases: + - harmful + - inappropriate + - '1' + SEVERE_TOXIC: + description: Text contains severely harmful content + title: Severe Toxic + is_a: TOXIC + OBSCENE: + description: Text contains obscene content + title: Obscene + is_a: TOXIC + THREAT: + description: Text contains threatening content + title: Threat + is_a: TOXIC + INSULT: + description: Text contains insulting content + title: Insult + is_a: TOXIC + IDENTITY_HATE: + description: Text contains identity-based hate + title: Identity Hate + is_a: TOXIC + is_a: TextClassificationSchemaEnum + annotations: + source_domain: data_science + source_schema: text_classification + IntentClassificationEnum: + title: Intent Classification + description: Common chatbot/NLU intent categories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GREETING: + description: User greeting or hello + title: Greeting + GOODBYE: + description: User saying goodbye + title: Goodbye + THANKS: + description: User expressing gratitude + title: Thanks + HELP: + description: User requesting help or assistance + title: Help + INFORMATION: + description: User requesting information + title: Information + COMPLAINT: + description: User expressing dissatisfaction + title: Complaint + FEEDBACK: + description: User providing feedback + title: Feedback + PURCHASE: + description: User intent to buy or purchase + title: Purchase + CANCEL: + description: User intent to cancel + title: Cancel + REFUND: + description: User requesting refund + title: Refund + is_a: TextClassificationSchemaEnum + annotations: + source_domain: data_science + source_schema: text_classification + EarthScienceDomainEnum: + description: Domain-level enum for earth_science value sets + is_a: ValueSetEnum + abstract: true + CollectionMethodsSchemaEnum: + description: Schema-level enum for collection_methods in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/collection_methods.yaml + SESARCollectionMethod: + title: SESAR Collection Method + description: Sample collection methods as defined by SESAR (System for Earth Sample Registration). These describe the + method by which a sample was collected. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.geosamples.org/vocabularies + permissible_values: + BLASTING: + description: Sample collected using blasting techniques + CAMERA_SLED: + description: Sample collected via camera sled or camera tow + annotations: + aliases: Camera tow + CORING: + description: Sample collected using coring techniques + CORING_BOX_CORER: + description: Sample collected using a box corer + annotations: + parent_method: Coring + CORING_CAMERA_MOUNTED: + description: Sample collected using camera-mounted corer + annotations: + parent_method: Coring + CORING_DRILL_CORER: + description: Sample collected using a drill corer + annotations: + parent_method: Coring + CORING_FREE_FALL_CORER: + description: Sample collected using a free-fall corer + annotations: + parent_method: Coring + CORING_GRAVITY: + description: Sample collected using a gravity corer + annotations: + parent_method: Coring + CORING_HAND_HELD: + description: Sample collected using a hand-held corer + annotations: + parent_method: Coring + CORING_KASTENLOT: + description: Sample collected using a kastenlot corer + annotations: + parent_method: Coring + CORING_MULTI: + description: Sample collected using a multi-corer + annotations: + parent_method: Coring + CORING_PISTON: + description: Sample collected using a piston corer + annotations: + parent_method: Coring + CORING_ROCK: + description: Sample collected using a rock corer + annotations: + parent_method: Coring + CORING_SIDE_SADDLE: + description: Sample collected using a side saddle corer + annotations: + parent_method: Coring + CORING_SUBMERSIBLE_MOUNTED: + description: Sample collected using a submersible-mounted corer + annotations: + parent_method: Coring + CORING_TRIGGER_WEIGHT: + description: Sample collected using a trigger weight corer + annotations: + parent_method: Coring + CORING_VIBRATING: + description: Sample collected using a vibrating corer + annotations: + parent_method: Coring + DREDGING: + description: Sample collected by dredging + DREDGING_CHAIN_BAG: + description: Sample collected using a chain bag dredge + annotations: + parent_method: Dredging + DREDGING_CHAIN_BAG_DREDGE: + description: Sample collected using a chain bag dredge + annotations: + parent_method: Dredging + EXPERIMENTAL_APPARATUS: + description: Sample collected using experimental apparatus + GRAB: + description: Sample collected using a grab sampler + GRAB_HOV: + description: Sample collected using Human-Occupied Vehicle grab + annotations: + parent_method: Grab + full_name: Human-Occupied Vehicle + GRAB_ROV: + description: Sample collected using Remotely Operated Vehicle grab + annotations: + parent_method: Grab + full_name: Remotely Operated Vehicle + MANUAL: + description: Sample collected manually + MANUAL_HAMMER: + description: Sample collected manually using a hammer + annotations: + parent_method: Manual + PROBE: + description: Sample collected using a probe + SEDIMENT_TRAP: + description: Sample collected using a sediment trap + SUSPENDED_SEDIMENT: + description: Suspended sediment sample + UNKNOWN: + description: Collection method unknown + is_a: CollectionMethodsSchemaEnum + annotations: + source_domain: earth_science + source_schema: collection_methods + FaoSoilSchemaEnum: + description: Schema-level enum for fao_soil in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/fao_soil.yaml + FAOSoilType: + title: FAO Soil Type + description: FAO World Reference Base (WRB) soil classification system. Based on the Harmonized World Soil Database (HWSD) + version 2. These represent the major soil groups according to the World Reference Base for Soil Resources. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.fao.org/soils-portal/data-hub/soil-classification/world-reference-base/en/ + - https://www.isric.org/explore/hwsd + permissible_values: + ACRISOLS: + description: Acrisols - soils with subsurface accumulation of low-activity clays and low base saturation + annotations: + symbol: AC + fao_id: 1 + color_rgb: 247,152,4 + ALISOLS: + description: Alisols - soils with high aluminium saturation and low base saturation + annotations: + symbol: AL + fao_id: 2 + color_rgb: 255,255,190 + ANDOSOLS: + title: andosol + description: Andosols - soils developed from volcanic ash with unique physical and chemical properties + meaning: ENVO:00002232 + annotations: + symbol: AN + fao_id: 3 + color_rgb: 254,0,0 + ARENOSOLS: + title: arenosol + description: Arenosols - sandy soils with weak horizon development + meaning: ENVO:00002229 + annotations: + symbol: AR + fao_id: 4 + color_rgb: 245,212,161 + ANTHROSOLS: + description: Anthrosols - soils strongly modified by human activities + annotations: + symbol: AT + fao_id: 5 + color_rgb: 207,152,4 + CHERNOZEMS: + description: Chernozems - very dark, fertile soils with thick mollic horizon + annotations: + symbol: CH + fao_id: 6 + color_rgb: 145,77,53 + CALCISOLS: + description: Calcisols - soils with secondary calcium carbonate accumulation + annotations: + symbol: CL + fao_id: 7 + color_rgb: 254,244,0 + CAMBISOLS: + description: Cambisols - soils with beginning of horizon differentiation + annotations: + symbol: CM + fao_id: 8 + color_rgb: 254,190,0 + CRYOSOLS: + title: cryosol + description: Cryosols - soils formed under permafrost conditions + meaning: ENVO:00002236 + annotations: + symbol: CR + fao_id: 9 + color_rgb: 75,61,172 + FLUVISOLS: + title: fluvisol + description: Fluvisols - soils developed from recent alluvial deposits + meaning: ENVO:00002273 + annotations: + symbol: FL + fao_id: 10 + color_rgb: 0,254,253 + FERRALSOLS: + description: Ferralsols - highly weathered soils with low-activity clay minerals + annotations: + symbol: FR + fao_id: 11 + color_rgb: 255,135,33 + GLACIERS: + title: glacier + description: Glaciers - areas covered by permanent ice + meaning: ENVO:00000133 + annotations: + symbol: GG + fao_id: 12 + color_rgb: 212,212,212 + GLEYSOLS: + title: gleysol + description: Gleysols - soils with permanent or temporary waterlogging + meaning: ENVO:00002244 + annotations: + symbol: GL + fao_id: 13 + color_rgb: 128,131,217 + GYPSISOLS: + description: Gypsisols - soils with secondary gypsum accumulation + annotations: + symbol: GY + fao_id: 14 + color_rgb: 254,246,164 + HISTOSOLS: + title: peat soil + description: Histosols - soils formed from organic materials (peat soils) + meaning: ENVO:00005774 + annotations: + symbol: HS + fao_id: 15 + color_rgb: 112,107,102 + KASTANOZEMS: + description: Kastanozems - soils with chestnut-colored mollic horizon + annotations: + symbol: KS + fao_id: 17 + color_rgb: 202,147,127 + LEPTOSOLS: + description: Leptosols - shallow soils over hard rock or highly calcareous material + annotations: + symbol: LP + fao_id: 18 + color_rgb: 209,209,209 + LUVISOLS: + description: Luvisols - soils with clay illuviation and high base saturation + annotations: + symbol: LV + fao_id: 19 + color_rgb: 250,132,132 + LIXISOLS: + description: Lixisols - soils with clay illuviation and low base saturation + annotations: + symbol: LX + fao_id: 20 + color_rgb: 255,190,190 + NITISOLS: + description: Nitisols - soils with deep, well-structured clay horizons + annotations: + symbol: NT + fao_id: 21 + color_rgb: 255,167,127 + PHAEOZEMS: + description: Phaeozems - soils with dark mollic horizon and high base saturation + annotations: + symbol: PH + fao_id: 22 + color_rgb: 189,100,70 + PLANOSOLS: + description: Planosols - soils with abrupt textural change and impermeable subsoil + annotations: + symbol: PL + fao_id: 23 + color_rgb: 247,125,58 + PLINTHOSOLS: + description: Plinthosols - soils with iron-rich, humus-poor mixture that hardens irreversibly + annotations: + symbol: PT + fao_id: 24 + color_rgb: 115,0,0 + PODZOLS: + description: Podzols - soils with subsurface accumulation of aluminium and iron complexes with organic matter (spodic + horizon) + annotations: + symbol: PZ + fao_id: 25 + color_rgb: 12,217,0 + REGOSOLS: + description: Regosols - weakly developed soils without significant horizon differentiation + annotations: + symbol: RG + fao_id: 26 + color_rgb: 254,227,164 + RETISOLS: + description: Retisols - soils with clay migration and tonguing of overlying material + annotations: + symbol: RT + fao_id: 27 + color_rgb: 254,194,194 + SOLONCHAKS: + title: solonchak + description: Solonchaks - soils with high salt content + meaning: ENVO:00002252 + annotations: + symbol: SC + fao_id: 28 + color_rgb: 254,0,250 + SOLONETZ: + description: Solonetz - soils with high exchangeable sodium content + annotations: + symbol: SN + fao_id: 29 + color_rgb: 249,194,254 + STAGNOSOLS: + description: Stagnosols - soils with seasonal waterlogging in upper horizons + annotations: + symbol: ST + fao_id: 30 + color_rgb: 64,192,233 + TECHNOSOLS: + description: Technosols - soils containing significant amounts of technical artifacts + annotations: + symbol: TC + fao_id: 31 + color_rgb: 145,0,157 + UMBRISOLS: + description: Umbrisols - soils with dark acidic surface horizon + annotations: + symbol: UM + fao_id: 32 + color_rgb: 115,142,127 + VERTISOLS: + title: vertisol + description: Vertisols - clay-rich soils with shrink-swell properties + meaning: ENVO:00002254 + annotations: + symbol: VR + fao_id: 33 + color_rgb: 197,0,255 + OPEN_INLAND_WATER: + title: fresh water body + description: Open inland water - areas covered by permanent water bodies + meaning: ENVO:01001320 + annotations: + symbol: WR + fao_id: 34 + color_rgb: 0,0,255 + NO_DATA: + description: No data - areas where soil data is not available + annotations: + symbol: ND + fao_id: 35 + color_rgb: 255,255,255 + is_a: FaoSoilSchemaEnum + annotations: + source_domain: earth_science + source_schema: fao_soil + HydrogeologySchemaEnum: + description: Schema-level enum for hydrogeology in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/hydrogeology.yaml + AquiferType: + title: Aquifer Type + description: Classification of aquifer types based on confinement, geology, and hydraulic characteristics. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + UNCONFINED: + description: An aquifer whose upper boundary is the water table, open to atmospheric pressure + CONFINED: + description: An aquifer bounded above and below by impermeable layers, under pressure greater than atmospheric + SEMI_CONFINED: + description: An aquifer partially bounded by layers of lower permeability that allow some vertical leakage + PERCHED: + description: A localized unconfined aquifer above the regional water table, supported by a low-permeability layer + ARTESIAN: + description: A confined aquifer in which the hydraulic pressure causes water to rise above the top of the aquifer + FRACTURED_ROCK: + description: An aquifer in which groundwater flows primarily through fractures in otherwise low-permeability rock + KARST: + description: An aquifer in soluble rock such as limestone where flow occurs through dissolution-enlarged conduits + and fractures + broad_mappings: + - ENVO:00000175 + ALLUVIAL: + description: An aquifer composed of unconsolidated alluvial deposits such as sand and gravel deposited by rivers + is_a: HydrogeologySchemaEnum + annotations: + source_domain: earth_science + source_schema: hydrogeology + GroundwaterProcessType: + title: Groundwater Process Type + description: Types of physical, chemical, and biological processes occurring in groundwater systems. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + RECHARGE: + description: The process by which water enters an aquifer from the surface or from an overlying formation + DISCHARGE: + description: The process by which groundwater exits an aquifer to the surface or to another formation + broad_mappings: + - ENVO:01001631 + BASEFLOW: + description: The portion of streamflow derived from groundwater discharge into surface water bodies + LATERAL_FLOW: + description: Horizontal movement of groundwater through an aquifer + broad_mappings: + - ENVO:01001632 + VERTICAL_LEAKAGE: + description: Vertical movement of groundwater between aquifers through semi-confining layers + SALTWATER_INTRUSION: + description: The movement of saline water into freshwater aquifers, typically in coastal areas + CONTAMINANT_TRANSPORT: + description: The movement and spreading of dissolved or suspended contaminants through groundwater + BIODEGRADATION: + description: The biological breakdown of contaminants in groundwater by microbial activity + broad_mappings: + - ENVO:06105014 + SORPTION: + description: The process by which dissolved substances are attached to solid surfaces in the aquifer matrix + PRECIPITATION_DISSOLUTION: + description: Chemical processes involving the formation or dissolution of mineral phases in groundwater + is_a: HydrogeologySchemaEnum + annotations: + source_domain: earth_science + source_schema: hydrogeology + HydrogeologyWellType: + title: Well Type + description: Classification of wells used for groundwater access, monitoring, and management. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MONITORING_WELL: + description: A well used to observe and measure groundwater conditions such as water level, quality, and flow + PRODUCTION_WELL: + description: A well used to extract groundwater for water supply purposes + INJECTION_WELL: + description: A well used to inject fluids into the subsurface for disposal, storage, or aquifer recharge + OBSERVATION_WELL: + description: A well used to observe hydrological parameters without significant water extraction + PIEZOMETER: + description: A device or small-diameter well used to measure hydraulic head at a specific point in the subsurface + EXTRACTION_WELL: + description: A well used to remove contaminated groundwater as part of remediation activities + RECHARGE_WELL: + description: A well used to artificially replenish groundwater by injecting treated water into an aquifer + GEOTHERMAL_WELL: + description: A well drilled to access geothermal resources for energy production or direct use + broad_mappings: + - ENVO:01000002 + is_a: HydrogeologySchemaEnum + annotations: + source_domain: earth_science + source_schema: hydrogeology + MaterialTypesSchemaEnum: + description: Schema-level enum for material_types in materials_science + is_a: MaterialsScienceDomainEnum + abstract: true + annotations: + source_file: materials_science/material_types.yaml + SESARMaterialType: + title: SESAR Material Type + description: Material types as defined by SESAR (System for Earth Sample Registration). These describe what a sample consists + of (e.g., rock, mineral, liquid). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.geosamples.org/vocabularies + permissible_values: + BIOLOGY: + description: Biological material or specimens + broad_mappings: + - ENVO:01000549 + GAS: + description: Gaseous material + broad_mappings: + - ENVO:01000797 + ICE: + description: Frozen water or ice samples + meaning: ENVO:01001125 + LIQUID_AQUEOUS: + description: Aqueous (water-based) liquid + broad_mappings: + - ENVO:00002006 + annotations: + sesar_label: Liquid>aqueous + LIQUID_ORGANIC: + description: Organic liquid + annotations: + sesar_label: Liquid>organic + MINERAL: + description: Mineral specimen + meaning: CHEBI:46662 + NOT_APPLICABLE: + description: Material type not applicable + annotations: + sesar_label: NotApplicable + ORGANIC_MATERIAL: + description: Organic material (non-living) + meaning: ENVO:01000155 + OTHER: + description: Other material type not listed + PARTICULATE: + description: Particulate matter + broad_mappings: + - ENVO:01000060 + PLANT_STRUCTURE: + description: Plant structure or tissue + meaning: PO:0009011 + ROCK: + description: Rock specimen + meaning: ENVO:00001995 + SEDIMENT: + description: Sediment sample + meaning: ENVO:00002007 + SOIL: + description: Soil sample + meaning: ENVO:00001998 + SYNTHETIC: + description: Synthetic or artificial material + broad_mappings: + - ENVO:06105123 + is_a: MaterialTypesSchemaEnum annotations: - source_domain: data_science - source_schema: emotion_classification - ExtendedEmotionEnum: - description: Extended emotion set including complex emotions - conforms_to: https://en.wikipedia.org/wiki/Emotion_classification + source_domain: earth_science + source_schema: material_types + PhysiographicFeaturesSchemaEnum: + description: Schema-level enum for physiographic_features in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/physiographic_features.yaml + SESARPhysiographicFeature: + title: SESAR Physiographic Feature + description: Physiographic feature types as defined by SESAR (System for Earth Sample Registration). These describe the + type of physical feature from which a sample was collected. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.geosamples.org/vocabularies + permissible_values: + ABYSSAL_FEATURE: + description: Deep ocean floor feature + ALLUVIAL_FAN: + description: Fan-shaped deposit formed by flowing water + ANTICLINE: + description: Upward-folded rock formation + AQUIFER: + description: Underground layer of water-bearing rock + ARCH: + description: Natural arch formation + annotations: + note: natural formation + ARROYO: + description: Steep-sided gully cut by running water + BADLANDS: + description: Dry terrain with eroded sedimentary rocks + BANK: + description: Raised area of seabed or riverbed + annotations: + note: hydrographic + BAR: + description: Elongated landform feature + annotations: + note: physiographic + BASIN: + description: Depression in the Earth's surface + BAY: + description: Body of water partly enclosed by land + BEACH: + description: Landform along a body of water + BIGHT: + description: Shallow bay or bend in a coastline + CANYON: + description: Deep gorge with steep sides + meaning: ENVO:00000169 + CAPE: + description: Pointed land projection into water + CAVE: + description: Natural underground chamber + meaning: ENVO:00000067 + CHANNEL: + description: Watercourse or strait + CIRQUE: + description: Amphitheater-like valley carved by glacial erosion + CLIFF: + description: Steep rock face + CONTINENTAL_DIVIDE: + description: Drainage divide on a continent + CONTINENTAL_MARGIN: + description: Zone between continental shelf and deep ocean + CRATER: + description: Bowl-shaped depression + DELTA: + description: Landform at river mouth + meaning: ENVO:00000101 + DRAINAGE_BASIN: + description: Area drained by a river system + DRUMLIN: + description: Elongated hill formed by glacial action + DUNE: + description: Hill of sand formed by wind or water + EARTHQUAKE_FEATURE: + description: Landform created by seismic activity + ESTUARY: + description: Partially enclosed coastal body of water + meaning: ENVO:00000045 + FAULT: + description: Fracture in rock with displacement + FAULT_ZONE: + description: Area containing multiple faults + FLAT: + description: Level land area + FLOODPLAIN: + description: Flat area adjacent to a river + FOLD: + description: Bend in rock layers + annotations: + note: geologic + FRACTURE_ZONE: + description: Area of crustal fractures + GAP: + description: Mountain pass or opening + GULF: + description: Large bay + GUT: + description: Narrow water passage + HYDROTHERMAL_VENT: + description: Fissure releasing geothermally heated water + meaning: ENVO:00000215 + ICE_MASS: + description: Large accumulation of ice + ISTHMUS: + description: Narrow strip of land connecting two larger areas + KARST_AREA: + description: Landscape formed by limestone dissolution + LAKE: + description: Body of standing water + meaning: ENVO:00000020 + LAVA_FIELD: + description: Area covered by lava flows + LEDGE: + description: Narrow horizontal surface projecting from rock + MASSIF: + description: Compact group of mountains + MESA: + description: Isolated flat-topped hill + MINERAL_DEPOSIT_AREA: + description: Area with concentrated mineral deposits + MORAINE: + description: Glacially formed accumulation of debris + MOUNTAIN: + description: Large natural elevation + meaning: ENVO:00000081 + MOUNTAIN_RANGE: + description: Series of connected mountains + meaning: ENVO:00000080 + MOUNTAIN_SUMMIT: + description: Highest point of a mountain + OCEAN_TRENCH: + description: Deep oceanic depression + OUTCROP: + description: Exposed rock formation + PLAIN: + description: Flat or gently rolling land + PLATEAU: + description: Elevated flat area + PLAYA: + description: Dried lake bed + REEF: + description: Ridge of rock or coral near water surface + meaning: ENVO:01001899 + RIDGE: + description: Long narrow elevation + RIFT_ZONE: + description: Area where Earth's crust is pulling apart + ROADCUT: + description: Artificial rock exposure along roadway + SEAMOUNT: + description: Underwater mountain + meaning: ENVO:00000264 + SEA: + description: Large body of salt water + STREAM: + description: Flowing body of water + SUBMARINE_CANYON: + description: Steep-sided valley on seafloor + meaning: ENVO:00000267 + SYNCLINE: + description: Downward-folded rock formation + THERMAL_FEATURE: + description: Geothermal feature + VALLEY: + description: Low area between hills or mountains + VOLCANO: + description: Vent in Earth's crust through which lava erupts + meaning: ENVO:00000247 + is_a: PhysiographicFeaturesSchemaEnum + annotations: + source_domain: earth_science + source_schema: physiographic_features + RemoteSensingSchemaEnum: + description: Schema-level enum for remote_sensing in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/remote_sensing.yaml + RemoteSensingPlatformType: + title: Remote Sensing Platform Type + description: Classification of platforms used to carry remote sensing instruments for earth observation and environmental + monitoring. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SATELLITE: + description: An artificial satellite orbiting Earth carrying remote sensing instruments + broad_mappings: + - ENVO:01001492 + AIRBORNE: + description: A manned aircraft carrying remote sensing instruments + UAV_DRONE: + description: An unmanned aerial vehicle or drone carrying remote sensing instruments + annotations: + aliases: UAV, drone + GROUND_BASED: + description: A stationary or mobile ground-based platform carrying remote sensing instruments + SHIPBORNE: + description: A watercraft carrying remote sensing instruments for maritime or coastal observation + is_a: RemoteSensingSchemaEnum + annotations: + source_domain: earth_science + source_schema: remote_sensing + RemoteSensingDataType: + title: Remote Sensing Data Type + description: Classification of data types acquired by remote sensing instruments, covering electromagnetic and potential + field measurements. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MULTISPECTRAL: + description: Imagery acquired in a limited number of discrete spectral bands across the electromagnetic spectrum + HYPERSPECTRAL: + description: Imagery acquired in many narrow, contiguous spectral bands providing detailed spectral information + SYNTHETIC_APERTURE_RADAR: + description: Radar imagery produced by synthesizing a large antenna aperture from a moving platform to achieve high + spatial resolution + annotations: + abbreviation: SAR + LIDAR: + description: Active remote sensing data acquired by measuring the time delay of reflected laser pulses to determine + distances and surface topography + annotations: + full_name: Light Detection And Ranging + THERMAL_INFRARED: + description: Imagery acquired in the thermal infrared portion of the spectrum, measuring emitted thermal radiation + MICROWAVE_RADIOMETRY: + description: Passive measurement of naturally emitted microwave radiation from the Earth's surface and atmosphere + GRAVIMETRY: + description: Measurement of variations in the gravitational field from airborne or satellite platforms + MAGNETOMETRY: + description: Measurement of variations in the magnetic field from airborne or satellite platforms + PHOTOGRAMMETRY: + description: The science of making measurements from photographs or imagery, typically to produce 3D models or maps + is_a: RemoteSensingSchemaEnum + annotations: + source_domain: earth_science + source_schema: remote_sensing + SampleTypesSchemaEnum: + description: Schema-level enum for sample_types in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/sample_types.yaml + SESARSampleType: + title: SESAR Sample Type + description: Sample object types as defined by SESAR (System for Earth Sample Registration). These describe the physical + form and collection context of samples. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.geosamples.org/vocabularies/sample-type-object + permissible_values: + CORE: + description: Long cylindrical cores + annotations: + sesar_definition: long cylindrical cores + CORE_CATCHER: + description: Material from core catcher treated as separate section + CORE_HALF_ROUND: + description: Half-cylindrical products of along-axis split of a whole round + CORE_PIECE: + description: Material occurring between unambiguous breaks in recovery + CORE_QUARTER_ROUND: + description: Quarter-cylindrical products of along-axis split of a half round + CORE_SECTION: + description: Arbitrarily cut segments of a core + CORE_SECTION_HALF: + description: Half-cylindrical products from section splits + CORE_SLAB: + description: Rectangular prism of material taken from a core with one dimension shorter + CORE_SUB_PIECE: + description: Mated portion of larger piece for curatorial management + CORE_U_CHANNEL: + description: Long rectangular prism of material for continuous measurement + CORE_WHOLE_ROUND: + description: Cylindrical segments of core or core section material + CTD: + description: A CTD (Conductivity, Temperature, and Depth) cast sample + annotations: + full_name: Conductivity Temperature Depth + CUTTINGS: + description: Loose, coarse, unconsolidated material suspended in drilling fluid + DREDGE: + description: A group of rocks collected by dragging a dredge along the seafloor + EXPERIMENTAL_SPECIMEN: + description: A synthetic material used during an experiment + GRAB: + description: Mechanically collected sample not necessarily representative + HOLE: + description: Hole cavity and walls surrounding that cavity + INDIVIDUAL_SAMPLE: + description: Single unit including rock samples or biological specimens + ORIENTED_CORE: + description: Core positioned identically to subsurface arrangement + OTHER: + description: Sample not fitting existing designations + ROCK_POWDER: + description: A sample created from pulverizing a rock to powder + SITE: + description: A place where a sample is collected + TERRESTRIAL_SECTION: + description: A sample of a section of the near-surface Earth, generally in the critical zone + is_a: SampleTypesSchemaEnum + annotations: + source_domain: earth_science + source_schema: sample_types + SubsurfaceSchemaEnum: + description: Schema-level enum for subsurface in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/subsurface.yaml + SubsurfaceFormationType: + title: Subsurface Formation Type + description: Classification of subsurface geological formations relevant to energy exploration, carbon storage, geothermal + systems, and groundwater resources. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AQUIFER: + description: An underground layer of water-bearing permeable rock or unconsolidated materials from which groundwater + can be extracted + meaning: ENVO:00012408 + AQUITARD: + description: A zone within the earth that restricts the flow of groundwater from one aquifer to another + RESERVOIR_ROCK: + description: A porous and permeable rock formation capable of storing and transmitting fluids such as oil, gas, or + water + CAPROCK: + description: An impermeable rock layer overlying a reservoir that prevents upward migration of fluids + FAULT_ZONE: + description: A zone of fracturing and deformation along a geological fault + broad_mappings: + - ENVO:01000668 + KARST: + description: A landscape formed from dissolution of soluble rocks such as limestone, dolomite, and gypsum, characterized + by sinkholes, caves, and underground drainage + meaning: ENVO:00000175 + PERMAFROST: + description: Soil or rock that remains at or below freezing for two or more consecutive years + meaning: ENVO:00000134 + UNCONSOLIDATED_SEDIMENT: + description: Loose, uncemented sedimentary material such as gravel, sand, silt, or clay + FRACTURED_BEDROCK: + description: Bedrock containing natural fractures that may serve as pathways for fluid flow + COAL_SEAM: + description: A stratum of coal within a sedimentary rock sequence + broad_mappings: + - ENVO:02000091 + SALT_DOME: + description: A dome-shaped intrusion of evaporite minerals formed by upward movement of a salt body through overlying + rock + meaning: ENVO:01000505 + SHALE: + description: A fine-grained sedimentary rock formed from compacted clay or mud, often serving as a seal or source + rock + meaning: ENVO:00002056 + is_a: SubsurfaceSchemaEnum + annotations: + source_domain: earth_science + source_schema: subsurface + GeophysicalMethodType: + title: Geophysical Method Type + description: Types of geophysical investigation methods used for subsurface characterization, resource exploration, and + environmental monitoring. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SEISMIC_REFLECTION: + description: A geophysical method using reflected seismic waves to image subsurface geological structures + SEISMIC_REFRACTION: + description: A geophysical method using refracted seismic waves to determine subsurface velocity structure and layer + boundaries + GROUND_PENETRATING_RADAR: + description: A geophysical method using radar pulses to image the shallow subsurface + ELECTRICAL_RESISTIVITY_TOMOGRAPHY: + description: A geophysical imaging technique that measures the electrical resistivity distribution of the subsurface + MAGNETOTELLURICS: + description: A geophysical method using natural electromagnetic fields to investigate the subsurface electrical conductivity + structure + GRAVITY_SURVEY: + description: A geophysical method measuring variations in the gravitational field to infer subsurface density distribution + MAGNETIC_SURVEY: + description: A geophysical method measuring variations in the magnetic field to detect subsurface magnetic anomalies + WELL_LOGGING: + description: Measurement of physical properties of rock formations traversed by a borehole using downhole instruments + DISTRIBUTED_ACOUSTIC_SENSING: + description: A monitoring technique using fiber optic cables to measure acoustic signals along a borehole or surface + deployment + DISTRIBUTED_TEMPERATURE_SENSING: + description: A monitoring technique using fiber optic cables to measure temperature profiles along a borehole or surface + deployment + CROSSWELL_TOMOGRAPHY: + description: A geophysical imaging method using sources and receivers in separate boreholes to image the intervening + subsurface + is_a: SubsurfaceSchemaEnum + annotations: + source_domain: earth_science + source_schema: subsurface + SubsurfacePropertyType: + title: Subsurface Property Type + description: Physical and hydraulic properties of subsurface formations relevant to resource characterization and reservoir + modeling. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + POROSITY: + description: The fraction of void space in a rock or sediment relative to its total volume + meaning: PATO:0000973 + PERMEABILITY: + description: The ability of a porous material to allow fluids to pass through it + meaning: PATO:0000970 + THERMAL_CONDUCTIVITY: + description: The rate at which heat is transferred through a material per unit area per unit temperature gradient + broad_mappings: + - PATO:0001756 + SPECIFIC_HEAT_CAPACITY: + description: The amount of heat energy required to raise the temperature of a unit mass of material by one degree + BULK_DENSITY: + description: The mass of a material divided by its total volume, including pore spaces + broad_mappings: + - PATO:0001019 + FLUID_SATURATION: + description: The fraction of pore space occupied by a specific fluid phase + PORE_PRESSURE: + description: The pressure of fluids within the pore spaces of rock or sediment + GEOTHERMAL_GRADIENT: + description: The rate of temperature increase with depth in the Earth's subsurface + HYDRAULIC_CONDUCTIVITY: + description: A measure of the ease with which water can move through a porous medium under a hydraulic gradient + ELASTIC_MODULUS: + description: A measure of the stiffness of a material, defined as the ratio of stress to strain + SEISMIC_VELOCITY: + description: The speed at which seismic waves propagate through a subsurface material + is_a: SubsurfaceSchemaEnum + annotations: + source_domain: earth_science + source_schema: subsurface + WaterResourcesSchemaEnum: + description: Schema-level enum for water_resources in earth_science + is_a: EarthScienceDomainEnum + abstract: true + annotations: + source_file: earth_science/water_resources.yaml + WaterResourceType: + title: Water Resource Type + description: Classification of water resources by source, quality, and origin. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SURFACE_WATER: + description: Water found on the surface of the Earth in rivers, lakes, reservoirs, and wetlands + meaning: ENVO:00002042 + GROUNDWATER: + description: Underground water located in pore spaces of rock or unconsolidated deposits + meaning: ENVO:01001004 + PRODUCED_WATER: + description: Water brought to the surface during oil, gas, or geothermal extraction operations + BRACKISH_WATER: + description: Water with salinity between freshwater and seawater + meaning: ENVO:00002019 + SEAWATER: + description: Water from the ocean or sea with characteristic salinity levels + broad_mappings: + - ENVO:00002149 + STORMWATER: + description: Water that accumulates on surfaces during precipitation events and snow or ice melt + meaning: ENVO:01001267 + WASTEWATER: + description: Water that has been adversely affected in quality by anthropogenic influence + broad_mappings: + - ENVO:01000964 + RECLAIMED_WATER: + description: Wastewater that has been treated to a level suitable for beneficial reuse + GLACIAL_MELTWATER: + description: Water released by the melting of glacial ice, ice sheets, or ice shelves + broad_mappings: + - ENVO:01000722 + is_a: WaterResourcesSchemaEnum + annotations: + source_domain: earth_science + source_schema: water_resources + WaterUseCategoryType: + title: Water Use Category Type + description: Classification of water use categories relevant to the water-energy nexus and national water resource planning. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AGRICULTURAL_IRRIGATION: + description: Water used for irrigation of crops and agricultural land + INDUSTRIAL_COOLING: + description: Water used for cooling processes in industrial facilities + MUNICIPAL_SUPPLY: + description: Water supplied for domestic, commercial, and public use by a municipal system + THERMOELECTRIC_POWER: + description: Water used in thermoelectric power generation for steam production and cooling + HYDROELECTRIC: + description: Water used for hydroelectric power generation + MINING: + description: Water used in mining operations for extraction, processing, and dust suppression + LIVESTOCK: + description: Water used for livestock watering, feedlots, and dairy operations + AQUACULTURE: + description: Water used for farming aquatic organisms including fish, shellfish, and plants + ENVIRONMENTAL_FLOW: + description: Water allocated to maintain or restore ecological health of rivers, wetlands, and other water-dependent + ecosystems + is_a: WaterResourcesSchemaEnum + annotations: + source_domain: earth_science + source_schema: water_resources + WaterQualityParameterType: + title: Water Quality Parameter Type + description: Physical, chemical, and biological parameters used to assess water quality for various applications. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ANGER: - description: Feeling of displeasure or hostility - title: Anger - meaning: MFOEM:000009 - DISGUST: - description: Feeling of revulsion - title: Disgust - meaning: MFOEM:000019 - FEAR: - description: Feeling of anxiety - title: Fear - meaning: MFOEM:000026 - HAPPINESS: - description: Feeling of pleasure - title: Happiness - meaning: MFOEM:000042 - SADNESS: - description: Feeling of sorrow - title: Sadness - meaning: MFOEM:000056 - SURPRISE: - description: Feeling of astonishment - title: Surprise - meaning: MFOEM:000032 - CONTEMPT: - description: Feeling that something is worthless - title: Contempt - meaning: MFOEM:000018 - ANTICIPATION: - description: Feeling of excitement about something that will happen - title: Erwartung - meaning: MFOEM:000175 - aliases: - - expectation - - expectant - TRUST: - description: Feeling of confidence in someone or something - title: Trust - meaning: MFOEM:000224 - LOVE: - description: Feeling of deep affection - title: Love - meaning: MFOEM:000048 - is_a: EmotionClassificationSchemaEnum + PH: + description: A measure of the hydrogen ion concentration indicating the acidity or alkalinity of water + broad_mappings: + - PATO:0001842 + DISSOLVED_OXYGEN: + description: The concentration of molecular oxygen dissolved in water + broad_mappings: + - CHEBI:15379 + TOTAL_DISSOLVED_SOLIDS: + description: The total concentration of dissolved inorganic and organic substances in water + TURBIDITY: + description: A measure of the degree to which water loses its transparency due to suspended particulates + CONDUCTIVITY: + description: The ability of water to conduct an electrical current, related to the concentration of dissolved ions + broad_mappings: + - PATO:0001757 + BIOLOGICAL_OXYGEN_DEMAND: + description: The amount of dissolved oxygen consumed by biological organisms during the decomposition of organic matter + CHEMICAL_OXYGEN_DEMAND: + description: The amount of oxygen required to chemically oxidize organic and inorganic matter in water + NITRATE: + description: The concentration of nitrate ions in water, an indicator of nutrient loading + meaning: CHEBI:17632 + PHOSPHATE: + description: The concentration of phosphate in water, an indicator of nutrient loading and eutrophication potential + meaning: CHEBI:26020 + HEAVY_METALS: + description: The concentration of heavy metals in water, including lead, mercury, cadmium, and arsenic + broad_mappings: + - CHEBI:5631 + COLIFORM_BACTERIA: + description: The presence and concentration of coliform bacteria as indicators of microbial contamination + TEMPERATURE: + description: The thermal energy of the water, affecting dissolved oxygen levels and biological activity + meaning: PATO:0000146 + is_a: WaterResourcesSchemaEnum annotations: - source_domain: data_science - source_schema: emotion_classification - PrioritySeveritySchemaEnum: - description: Schema-level enum for priority_severity in data_science - is_a: DataScienceDomainEnum + source_domain: earth_science + source_schema: water_resources + EnergyDomainEnum: + description: Domain-level enum for energy value sets + is_a: ValueSetEnum + abstract: true + EnergySchemaEnum: + description: Schema-level enum for energy in energy + is_a: EnergyDomainEnum abstract: true annotations: - source_file: data_science/priority_severity.yaml - PriorityLevelEnum: - description: Standard priority levels for task/issue classification + source_file: energy/energy.yaml + EnergySource: + title: Energy Source + description: Types of energy sources and generation methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - CRITICAL: - description: Highest priority, requires immediate attention - title: Critical - aliases: - - P0 - - urgent - - blocker - - '1' - HIGH: - description: High priority, should be addressed soon - title: High - aliases: - - P1 - - important - - '2' - MEDIUM: - description: Medium priority, normal workflow - title: Medium - aliases: - - P2 - - normal - - '3' - LOW: - description: Low priority, can be deferred - title: Low + SOLAR: + title: Solar energy (photovoltaic and thermal) aliases: - - P3 - - minor - - '4' - TRIVIAL: - description: Lowest priority, nice to have - title: Trivial + - Solar radiation + meaning: ENVO:01001862 + exact_mappings: + - OEO:00000384 + related_mappings: + - brick:Solar_Thermal_Collector + annotations: + renewable: true + emission_free: true + oeo_label: solar energy + brick_label: Solar Thermal Collector + WIND: + title: Wind power aliases: - - P4 - - cosmetic - - '5' - is_a: PrioritySeveritySchemaEnum - annotations: - source_domain: data_science - source_schema: priority_severity - SeverityLevelEnum: - description: Severity levels for incident/bug classification - permissible_values: - CRITICAL: - description: System is unusable, data loss possible - title: Critical + - wind wave energy + related_mappings: + - ENVO:2000033 + broad_mappings: + - sweet:phenAtmoWind/Wind + exact_mappings: + - OEO:00000446 + annotations: + renewable: true + emission_free: true + oeo_label: wind energy + HYDROELECTRIC: + title: Hydroelectric power aliases: - - S1 - - blocker - - showstopper - MAJOR: - description: Major functionality impaired - title: Major + - hydroelectric dam + related_mappings: + - ENVO:00000468 + exact_mappings: + - OEO:00000218 + annotations: + renewable: true + emission_free: true + oeo_label: hydro energy + GEOTHERMAL: + title: Geothermal energy aliases: - - S2 - - severe - - high - MINOR: - description: Minor functionality impaired - title: Minor + - geothermal energy + meaning: ENVO:2000034 + close_mappings: + - sweet:phenEnergy/Geothermal + exact_mappings: + - OEO:00000191 + annotations: + renewable: true + emission_free: true + oeo_label: geothermal energy + BIOMASS: + title: Biomass and bioenergy aliases: - - S3 - - moderate - - medium - TRIVIAL: - description: Cosmetic issue, minimal impact - title: Trivial + - organic material + related_mappings: + - ENVO:01000155 + close_mappings: + - sweet:matrBiomass/Biomass + exact_mappings: + - OEO:00010258 + annotations: + renewable: true + emission_free: false + oeo_label: bioenergy + BIOFUEL: + title: Biofuels (ethanol, biodiesel) + close_mappings: + - sweet:matrEnergy/Biofuel + exact_mappings: + - OEO:00000072 + annotations: + renewable: true + emission_free: false + oeo_label: biofuel + TIDAL: + title: Tidal and wave energy + close_mappings: + - OEO:00010100 + - OEO:00010102 + annotations: + renewable: true + emission_free: true + oeo_label: marine tidal energy, marine wave energy + HYDROGEN: + title: Hydrogen fuel aliases: - - S4 - - cosmetic - - low - is_a: PrioritySeveritySchemaEnum - annotations: - source_domain: data_science - source_schema: priority_severity - ConfidenceLevelEnum: - description: Confidence levels for predictions and classifications - permissible_values: - VERY_HIGH: - description: Very high confidence (>95%) - title: Very High + - dihydrogen + meaning: CHEBI:18276 + broad_mappings: + - sweet:matrElement/Hydrogen + exact_mappings: + - OEO:00000220 + annotations: + renewable: depends + emission_free: true + oeo_label: hydrogen + COAL: + title: Coal + meaning: ENVO:02000091 + close_mappings: + - sweet:matrNaturalResource/Coal + exact_mappings: + - OEO:00000088 + annotations: + renewable: false + emission_free: false + fossil_fuel: true + oeo_label: coal + NATURAL_GAS: + title: Natural gas + meaning: ENVO:01000552 + close_mappings: + - sweet:matrNaturalResource/NaturalGas + exact_mappings: + - OEO:00000292 + annotations: + renewable: false + emission_free: false + fossil_fuel: true + oeo_label: natural gas + PETROLEUM: + title: Petroleum/oil + meaning: ENVO:00002984 + close_mappings: + - sweet:matrNaturalResource/Petroleum + - OEO:00000115 + annotations: + renewable: false + emission_free: false + fossil_fuel: true + oeo_label: crude oil + DIESEL: + title: Diesel fuel aliases: - - certain - - '5' - HIGH: - description: High confidence (80-95%) - title: High + - diesel fuel + meaning: ENVO:03510006 + exact_mappings: + - OEO:00010242 + annotations: + renewable: false + emission_free: false + fossil_fuel: true + oeo_label: diesel fuel + GASOLINE: + title: Gasoline/petrol aliases: - - confident - - '4' - MEDIUM: - description: Medium confidence (60-80%) - title: Medium + - fuel oil + related_mappings: + - ENVO:00002983 + exact_mappings: + - OEO:00010241 + annotations: + renewable: false + emission_free: false + fossil_fuel: true + oeo_label: gasoline fuel + PROPANE: + title: Propane/LPG aliases: - - moderate - - '3' - LOW: - description: Low confidence (40-60%) - title: Low + - liquefied petroleum gas + meaning: ENVO:01000553 + annotations: + renewable: false + emission_free: false + fossil_fuel: true + NUCLEAR_FISSION: + title: Nuclear fission aliases: - - uncertain - - '2' - VERY_LOW: - description: Very low confidence (<40%) - title: Very Low + - nuclear energy + related_mappings: + - ENVO:2000025 + exact_mappings: + - CHEBI:35231 + close_mappings: + - OEO:00000302 + annotations: + renewable: false + emission_free: true + oeo_label: nuclear fuel + NUCLEAR_FUSION: + title: Nuclear fusion (experimental) aliases: - - guess - - '1' - is_a: PrioritySeveritySchemaEnum + - nuclear energy + related_mappings: + - ENVO:2000025 + annotations: + renewable: false + emission_free: true + GRID_MIX: + title: Grid electricity (mixed sources) + close_mappings: + - OEO:00000200 + annotations: + renewable: partial + oeo_label: supply grid + BATTERY_STORAGE: + description: Battery storage systems + close_mappings: + - OEO:00000068 + annotations: + storage: true + oeo_label: battery + is_a: EnergySchemaEnum annotations: - source_domain: data_science - source_schema: priority_severity - QualityControlSchemaEnum: - description: Schema-level enum for quality_control in data_science - is_a: DataScienceDomainEnum - abstract: true + source_domain: energy + source_schema: energy + EnergyUnit: + title: Energy Unit + description: Units for measuring energy + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + JOULE: + description: Joule (J) + meaning: QUDT:J + annotations: + symbol: J + ucum: J + si_base: true + KILOJOULE: + description: Kilojoule (kJ) + meaning: QUDT:KiloJ + annotations: + symbol: kJ + ucum: kJ + joules: 1000 + MEGAJOULE: + description: Megajoule (MJ) + meaning: QUDT:MegaJ + annotations: + symbol: MJ + ucum: MJ + joules: 1e6 + GIGAJOULE: + description: Gigajoule (GJ) + meaning: QUDT:GigaJ + annotations: + symbol: GJ + ucum: GJ + joules: 1e9 + WATT_HOUR: + description: Watt-hour (Wh) + meaning: QUDT:W-HR + annotations: + symbol: Wh + ucum: W.h + joules: 3600 + KILOWATT_HOUR: + description: Kilowatt-hour (kWh) + meaning: QUDT:KiloW-HR + annotations: + symbol: kWh + ucum: kW.h + joules: 3.6e6 + MEGAWATT_HOUR: + description: Megawatt-hour (MWh) + meaning: QUDT:MegaW-HR + annotations: + symbol: MWh + ucum: MW.h + joules: 3.6e9 + GIGAWATT_HOUR: + description: Gigawatt-hour (GWh) + meaning: QUDT:GigaW-HR + annotations: + symbol: GWh + ucum: GW.h + joules: 3.6e12 + TERAWATT_HOUR: + description: Terawatt-hour (TWh) + meaning: QUDT:TeraW-HR + annotations: + symbol: TWh + ucum: TW.h + joules: 3.6e15 + CALORIE: + description: Calorie (cal) + meaning: QUDT:CAL + annotations: + symbol: cal + ucum: cal + joules: 4.184 + KILOCALORIE: + description: Kilocalorie (kcal) + meaning: QUDT:KiloCAL + annotations: + symbol: kcal + ucum: kcal + joules: 4184 + BTU: + description: British thermal unit + meaning: QUDT:BTU_IT + annotations: + symbol: BTU + ucum: '[Btu_IT]' + joules: 1055.06 + THERM: + description: Therm + meaning: QUDT:THM_US + annotations: + symbol: thm + ucum: '[thm_us]' + joules: 1.055e8 + ELECTRON_VOLT: + description: Electron volt (eV) + meaning: QUDT:EV + annotations: + symbol: eV + ucum: eV + joules: 1.602e-19 + TOE: + description: Tonne of oil equivalent + meaning: QUDT:TOE + annotations: + symbol: toe + ucum: toe + joules: 4.187e10 + TCE: + description: Tonne of coal equivalent + annotations: + symbol: tce + ucum: tce + joules: 2.93e10 + is_a: EnergySchemaEnum + annotations: + source_domain: energy + source_schema: energy + PowerUnit: + title: Power Unit + description: Units for measuring power (energy per time) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + WATT: + description: Watt (W) + meaning: QUDT:W + annotations: + symbol: W + ucum: W + si_base: true + KILOWATT: + description: Kilowatt (kW) + meaning: QUDT:KiloW + annotations: + symbol: kW + ucum: kW + watts: 1000 + MEGAWATT: + description: Megawatt (MW) + meaning: QUDT:MegaW + annotations: + symbol: MW + ucum: MW + watts: 1e6 + GIGAWATT: + description: Gigawatt (GW) + meaning: QUDT:GigaW + annotations: + symbol: GW + ucum: GW + watts: 1e9 + TERAWATT: + description: Terawatt (TW) + meaning: QUDT:TeraW + annotations: + symbol: TW + ucum: TW + watts: 1e12 + HORSEPOWER: + description: Horsepower + meaning: QUDT:HP + annotations: + symbol: hp + ucum: '[HP]' + watts: 745.7 + BTU_PER_HOUR: + description: BTU per hour + annotations: + symbol: BTU/h + ucum: '[Btu_IT]/h' + watts: 0.293 + is_a: EnergySchemaEnum annotations: - source_file: data_science/quality_control.yaml - QualityControlEnum: - description: Quality control classification labels + source_domain: energy + source_schema: energy + EnergyEfficiencyRating: + title: Energy Efficiency Rating + description: Energy efficiency ratings and standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - PASS: - description: Item meets quality standards - title: Pass - meaning: NCIT:C81275 - aliases: - - passed - - acceptable - - ok - - '1' - FAIL: - description: Item does not meet quality standards - title: Fail - meaning: NCIT:C44281 - aliases: - - failed - - reject - - defective - - '0' - is_a: QualityControlSchemaEnum + A_PLUS_PLUS_PLUS: + description: A+++ (highest efficiency) + annotations: + rank: 1 + region: EU + A_PLUS_PLUS: + description: A++ + annotations: + rank: 2 + region: EU + A_PLUS: + description: A+ + annotations: + rank: 3 + region: EU + A: + description: A + annotations: + rank: 4 + region: EU + B: + description: B + annotations: + rank: 5 + region: EU + C: + description: C + annotations: + rank: 6 + region: EU + D: + description: D + annotations: + rank: 7 + region: EU + E: + description: E + annotations: + rank: 8 + region: EU + F: + description: F + annotations: + rank: 9 + region: EU + G: + description: G (lowest efficiency) + annotations: + rank: 10 + region: EU + ENERGY_STAR: + description: Energy Star certified + annotations: + region: US + ENERGY_STAR_MOST_EFFICIENT: + description: Energy Star Most Efficient + annotations: + region: US + is_a: EnergySchemaEnum annotations: - source_domain: data_science - source_schema: quality_control - DefectClassificationEnum: - description: Manufacturing defect classification + source_domain: energy + source_schema: energy + BuildingEnergyStandard: + title: Building Energy Standard + description: Building energy efficiency standards and certifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - NO_DEFECT: - description: No defect detected - title: No Defect - meaning: NCIT:C14165 - aliases: - - good - - normal - - '0' - MINOR_DEFECT: - description: Minor defect that doesn't affect functionality - title: Minor Defect - aliases: - - minor - - cosmetic - - '1' - MAJOR_DEFECT: - description: Major defect affecting functionality - title: Major Defect - aliases: - - major - - functional - - '2' - CRITICAL_DEFECT: - description: Critical defect rendering item unusable or unsafe - title: Critical Defect - aliases: - - critical - - severe - - '3' - is_a: QualityControlSchemaEnum - annotations: - source_domain: data_science - source_schema: quality_control - SentimentAnalysisSchemaEnum: - description: Schema-level enum for sentiment_analysis in data_science - is_a: DataScienceDomainEnum - abstract: true + PASSIVE_HOUSE: + description: Passive House (Passivhaus) standard + LEED_PLATINUM: + description: LEED Platinum certification + LEED_GOLD: + description: LEED Gold certification + LEED_SILVER: + description: LEED Silver certification + LEED_CERTIFIED: + description: LEED Certified + BREEAM_OUTSTANDING: + description: BREEAM Outstanding + BREEAM_EXCELLENT: + description: BREEAM Excellent + BREEAM_VERY_GOOD: + description: BREEAM Very Good + BREEAM_GOOD: + description: BREEAM Good + BREEAM_PASS: + description: BREEAM Pass + NET_ZERO: + description: Net Zero Energy Building + ENERGY_POSITIVE: + description: Energy Positive Building + ZERO_CARBON: + description: Zero Carbon Building + is_a: EnergySchemaEnum annotations: - source_file: data_science/sentiment_analysis.yaml - SentimentClassificationEnum: - description: Standard labels for sentiment analysis classification tasks + source_domain: energy + source_schema: energy + GridType: + title: Grid Type + description: Types of electrical grid systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - POSITIVE: - description: Positive sentiment or opinion - title: Positive Finding - meaning: NCIT:C38758 - aliases: - - pos - - '1' - - + - NEGATIVE: - description: Negative sentiment or opinion - title: Negative Test Result - meaning: NCIT:C35681 - aliases: - - neg - - '0' - - '-' - NEUTRAL: - description: Neutral sentiment, neither positive nor negative - title: Normal - meaning: NCIT:C14165 - aliases: - - neu - - '2' - is_a: SentimentAnalysisSchemaEnum + MAIN_GRID: + description: Main utility grid + exact_mappings: + - OEO:00000200 + annotations: + oeo_label: supply grid + MICROGRID: + description: Microgrid + OFF_GRID: + description: Off-grid/standalone + SMART_GRID: + description: Smart grid + MINI_GRID: + description: Mini-grid + VIRTUAL_POWER_PLANT: + description: Virtual power plant + is_a: EnergySchemaEnum annotations: - source_domain: data_science - source_schema: sentiment_analysis - FineSentimentClassificationEnum: - description: Fine-grained sentiment analysis labels with intensity levels - permissible_values: - VERY_POSITIVE: - description: Strongly positive sentiment - title: Positive Finding - is_a: POSITIVE - meaning: NCIT:C38758 - aliases: - - '5' - - ++ - POSITIVE: - description: Positive sentiment - title: Positive Finding - meaning: NCIT:C38758 - aliases: - - '4' - - + - NEUTRAL: - description: Neutral sentiment - title: Normal - meaning: NCIT:C14165 - aliases: - - '3' - - '0' - NEGATIVE: - description: Negative sentiment - title: Negative Test Result - meaning: NCIT:C35681 + source_domain: energy + source_schema: energy + BatteryType: + title: Battery Type + description: Types of battery technologies for energy storage + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + exact_mappings: + - OEO:00000068 + - brick:Battery + permissible_values: + LITHIUM_ION: + description: Lithium-ion battery aliases: - - '2' - - '-' - VERY_NEGATIVE: - description: Strongly negative sentiment - title: Negative Test Result - is_a: NEGATIVE - meaning: NCIT:C35681 + - Li-ion + - LIB + annotations: + chemistry: lithium + LITHIUM_IRON_PHOSPHATE: + description: Lithium iron phosphate (LFP) battery aliases: - - '1' - - -- - is_a: SentimentAnalysisSchemaEnum - annotations: - source_domain: data_science - source_schema: sentiment_analysis - TextClassificationSchemaEnum: - description: Schema-level enum for text_classification in data_science - is_a: DataScienceDomainEnum - abstract: true - annotations: - source_file: data_science/text_classification.yaml - NewsTopicCategoryEnum: - description: Common news article topic categories - permissible_values: - POLITICS: - description: Political news and government affairs - title: Politics - BUSINESS: - description: Business, finance, and economic news - title: Business + - LFP + - LiFePO4 + annotations: + chemistry: lithium + LITHIUM_POLYMER: + description: Lithium polymer battery aliases: - - finance - - economy - TECHNOLOGY: - description: Technology and computing news - title: Technology + - LiPo + annotations: + chemistry: lithium + LEAD_ACID: + description: Lead-acid battery aliases: - - tech - - IT - SPORTS: - description: Sports news and events - title: Sports - ENTERTAINMENT: - description: Entertainment and celebrity news - title: Entertainment + - Pb-acid + annotations: + chemistry: lead + NICKEL_METAL_HYDRIDE: + description: Nickel-metal hydride battery aliases: - - showbiz - SCIENCE: - description: Scientific discoveries and research - title: Science - HEALTH: - description: Health, medicine, and wellness news - title: Health + - NiMH + annotations: + chemistry: nickel + NICKEL_CADMIUM: + description: Nickel-cadmium battery aliases: - - medical - WORLD: - description: International news and events - title: World + - NiCd + annotations: + chemistry: nickel + SODIUM_ION: + description: Sodium-ion battery aliases: - - international - - global - LOCAL: - description: Local and regional news - title: Local + - Na-ion + annotations: + chemistry: sodium + SOLID_STATE: + description: Solid-state battery + annotations: + chemistry: various + VANADIUM_REDOX_FLOW: + description: Vanadium redox flow battery aliases: - - regional - is_a: TextClassificationSchemaEnum + - VRB + - VRFB + annotations: + chemistry: vanadium + type: flow + ZINC_BROMINE_FLOW: + description: Zinc-bromine flow battery + aliases: + - ZnBr + annotations: + chemistry: zinc + type: flow + IRON_AIR: + description: Iron-air battery + annotations: + chemistry: iron + ZINC_AIR: + description: Zinc-air battery + annotations: + chemistry: zinc + is_a: EnergySchemaEnum annotations: - source_domain: data_science - source_schema: text_classification - ToxicityClassificationEnum: - description: Text toxicity classification labels - permissible_values: - NON_TOXIC: - description: Text is appropriate and non-harmful - title: Non-Toxic - meaning: SIO:001010 + source_domain: energy + source_schema: energy + PVCellType: + title: Photovoltaic Cell Type + description: Types of photovoltaic cell technologies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - OEO:00000348 + permissible_values: + MONOCRYSTALLINE_SILICON: + description: Monocrystalline silicon (mono-Si) cells + aliases: + - mono-Si + - single-crystal silicon + related_mappings: + - CHEBI:27573 + annotations: + material: silicon + efficiency_range: 17-22% + POLYCRYSTALLINE_SILICON: + description: Polycrystalline silicon (poly-Si) cells aliases: - - safe - - clean - - '0' - TOXIC: - description: Text contains harmful or inappropriate content - title: Toxic + - poly-Si + - multi-crystalline silicon + related_mappings: + - CHEBI:27573 + annotations: + material: silicon + efficiency_range: 15-17% + PASSIVATED_EMITTER_REAR_CELL: + description: Passivated Emitter and Rear Cell (PERC) aliases: - - harmful - - inappropriate - - '1' - SEVERE_TOXIC: - description: Text contains severely harmful content - title: Severe Toxic - is_a: TOXIC - OBSCENE: - description: Text contains obscene content - title: Obscene - is_a: TOXIC - THREAT: - description: Text contains threatening content - title: Threat - is_a: TOXIC - INSULT: - description: Text contains insulting content - title: Insult - is_a: TOXIC - IDENTITY_HATE: - description: Text contains identity-based hate - title: Identity Hate - is_a: TOXIC - is_a: TextClassificationSchemaEnum - annotations: - source_domain: data_science - source_schema: text_classification - IntentClassificationEnum: - description: Common chatbot/NLU intent categories - permissible_values: - GREETING: - description: User greeting or hello - title: Greeting - GOODBYE: - description: User saying goodbye - title: Goodbye - THANKS: - description: User expressing gratitude - title: Thanks - HELP: - description: User requesting help or assistance - title: Help - INFORMATION: - description: User requesting information - title: Information - COMPLAINT: - description: User expressing dissatisfaction - title: Complaint - FEEDBACK: - description: User providing feedback - title: Feedback - PURCHASE: - description: User intent to buy or purchase - title: Purchase - CANCEL: - description: User intent to cancel - title: Cancel - REFUND: - description: User requesting refund - title: Refund - is_a: TextClassificationSchemaEnum - annotations: - source_domain: data_science - source_schema: text_classification - EnergyDomainEnum: - description: Domain-level enum for energy value sets - is_a: ValueSetEnum - abstract: true - EnergySchemaEnum: - description: Schema-level enum for energy in energy - is_a: EnergyDomainEnum - abstract: true - annotations: - source_file: energy/energy.yaml - EnergySource: - description: Types of energy sources and generation methods - permissible_values: - SOLAR: - title: Solar energy (photovoltaic and thermal) + - PERC + annotations: + material: silicon + efficiency_range: 19-22% + HETEROJUNCTION: + description: Heterojunction (HJT) cells aliases: - - Solar radiation - meaning: ENVO:01001862 + - HJT + - HIT annotations: - renewable: true - emission_free: true - WIND: - title: Wind power + material: silicon + efficiency_range: 21-24% + TUNNEL_OXIDE_PASSIVATED_CONTACT: + description: Tunnel Oxide Passivated Contact (TOPCon) cells aliases: - - wind wave energy - related_mappings: - - ENVO:2000033 + - TOPCon annotations: - renewable: true - emission_free: true - HYDROELECTRIC: - title: Hydroelectric power + material: silicon + efficiency_range: 22-24% + INTERDIGITATED_BACK_CONTACT: + description: Interdigitated Back Contact (IBC) cells aliases: - - hydroelectric dam - related_mappings: - - ENVO:00000468 + - IBC annotations: - renewable: true - emission_free: true - GEOTHERMAL: - title: Geothermal energy + material: silicon + efficiency_range: 22-24% + CADMIUM_TELLURIDE: + description: Cadmium telluride (CdTe) thin-film cells aliases: - - geothermal energy - meaning: ENVO:2000034 + - CdTe + exact_mappings: + - CHEBI:232800 annotations: - renewable: true - emission_free: true - BIOMASS: - title: Biomass and bioenergy + material: cadmium_telluride + type: thin-film + efficiency_range: 16-18% + COPPER_INDIUM_GALLIUM_SELENIDE: + description: Copper indium gallium selenide (CIGS) thin-film cells aliases: - - organic material + - CIGS + - CIS + annotations: + material: CIGS + type: thin-film + efficiency_range: 15-20% + AMORPHOUS_SILICON: + description: Amorphous silicon (a-Si) thin-film cells + aliases: + - a-Si related_mappings: - - ENVO:01000155 + - CHEBI:27573 annotations: - renewable: true - emission_free: false - BIOFUEL: - title: Biofuels (ethanol, biodiesel) + material: silicon + type: thin-film + efficiency_range: 6-8% + GALLIUM_ARSENIDE: + description: Gallium arsenide (GaAs) cells + aliases: + - GaAs annotations: - renewable: true - emission_free: false - TIDAL: - title: Tidal and wave energy + material: gallium_arsenide + efficiency_range: 25-30% + application: space, concentrator + PEROVSKITE: + description: Perovskite solar cells annotations: - renewable: true - emission_free: true - HYDROGEN: - title: Hydrogen fuel + material: perovskite + efficiency_range: 20-25% + status: emerging + ORGANIC: + description: Organic photovoltaic (OPV) cells aliases: - - dihydrogen - meaning: CHEBI:18276 + - OPV annotations: - renewable: depends - emission_free: true - COAL: - title: Coal - meaning: ENVO:02000091 + material: organic + type: thin-film + efficiency_range: 10-15% + status: emerging + TANDEM: + description: Tandem/multi-junction cells + aliases: + - multi-junction annotations: - renewable: false - emission_free: false - fossil_fuel: true - NATURAL_GAS: - title: Natural gas - meaning: ENVO:01000552 + efficiency_range: 25-35% + is_a: EnergySchemaEnum + annotations: + source_domain: energy + source_schema: energy + PVSystemType: + title: Photovoltaic System Type + description: Types of photovoltaic system installations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + exact_mappings: + - OEO:00000324 + permissible_values: + ROOFTOP_RESIDENTIAL: + description: Residential rooftop PV system + broad_mappings: + - OEO:00000361 annotations: - renewable: false - emission_free: false - fossil_fuel: true - PETROLEUM: - title: Petroleum/oil - meaning: ENVO:00002984 + scale: residential + mounting: rooftop + ROOFTOP_COMMERCIAL: + description: Commercial/industrial rooftop PV system + broad_mappings: + - OEO:00000361 annotations: - renewable: false - emission_free: false - fossil_fuel: true - DIESEL: - title: Diesel fuel + scale: commercial + mounting: rooftop + GROUND_MOUNTED: + description: Ground-mounted utility-scale PV system + exact_mappings: + - OEO:00000165 + annotations: + scale: utility + mounting: ground + FLOATING: + description: Floating PV system (floatovoltaics) aliases: - - diesel fuel - meaning: ENVO:03510006 + - floatovoltaics + - FPV annotations: - renewable: false - emission_free: false - fossil_fuel: true - GASOLINE: - title: Gasoline/petrol + scale: utility + mounting: floating + BUILDING_INTEGRATED: + description: Building-integrated PV (BIPV) aliases: - - fuel oil - related_mappings: - - ENVO:00002983 + - BIPV annotations: - renewable: false - emission_free: false - fossil_fuel: true - PROPANE: - title: Propane/LPG + mounting: integrated + AGRIVOLTAICS: + description: Agrivoltaic system (dual-use with agriculture) aliases: - - liquefied petroleum gas - meaning: ENVO:01000553 + - agrophotovoltaics + - APV annotations: - renewable: false - emission_free: false - fossil_fuel: true - NUCLEAR_FISSION: - title: Nuclear fission + scale: utility + dual_use: agriculture + CARPORT: + description: Solar carport/parking canopy + annotations: + mounting: canopy + dual_use: parking + TRACKER_SINGLE_AXIS: + description: Single-axis tracking system + annotations: + tracking: single_axis + TRACKER_DUAL_AXIS: + description: Dual-axis tracking system + annotations: + tracking: dual_axis + CONCENTRATING: + description: Concentrating PV (CPV) system aliases: - - nuclear energy - related_mappings: - - ENVO:2000025 + - CPV + annotations: + type: concentrating + is_a: EnergySchemaEnum + annotations: + source_domain: energy + source_schema: energy + EnergyStorageType: + title: Energy Storage Type + description: Types of energy storage systems (categories) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BATTERY: + description: Battery storage (see BatteryType for specific chemistries) exact_mappings: - - CHEBI:35231 + - OEO:00000068 + - brick:Battery annotations: - renewable: false - emission_free: true - NUCLEAR_FUSION: - title: Nuclear fusion (experimental) - aliases: - - nuclear energy - related_mappings: - - ENVO:2000025 + category: electrochemical + PUMPED_HYDRO: + description: Pumped hydroelectric storage + exact_mappings: + - OEO:00010089 annotations: - renewable: false - emission_free: true - GRID_MIX: - title: Grid electricity (mixed sources) + category: mechanical + oeo_label: pumped hydro storage power plant + COMPRESSED_AIR: + description: Compressed air energy storage (CAES) + close_mappings: + - OEO:00000102 annotations: - renewable: partial - BATTERY_STORAGE: - description: Battery storage systems + category: mechanical + oeo_label: compressed air + FLYWHEEL: + description: Flywheel energy storage annotations: - storage: true + category: mechanical + GRAVITY_STORAGE: + description: Gravity-based storage + annotations: + category: mechanical + MOLTEN_SALT: + description: Molten salt thermal storage + annotations: + category: thermal + ICE_STORAGE: + description: Ice thermal storage + annotations: + category: thermal + PHASE_CHANGE: + description: Phase change materials + annotations: + category: thermal + HYDROGEN_STORAGE: + description: Hydrogen storage + close_mappings: + - OEO:00000220 + annotations: + category: chemical + oeo_label: hydrogen + SYNTHETIC_FUEL: + description: Synthetic fuel storage + close_mappings: + - OEO:00010017 + annotations: + category: chemical + oeo_label: synthetic fuel + SUPERCAPACITOR: + description: Supercapacitor + annotations: + category: electrical + SUPERCONDUCTING: + description: Superconducting magnetic energy storage (SMES) + annotations: + category: electrical is_a: EnergySchemaEnum annotations: source_domain: energy source_schema: energy - EnergyUnit: - description: Units for measuring energy + EmissionScope: + title: Emission Scope + description: Greenhouse gas emission scopes (GHG Protocol) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - OEO:00000147 + - OEO:00000020 permissible_values: - JOULE: - description: Joule (J) - meaning: QUDT:J - annotations: - symbol: J - ucum: J - si_base: true - KILOJOULE: - description: Kilojoule (kJ) - meaning: QUDT:KiloJ + SCOPE_1: + description: Direct emissions from owned or controlled sources + related_mappings: + - OEO:00000199 annotations: - symbol: kJ - ucum: kJ - joules: 1000 - MEGAJOULE: - description: Megajoule (MJ) - meaning: QUDT:MegaJ + ghg_protocol: Scope 1 + oeo_label: greenhouse gas emission + SCOPE_2: + description: Indirect emissions from purchased energy + related_mappings: + - OEO:00000199 annotations: - symbol: MJ - ucum: MJ - joules: 1e6 - GIGAJOULE: - description: Gigajoule (GJ) - meaning: QUDT:GigaJ + ghg_protocol: Scope 2 + oeo_label: greenhouse gas emission + SCOPE_3: + description: All other indirect emissions in value chain + related_mappings: + - OEO:00000199 annotations: - symbol: GJ - ucum: GJ - joules: 1e9 - WATT_HOUR: - description: Watt-hour (Wh) - meaning: QUDT:W-HR + ghg_protocol: Scope 3 + oeo_label: greenhouse gas emission + SCOPE_3_UPSTREAM: + description: Upstream Scope 3 emissions + related_mappings: + - OEO:00000199 annotations: - symbol: Wh - ucum: W.h - joules: 3600 - KILOWATT_HOUR: - description: Kilowatt-hour (kWh) - meaning: QUDT:KiloW-HR + ghg_protocol: Scope 3 + oeo_label: greenhouse gas emission + SCOPE_3_DOWNSTREAM: + description: Downstream Scope 3 emissions + related_mappings: + - OEO:00000199 annotations: - symbol: kWh - ucum: kW.h - joules: 3.6e6 - MEGAWATT_HOUR: - description: Megawatt-hour (MWh) - meaning: QUDT:MegaW-HR + ghg_protocol: Scope 3 + oeo_label: greenhouse gas emission + is_a: EnergySchemaEnum + annotations: + source_domain: energy + source_schema: energy + CarbonIntensity: + title: Carbon Intensity + description: Carbon intensity levels for energy sources + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ZERO_CARBON: + description: Zero carbon emissions annotations: - symbol: MWh - ucum: MW.h - joules: 3.6e9 - GIGAWATT_HOUR: - description: Gigawatt-hour (GWh) - meaning: QUDT:GigaW-HR + gCO2_per_kWh: 0 + VERY_LOW_CARBON: + description: Very low carbon (< 50 gCO2/kWh) annotations: - symbol: GWh - ucum: GW.h - joules: 3.6e12 - TERAWATT_HOUR: - description: Terawatt-hour (TWh) - meaning: QUDT:TeraW-HR + gCO2_per_kWh: 0-50 + LOW_CARBON: + description: Low carbon (50-200 gCO2/kWh) annotations: - symbol: TWh - ucum: TW.h - joules: 3.6e15 - CALORIE: - description: Calorie (cal) - meaning: QUDT:CAL + gCO2_per_kWh: 50-200 + MEDIUM_CARBON: + description: Medium carbon (200-500 gCO2/kWh) annotations: - symbol: cal - ucum: cal - joules: 4.184 - KILOCALORIE: - description: Kilocalorie (kcal) - meaning: QUDT:KiloCAL + gCO2_per_kWh: 200-500 + HIGH_CARBON: + description: High carbon (500-1000 gCO2/kWh) annotations: - symbol: kcal - ucum: kcal - joules: 4184 - BTU: - description: British thermal unit - meaning: QUDT:BTU_IT + gCO2_per_kWh: 500-1000 + VERY_HIGH_CARBON: + description: Very high carbon (> 1000 gCO2/kWh) annotations: - symbol: BTU - ucum: '[Btu_IT]' - joules: 1055.06 - THERM: - description: Therm - meaning: QUDT:THM_US + gCO2_per_kWh: 1000+ + is_a: EnergySchemaEnum + annotations: + source_domain: energy + source_schema: energy + ElectricityMarket: + title: Electricity Market + description: Types of electricity markets and pricing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SPOT_MARKET: + description: Spot market/real-time pricing + DAY_AHEAD: + description: Day-ahead market + INTRADAY: + description: Intraday market + FUTURES: + description: Futures market + CAPACITY_MARKET: + description: Capacity market + ANCILLARY_SERVICES: + description: Ancillary services market + BILATERAL: + description: Bilateral contracts + FEED_IN_TARIFF: + description: Feed-in tariff + NET_METERING: + description: Net metering + POWER_PURCHASE_AGREEMENT: + description: Power purchase agreement (PPA) + is_a: EnergySchemaEnum + annotations: + source_domain: energy + source_schema: energy + CapabilityStatus: + title: Capability Status + description: Operational status of a capability, facility, or infrastructure. Applicable to energy facilities, research + capabilities, and other infrastructure throughout their lifecycle. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.wikidata.org/wiki/Property:P5817 + - https://www.iaea.org/topics/nuclear-power-plant-life-cycle + - https://schema.org/ItemAvailability + - https://www.iso.org/standard/83053.html + permissible_values: + OPERATIONAL: + title: Operational + description: Fully operational and available to users + exact_mappings: + - wikidata:Q55654238 + annotations: + wikidata_label: in use + lifecycle_phase: operation + COMING_ONLINE: + title: Coming Online + description: Being commissioned, coming online soon + related_mappings: + - wikidata:Q811686 annotations: - symbol: thm - ucum: '[thm_us]' - joules: 1.055e8 - ELECTRON_VOLT: - description: Electron volt (eV) - meaning: QUDT:EV + wikidata_label: building process + lifecycle_phase: commissioning + iaea_equivalent: commissioning + PILOT: + title: Pilot + description: In pilot phase with limited access + related_mappings: + - schema:LimitedAvailability annotations: - symbol: eV - ucum: eV - joules: 1.602e-19 - TOE: - description: Tonne of oil equivalent - meaning: QUDT:TOE + availability: limited + lifecycle_phase: testing + UNDER_DEVELOPMENT: + title: Under Development + description: Under development, not yet available + exact_mappings: + - wikidata:Q811683 annotations: - symbol: toe - ucum: toe - joules: 4.187e10 - TCE: - description: Tonne of coal equivalent + wikidata_label: proposed building or structure + lifecycle_phase: planning/construction + DECOMMISSIONED: + title: Decommissioned + description: No longer available, permanently shut down + related_mappings: + - schema:Discontinued annotations: - symbol: tce - ucum: tce - joules: 2.93e10 + lifecycle_phase: end-of-life + iaea_equivalent: decommissioned is_a: EnergySchemaEnum annotations: source_domain: energy source_schema: energy - PowerUnit: - description: Units for measuring power (energy per time) + FossilFuelsSchemaEnum: + description: Schema-level enum for fossil_fuels in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/fossil_fuels.yaml + FossilFuelTypeEnum: + title: Fossil Fuel Type + description: Types of fossil fuels used for energy generation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - WATT: - description: Watt (W) - meaning: QUDT:W - annotations: - symbol: W - ucum: W - si_base: true - KILOWATT: - description: Kilowatt (kW) - meaning: QUDT:KiloW - annotations: - symbol: kW - ucum: kW - watts: 1000 - MEGAWATT: - description: Megawatt (MW) - meaning: QUDT:MegaW - annotations: - symbol: MW - ucum: MW - watts: 1e6 - GIGAWATT: - description: Gigawatt (GW) - meaning: QUDT:GigaW + COAL: + description: Coal + title: Coal + meaning: ENVO:02000091 + NATURAL_GAS: + description: Natural gas + title: Natural Gas + meaning: ENVO:01000552 + PETROLEUM: + description: Petroleum + title: Petroleum + meaning: ENVO:00002984 + is_a: FossilFuelsSchemaEnum + annotations: + source_domain: energy + source_schema: fossil_fuels + GridSchemaEnum: + description: Schema-level enum for grid in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/grid.yaml + GridComponentType: + title: Grid Component Type + description: Types of physical components in electrical transmission and distribution grids + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TRANSMISSION_LINE: + description: High-voltage conductors that carry electricity over long distances from generation to substations + related_mappings: + - OEO:00410056 + DISTRIBUTION_LINE: + description: Medium- and low-voltage conductors that deliver electricity from substations to end users + related_mappings: + - OEO:00410057 + TRANSFORMER: + title: Transformer Device + description: Device that changes voltage levels between transmission and distribution systems + meaning: NCIT:C50227 + close_mappings: + - OEO:00000420 + SUBSTATION: + description: Facility that switches, transforms, and regulates electrical power in the grid + CIRCUIT_BREAKER: + description: Protective device that automatically interrupts current flow during fault conditions + CAPACITOR_BANK: + description: Array of capacitors used for reactive power compensation and voltage regulation + FACTS_DEVICE: + description: Flexible AC Transmission System device for controlling power flow and improving grid stability + SMART_METER: + description: Advanced metering device that records energy consumption and communicates with the utility + INVERTER: + description: Device that converts direct current (DC) to alternating current (AC) for grid connection + RELAY: + description: Protective device that detects abnormal conditions and triggers circuit breakers + is_a: GridSchemaEnum + annotations: + source_domain: energy + source_schema: grid + GridEnergyStorageType: + title: Energy Storage Type + description: Types of energy storage technologies used for grid-scale and distributed applications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LITHIUM_ION_BATTERY: + title: lithium-ion battery + description: Rechargeable battery using lithium ion intercalation in electrode materials + meaning: OEO:00000248 + FLOW_BATTERY: + title: flow battery + description: Rechargeable battery using liquid electrolytes stored in external tanks for scalable capacity + meaning: OEO:00000169 + PUMPED_HYDROELECTRIC: + description: Energy storage by pumping water to an elevated reservoir and releasing it through turbines + close_mappings: + - OEO:00010089 + COMPRESSED_AIR: + title: compressed-air energy storage unit + description: Energy storage by compressing air into underground caverns or tanks for later expansion through turbines + close_mappings: + - OEO:00020249 + FLYWHEEL: + description: Energy storage as rotational kinetic energy in a spinning mass + broad_mappings: + - OEO:00020364 + SUPERCAPACITOR: + description: Electrochemical capacitor providing high power density with rapid charge and discharge cycles + THERMAL_STORAGE: + description: Energy storage as heat in materials such as molten salt, concrete, or phase-change materials + close_mappings: + - OEO:00020365 + HYDROGEN_STORAGE: + description: Energy storage by producing hydrogen via electrolysis for later use in fuel cells or turbines + related_mappings: + - OEO:00000429 + GRAVITY_STORAGE: + description: Energy storage by raising heavy masses to height and lowering them to generate electricity + SODIUM_ION_BATTERY: + title: sodium-ion battery + description: Rechargeable battery using sodium ion intercalation as a lower-cost alternative to lithium-ion + meaning: OEO:00000376 + is_a: GridSchemaEnum + annotations: + source_domain: energy + source_schema: grid + GridManagementStrategyType: + title: Grid Management Strategy Type + description: Strategies for managing and optimizing the operation of electrical grids + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + DEMAND_RESPONSE: + description: Adjusting consumer electricity demand in response to supply conditions or price signals + LOAD_BALANCING: + description: Distributing electrical load across generation sources to maintain grid stability + FREQUENCY_REGULATION: + description: Maintaining grid frequency at nominal levels by balancing generation and load in real time + VOLTAGE_CONTROL: + description: Maintaining voltage levels within acceptable ranges across the grid + PEAK_SHAVING: + description: Reducing peak electricity demand through storage dispatch or demand reduction programs + DISTRIBUTED_GENERATION: + description: Generating electricity from many small sources close to the point of consumption + MICROGRID_OPERATION: + description: Operating a localized energy grid that can function independently or connected to the main grid + VIRTUAL_POWER_PLANT: + description: Aggregating distributed energy resources to operate as a single coordinated power source + GRID_SCALE_STORAGE_DISPATCH: + description: Coordinating charge and discharge of large-scale energy storage assets for grid optimization + is_a: GridSchemaEnum + annotations: + source_domain: energy + source_schema: grid + FusionSchemaEnum: + description: Schema-level enum for fusion in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/fusion.yaml + FusionConfinementType: + title: Fusion Confinement Type + description: Methods for confining plasma in fusion energy experiments and reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MAGNETIC_CONFINEMENT_TOKAMAK: + description: Magnetic confinement using a toroidal chamber with an axial magnetic field and plasma current (tokamak) + MAGNETIC_CONFINEMENT_STELLARATOR: + description: Magnetic confinement using external coils to generate a twisted toroidal magnetic field (stellarator) + INERTIAL_CONFINEMENT: + description: Confinement by compressing fuel pellets to extreme densities using lasers or particle beams + MAGNETO_INERTIAL: + description: Hybrid approach combining magnetic field compression with inertial confinement + LASER_DRIVEN: + description: Fusion driven by high-power laser systems to compress and heat fuel targets + Z_PINCH: + description: Confinement using the magnetic field generated by a large axial current through the plasma + FIELD_REVERSED_CONFIGURATION: + description: Compact toroidal confinement where the magnetic field reverses direction inside the plasma + SPHEROMAK: + description: Compact toroidal confinement with toroidal and poloidal magnetic fields of comparable strength + is_a: FusionSchemaEnum + annotations: + source_domain: energy + source_schema: fusion + FusionFuelType: + title: Fusion Fuel Type + description: Types of nuclear fuel mixtures used in fusion reactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + DEUTERIUM_TRITIUM: + description: Deuterium-tritium (D-T) fuel, the most studied fusion fuel with the lowest ignition temperature + annotations: + reactants: deuterium + tritium + products: helium-4 + neutron + energy_release: 17.6 MeV + DEUTERIUM_DEUTERIUM: + description: Deuterium-deuterium (D-D) fuel, avoiding the need for scarce tritium + annotations: + reactants: deuterium + deuterium + products: helium-3 + neutron OR tritium + proton + DEUTERIUM_HELIUM3: + description: Deuterium-helium-3 (D-He3) fuel, producing fewer neutrons than D-T + annotations: + reactants: deuterium + helium-3 + products: helium-4 + proton + energy_release: 18.3 MeV + PROTON_BORON11: + description: Proton-boron-11 (p-B11) aneutronic fuel producing only charged particles + annotations: + reactants: proton + boron-11 + products: 3 helium-4 + energy_release: 8.7 MeV + is_a: FusionSchemaEnum + annotations: + source_domain: energy + source_schema: fusion + FusionPlasmaParameterType: + title: Fusion Plasma Parameter Type + description: Key physical parameters measured and optimized in fusion plasma experiments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PLASMA_TEMPERATURE: + description: Temperature of the plasma, typically measured in electron-volts (eV) or kelvin + broad_mappings: + - PATO:0000146 + PLASMA_DENSITY: + description: Number density of particles in the plasma, measured in particles per cubic meter + broad_mappings: + - PATO:0001019 + CONFINEMENT_TIME: + description: Average time a particle or unit of energy remains confined in the plasma + BETA_VALUE: + description: Ratio of plasma kinetic pressure to magnetic pressure, a key performance metric + ENERGY_GAIN_FACTOR_Q: + description: Ratio of fusion power output to external heating power input (Q factor) + LAWSON_CRITERION: + description: Product of plasma density and confinement time required for net energy gain + PLASMA_CURRENT: + description: Electric current flowing through the plasma, important for tokamak confinement + MAGNETIC_FIELD_STRENGTH: + title: Magnetic Field Strength + description: Strength of the magnetic field used to confine the plasma + meaning: NCIT:C156494 + is_a: FusionSchemaEnum + annotations: + source_domain: energy + source_schema: fusion + NuclearCleanupSchemaEnum: + description: Schema-level enum for nuclear_cleanup in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_cleanup.yaml + NuclearRemediationType: + title: Nuclear Remediation Type + description: Methods for remediating radioactive contamination at nuclear sites + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SOIL_EXCAVATION: + description: Physical removal and disposal of contaminated soil + GROUNDWATER_PUMP_AND_TREAT: + description: Pumping contaminated groundwater to the surface for treatment and reinjection + IN_SITU_BIOREMEDIATION: + description: Using microorganisms in place to degrade or immobilize radioactive contaminants + VITRIFICATION: + description: Immobilizing radioactive waste by incorporating it into a glass matrix + STABILIZATION: + description: Chemical or physical treatment to reduce the mobility of contaminants in soil or waste + CAPPING: + description: Placing an engineered barrier over contaminated material to prevent migration and exposure + PHYTOREMEDIATION: + description: Using plants to extract, contain, or degrade radioactive contaminants from soil and water + ELECTROKINETIC_REMEDIATION: + description: Applying electric fields to move and concentrate contaminants in soil for removal + CHEMICAL_OXIDATION: + description: Using chemical oxidants to destroy or transform organic contaminants at nuclear sites + MONITORED_NATURAL_ATTENUATION: + description: Monitoring natural processes that reduce contaminant concentrations without active intervention + is_a: NuclearCleanupSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_cleanup + DecommissioningPhaseType: + title: Decommissioning Phase Type + description: Phases in the decommissioning lifecycle of nuclear facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CHARACTERIZATION: + description: Surveying and characterizing radiological and hazardous conditions at the facility + DECONTAMINATION: + title: Decontamination + description: Removing radioactive contamination from surfaces, equipment, and structures + meaning: NCIT:C68769 + DISMANTLEMENT: + description: Physical demolition and removal of contaminated structures and equipment + WASTE_MANAGEMENT: + description: Processing, packaging, transporting, and disposing of radioactive waste + SITE_RESTORATION: + description: Restoring the site to a condition suitable for future use + LONG_TERM_MONITORING: + description: Ongoing environmental monitoring after initial cleanup is complete + broad_mappings: + - ENVO:02500041 + LICENSE_TERMINATION: + description: Final regulatory review and release of the site from nuclear licensing requirements + is_a: NuclearCleanupSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_cleanup + RadioactiveContaminantType: + title: Radioactive Contaminant Type + description: Common radioactive contaminants found at nuclear cleanup sites + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CESIUM_137: + title: caesium-137 + description: Cesium-137, a beta and gamma emitter with a half-life of approximately 30 years + meaning: CHEBI:196959 + annotations: + half_life: 30.17 years + decay_mode: beta, gamma + STRONTIUM_90: + title: Strontium Sr-90 + description: Strontium-90, a beta emitter with a half-life of approximately 29 years + meaning: NCIT:C29776 + annotations: + half_life: 28.8 years + decay_mode: beta + TECHNETIUM_99: + description: Technetium-99, a long-lived beta emitter produced in fission reactors + meaning: CHEBI:33371 + annotations: + half_life: 211100 years + decay_mode: beta + TRITIUM: + title: tritium atom + description: Tritium (hydrogen-3), a low-energy beta emitter with a half-life of approximately 12 years + meaning: CHEBI:29238 + annotations: + half_life: 12.33 years + decay_mode: beta + URANIUM: + title: uranium atom + description: Uranium isotopes, alpha emitters with very long half-lives + meaning: CHEBI:27214 annotations: - symbol: GW - ucum: GW - watts: 1e9 - TERAWATT: - description: Terawatt (TW) - meaning: QUDT:TeraW + decay_mode: alpha + PLUTONIUM: + title: plutonium atom + description: Plutonium isotopes, alpha emitters with long half-lives and high radiotoxicity + meaning: CHEBI:33388 + annotations: + decay_mode: alpha + AMERICIUM_241: + title: americium atom + description: Americium-241, an alpha emitter with a half-life of approximately 432 years + meaning: CHEBI:33389 + annotations: + half_life: 432.2 years + decay_mode: alpha + IODINE_129: + title: iodine-129 atom + description: Iodine-129, a long-lived beta and gamma emitter produced in nuclear fission + meaning: CHEBI:52636 + annotations: + half_life: 15.7 million years + decay_mode: beta, gamma + COBALT_60: + title: Cobalt Co-60 + description: Cobalt-60, a gamma emitter with a half-life of approximately 5 years + meaning: NCIT:C28239 + annotations: + half_life: 5.27 years + decay_mode: beta, gamma + RADIUM_226: + description: Radium-226, an alpha emitter with a half-life of approximately 1600 years + meaning: CHEBI:80504 + annotations: + half_life: 1600 years + decay_mode: alpha + is_a: NuclearCleanupSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_cleanup + NuclearFacilitiesSchemaEnum: + description: Schema-level enum for nuclear_facilities in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_facilities.yaml + NuclearFacilityTypeEnum: + title: Nuclear Facility Type + description: Types of nuclear facilities and infrastructure + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + COMMERCIAL_POWER_PLANT: + title: Commercial Nuclear Power Plant + description: Large-scale commercial reactor for electricity generation + annotations: + primary_purpose: electricity generation + power_output: typically 300-1600 MWe + operator_type: utility company + regulatory_oversight: extensive + RESEARCH_REACTOR: + title: Research Reactor + description: Reactor designed for research, training, and isotope production + annotations: + primary_purpose: research, training, isotope production + power_output: typically <100 MWt + neutron_flux: optimized for research needs + fuel_type: various, often HEU or LEU + TEST_REACTOR: + title: Test Reactor + description: Reactor for testing materials and components + annotations: + primary_purpose: materials and component testing + test_capabilities: irradiation testing + neutron_spectrum: variable for testing needs + PROTOTYPE_REACTOR: + title: Prototype Reactor + description: Reactor for demonstrating new technology + annotations: + primary_purpose: technology demonstration + scale: smaller than commercial + innovation_focus: new reactor concepts + NAVAL_REACTOR: + title: Naval Reactor + description: Reactor for ship or submarine propulsion + annotations: + primary_purpose: vessel propulsion + compactness: highly compact design + fuel_enrichment: typically HEU + operation_mode: mobile platform + SPACE_REACTOR: + title: Space Nuclear Reactor + description: Reactor designed for space applications + annotations: + primary_purpose: space power or propulsion + mass_constraints: extremely lightweight + cooling: radiative cooling + power_output: typically <10 MWt + PRODUCTION_REACTOR: + title: Production Reactor + description: Reactor for producing nuclear materials + annotations: + primary_purpose: isotope or material production + products: tritium, plutonium, medical isotopes + operation_mode: specialized for production + URANIUM_MINE: + title: Uranium Mine + description: Facility for extracting uranium ore + annotations: + extraction_method: underground or open pit + product: uranium ore + processing: may include milling + URANIUM_MILL: + title: Uranium Mill + description: Facility for processing uranium ore into yellowcake + annotations: + input_material: uranium ore + output_product: uranium concentrate (U3O8) + process: chemical extraction and purification + CONVERSION_FACILITY: + title: Conversion Facility + description: Facility for converting yellowcake to UF6 + annotations: + input_material: uranium concentrate (U3O8) + output_product: uranium hexafluoride (UF6) + process: chemical conversion + ENRICHMENT_FACILITY: + title: Enrichment Facility + description: Facility for increasing U-235 concentration + annotations: + input_material: natural UF6 + output_product: enriched UF6 + process: isotope separation (centrifuge, diffusion) + sensitive_technology: proliferation-sensitive + FUEL_FABRICATION_FACILITY: + title: Fuel Fabrication Facility + description: Facility for manufacturing nuclear fuel assemblies + annotations: + input_material: enriched UF6 + output_product: fuel assemblies + process: pellet and rod manufacturing + REPROCESSING_FACILITY: + title: Reprocessing Facility + description: Facility for separating spent fuel components + annotations: + input_material: spent nuclear fuel + output_products: uranium, plutonium, waste + process: chemical separation (PUREX, UREX+) + proliferation_sensitivity: high + INTERIM_STORAGE_FACILITY: + title: Interim Storage Facility + description: Facility for temporary storage of nuclear materials + annotations: + storage_duration: intermediate term (5-100 years) + storage_medium: pools, dry casks + typical_materials: spent fuel, waste + GEOLOGICAL_REPOSITORY: + title: Geological Repository + description: Deep underground facility for permanent waste disposal + annotations: + storage_duration: permanent (thousands of years) + depth: typically >300 meters underground + waste_types: high-level waste, spent fuel + DECOMMISSIONING_SITE: + title: Decommissioning Site + description: Nuclear facility undergoing dismantlement + annotations: + facility_status: being dismantled + activities: decontamination, demolition + duration: typically 10-50 years + NUCLEAR_LABORATORY: + title: Nuclear Laboratory + description: Laboratory facility handling radioactive materials + annotations: + activities: research, analysis, small-scale production + materials: various radioactive substances + scale: laboratory scale + RADIOISOTOPE_PRODUCTION_FACILITY: + title: Radioisotope Production Facility + description: Facility for producing medical and industrial isotopes + annotations: + products: medical isotopes, industrial tracers + production_methods: reactor irradiation, accelerator + market: medical and industrial applications + is_a: NuclearFacilitiesSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_facilities + PowerPlantStatusEnum: + title: Power Plant Status + description: Operational status of nuclear power plants + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + UNDER_CONSTRUCTION: + title: Under Construction + description: Plant currently being built + annotations: + construction_phase: civil and mechanical work ongoing + licensing_status: construction permit issued + commercial_operation: not yet started + COMMISSIONING: + title: Commissioning + description: Plant undergoing testing before commercial operation + annotations: + testing_phase: systems testing and startup + fuel_loading: may have occurred + commercial_operation: not yet achieved + COMMERCIAL_OPERATION: + title: Commercial Operation + description: Plant operating commercially for electricity generation + annotations: + operational_status: fully operational + power_generation: commercial electricity production + licensing_status: operating license active + REFUELING_OUTAGE: + title: Refueling Outage + description: Plant temporarily shut down for fuel replacement and maintenance + annotations: + shutdown_reason: scheduled refueling + duration: typically 30-60 days + activities: fuel replacement, maintenance, inspection + EXTENDED_OUTAGE: + title: Extended Outage + description: Plant shut down for extended period for major work + annotations: + shutdown_duration: months to years + work_scope: major modifications or repairs + return_to_service: planned + PERMANENTLY_SHUTDOWN: + title: Permanently Shutdown + description: Plant permanently ceased operation + annotations: + operational_status: permanently ceased + fuel_removal: may be ongoing or completed + decommissioning: may be planned or ongoing + DECOMMISSIONING: + title: Decommissioning + description: Plant undergoing dismantlement + annotations: + decommissioning_phase: active dismantlement + radioactive_cleanup: ongoing + site_restoration: planned + DECOMMISSIONED: + title: Decommissioned + description: Plant completely dismantled and site restored + annotations: + dismantlement_status: completed + site_condition: restored for unrestricted use + radioactive_materials: removed + is_a: NuclearFacilitiesSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_facilities + ResearchReactorTypeEnum: + title: Research Reactor Type + description: Types of research reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + POOL_TYPE: + title: Pool-Type Research Reactor + description: Reactor with fuel in open pool of water + annotations: + design: open pool with underwater fuel + power_level: typically 1-20 MW + applications: neutron beam experiments, training + TANK_TYPE: + title: Tank-Type Research Reactor + description: Reactor with fuel in enclosed tank + annotations: + design: fuel in pressurized or unpressurized tank + power_level: variable + containment: more enclosed than pool type + HOMOGENEOUS: + title: Homogeneous Research Reactor + description: Reactor with fuel in liquid form + annotations: + fuel_form: aqueous solution + design: fuel dissolved in moderator + power_level: typically low + FAST_RESEARCH_REACTOR: + title: Fast Research Reactor + description: Research reactor using fast neutrons + annotations: + neutron_spectrum: fast neutrons + moderator: none or minimal + applications: fast neutron research + PULSED_REACTOR: + title: Pulsed Research Reactor + description: Reactor designed for pulsed operation + annotations: + operation_mode: short intense pulses + power_level: very high peak power + applications: transient testing, physics research + CRITICAL_ASSEMBLY: + title: Critical Assembly + description: Minimal reactor for criticality studies + annotations: + power_level: essentially zero + purpose: criticality experiments, training + design: minimal critical configuration + SUBCRITICAL_ASSEMBLY: + title: Subcritical Assembly + description: Neutron source-driven subcritical system + annotations: + criticality: subcritical + neutron_source: external source required + applications: research, training, transmutation studies + is_a: NuclearFacilitiesSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_facilities + FuelCycleFacilityTypeEnum: + title: Fuel Cycle Facility Type + description: Types of nuclear fuel cycle facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + IN_SITU_LEACH_MINE: + title: In-Situ Leach Mine + description: Uranium extraction by solution mining + annotations: + extraction_method: chemical leaching in ground + environmental_impact: lower surface disturbance + geology_requirement: permeable ore deposits + CONVENTIONAL_MINE: + title: Conventional Mine + description: Traditional underground or open-pit uranium mining + annotations: + extraction_method: physical excavation + mine_types: underground or open pit + ore_grade: variable + HEAP_LEACH_FACILITY: + title: Heap Leach Facility + description: Uranium extraction from low-grade ores by heap leaching + annotations: + ore_grade: low-grade ores + process: chemical leaching of ore piles + economics: cost-effective for low grades + GASEOUS_DIFFUSION_PLANT: + title: Gaseous Diffusion Enrichment Plant + description: Uranium enrichment using gaseous diffusion + annotations: + enrichment_method: gaseous diffusion + energy_consumption: very high + status: mostly retired technology + GAS_CENTRIFUGE_PLANT: + title: Gas Centrifuge Enrichment Plant + description: Uranium enrichment using centrifuge technology + annotations: + enrichment_method: gas centrifuge + energy_consumption: lower than diffusion + technology_status: current standard technology + LASER_ENRICHMENT_FACILITY: + title: Laser Enrichment Facility + description: Uranium enrichment using laser isotope separation + annotations: + enrichment_method: laser isotope separation + technology_status: under development + energy_consumption: potentially lower + MOX_FUEL_FABRICATION: + title: MOX Fuel Fabrication Facility + description: Facility for manufacturing mixed oxide fuel + annotations: + fuel_type: mixed oxide (uranium and plutonium) + input_materials: plutonium dioxide, uranium dioxide + special_handling: plutonium handling required + AQUEOUS_REPROCESSING: + title: Aqueous Reprocessing Plant + description: Spent fuel reprocessing using aqueous methods + annotations: + process_type: PUREX or similar aqueous process + separation_products: uranium, plutonium, waste + technology_maturity: commercially proven + PYROPROCESSING_FACILITY: + title: Pyroprocessing Facility + description: Spent fuel reprocessing using electrochemical methods + annotations: + process_type: electrochemical separation + temperature: high temperature operation + technology_status: under development + is_a: NuclearFacilitiesSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_facilities + WasteFacilityTypeEnum: + title: Waste Facility Type + description: Types of nuclear waste management facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SPENT_FUEL_POOL: + title: Spent Fuel Pool + description: Water-filled pool for cooling spent fuel + annotations: + cooling_medium: water + location: typically at reactor site + storage_duration: 5-10 years typical + DRY_CASK_STORAGE: + title: Dry Cask Storage + description: Air-cooled storage in sealed containers + annotations: + cooling_medium: air circulation + storage_duration: 20-100 years + location: on-site or centralized + CENTRALIZED_INTERIM_STORAGE: + title: Centralized Interim Storage Facility + description: Large-scale interim storage away from reactor sites + annotations: + scale: multiple reactor's worth of fuel + storage_duration: decades + transportation: rail or truck access required + LOW_LEVEL_WASTE_DISPOSAL: + title: Low-Level Waste Disposal Site + description: Near-surface disposal for low-level waste + annotations: + waste_category: Class A, B, C low-level waste + disposal_depth: near-surface (<30 meters) + institutional_control: 100 years minimum + GREATER_THAN_CLASS_C_STORAGE: + title: Greater Than Class C Storage + description: Storage for waste exceeding Class C limits + annotations: + waste_category: greater than Class C waste + storage_type: interim storage pending disposal + disposal_requirements: deep disposal likely required + TRANSURANIC_WASTE_REPOSITORY: + title: Transuranic Waste Repository + description: Deep geological repository for TRU waste + annotations: + waste_category: transuranic waste + disposal_depth: deep underground + example: Waste Isolation Pilot Plant (WIPP) + HIGH_LEVEL_WASTE_REPOSITORY: + title: High-Level Waste Repository + description: Deep geological repository for high-level waste + annotations: + waste_category: high-level waste, spent fuel + disposal_depth: typically >300 meters + containment_period: thousands of years + WASTE_TREATMENT_FACILITY: + title: Waste Treatment Facility + description: Facility for processing and conditioning waste + annotations: + purpose: volume reduction, stabilization + processes: incineration, compaction, solidification + output: treated waste for disposal + DECONTAMINATION_FACILITY: + title: Decontamination Facility + description: Facility for cleaning contaminated materials + annotations: + purpose: remove radioactive contamination + materials: equipment, clothing, tools + methods: chemical, physical decontamination + is_a: NuclearFacilitiesSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_facilities + NuclearShipTypeEnum: + title: Nuclear Ship Type + description: Types of nuclear-powered vessels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AIRCRAFT_CARRIER: + title: Nuclear Aircraft Carrier + description: Large naval vessel with nuclear propulsion and aircraft operations + annotations: + propulsion: nuclear steam turbine + size: very large (>80,000 tons) + mission: power projection, aircraft operations + reactor_count: typically 2 + SUBMARINE: + title: Nuclear Submarine + description: Underwater vessel with nuclear propulsion + annotations: + propulsion: nuclear steam turbine + operational_environment: submerged + mission: various (attack, ballistic missile, cruise missile) + reactor_count: typically 1 + CRUISER: + title: Nuclear Cruiser + description: Large surface combatant with nuclear propulsion + annotations: + propulsion: nuclear steam turbine + mission: escort, surface warfare + size: large surface vessel + status: mostly retired + ICEBREAKER: + title: Nuclear Icebreaker + description: Vessel designed to break ice using nuclear power + annotations: + propulsion: nuclear steam turbine or electric + mission: ice breaking, Arctic operations + operational_environment: polar regions + reactor_count: 1-3 + MERCHANT_SHIP: + title: Nuclear Merchant Ship + description: Commercial cargo vessel with nuclear propulsion + annotations: + propulsion: nuclear steam turbine + mission: cargo transport + commercial_viability: limited due to costs + examples: NS Savannah, few others + RESEARCH_VESSEL: + title: Nuclear Research Vessel + description: Ship designed for oceanographic research with nuclear power + annotations: + propulsion: nuclear + mission: scientific research + duration: extended operations without refueling + examples: limited number built + is_a: NuclearFacilitiesSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_facilities + NuclearForensicsSchemaEnum: + description: Schema-level enum for nuclear_forensics in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_forensics.yaml + NuclearForensicsMethodType: + title: Nuclear Forensics Method Type + description: Analytical methods used in nuclear forensics for material characterization and attribution + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ISOTOPE_RATIO_ANALYSIS: + description: Measurement of relative abundances of isotopes to determine material origin and processing history + title: isotope ratio mass spectrometry + meaning: CHMO:0000506 + close_mappings: + - MS:1000263 + MASS_SPECTROMETRY: + description: Analytical technique measuring mass-to-charge ratios for elemental and isotopic composition + title: mass spectrometry + meaning: CHMO:0000470 + GAMMA_SPECTROSCOPY: + description: Measurement of gamma-ray energies emitted by radioactive materials for isotope identification + title: gamma-ray spectroscopy + meaning: CHMO:0000414 + ALPHA_SPECTROSCOPY: + description: Measurement of alpha particle energies for characterizing alpha-emitting radionuclides + title: alpha-particle spectroscopy + meaning: CHMO:0000230 + NEUTRON_ACTIVATION_ANALYSIS: + description: Elemental analysis by irradiating samples with neutrons and measuring induced radioactivity + title: neutron activation analysis + meaning: CHMO:0000782 + RADIOCHEMICAL_SEPARATION: + description: Chemical separation of radionuclides from a sample matrix for individual measurement + ELECTRON_MICROSCOPY: + description: Microscopic imaging and analysis of nuclear material morphology and microstructure + title: electron microscopy + meaning: CHMO:0000068 + X_RAY_FLUORESCENCE: + description: Elemental analysis by measuring characteristic X-rays emitted after X-ray excitation + title: X-ray emission spectroscopy + meaning: CHMO:0000307 + AGE_DATING: + description: Determination of the time since last chemical purification of nuclear material using parent-daughter + ratios + is_a: NuclearForensicsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_forensics + NuclearThreatCategoryType: + title: Nuclear Threat Category Type + description: Categories of nuclear and radiological threat scenarios for security assessment + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + IMPROVISED_NUCLEAR_DEVICE: + title: Improvised Nuclear Device + description: A crude nuclear weapon constructed from diverted or stolen fissile material + meaning: NCIT:C120576 + RADIOLOGICAL_DISPERSAL_DEVICE: + title: Radiological Dispersal Device + description: A device that disperses radioactive material using conventional explosives or other means + meaning: NCIT:C120580 + NUCLEAR_FACILITY_SABOTAGE: + description: Deliberate sabotage of a nuclear facility to cause radiological release + NUCLEAR_MATERIAL_THEFT: + description: Theft or diversion of nuclear or radioactive material from authorized control + NUCLEAR_SMUGGLING: + description: Illicit trafficking and transport of nuclear or radioactive materials across borders + ENVIRONMENTAL_RELEASE: + description: Unauthorized or accidental release of radioactive material into the environment + is_a: NuclearForensicsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_forensics + NuclearFuelCycleSchemaEnum: + description: Schema-level enum for nuclear_fuel_cycle in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_fuel_cycle.yaml + NuclearFuelCycleStageEnum: + title: Nuclear Fuel Cycle Stage + description: Stages in the nuclear fuel cycle from mining to disposal + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MINING: + description: Uranium ore mining and extraction + MILLING: + description: Processing uranium ore into yellowcake (U3O8) + CONVERSION: + description: Converting yellowcake to uranium hexafluoride (UF6) + ENRICHMENT: + description: Increasing U-235 concentration in uranium + FUEL_FABRICATION: + description: Manufacturing nuclear fuel assemblies + REACTOR_OPERATION: + description: Nuclear fission in reactor core + INTERIM_STORAGE: + description: Temporary storage of spent nuclear fuel + REPROCESSING: + description: Chemical separation of useful materials from spent fuel + FINAL_DISPOSAL: + description: Permanent disposal of nuclear waste + is_a: NuclearFuelCycleSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuel_cycle + NuclearFuelFormEnum: + title: Nuclear Fuel Form + description: Different forms of nuclear fuel throughout the cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + URANIUM_ORE: + description: Natural uranium ore containing uranium minerals + YELLOWCAKE: + description: Uranium oxide concentrate (U3O8) + URANIUM_HEXAFLUORIDE: + description: Gaseous uranium compound (UF6) used for enrichment + ENRICHED_URANIUM: + description: Uranium with increased U-235 concentration + URANIUM_DIOXIDE: + description: Ceramic uranium fuel pellets (UO2) + FUEL_PELLETS: + description: Sintered uranium dioxide pellets + FUEL_RODS: + description: Zircaloy tubes containing fuel pellets + FUEL_ASSEMBLIES: + description: Bundled fuel rods ready for reactor loading + SPENT_FUEL: + description: Used nuclear fuel removed from reactor + MIXED_OXIDE_FUEL: + description: MOX fuel containing plutonium and uranium oxides + is_a: NuclearFuelCycleSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuel_cycle + EnrichmentProcessEnum: + title: Enrichment Process + description: Methods for enriching uranium to increase U-235 concentration + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GAS_DIFFUSION: + description: Gaseous diffusion enrichment process + GAS_CENTRIFUGE: + description: Gas centrifuge enrichment process + LASER_ISOTOPE_SEPARATION: + description: Laser-based uranium isotope separation + ELECTROMAGNETIC_SEPARATION: + description: Electromagnetic isotope separation (EMIS) + AERODYNAMIC_SEPARATION: + description: Aerodynamic enrichment processes + is_a: NuclearFuelCycleSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuel_cycle + NuclearFuelsSchemaEnum: + description: Schema-level enum for nuclear_fuels in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_fuels.yaml + NuclearFuelTypeEnum: + title: Nuclear Fuel Type + description: Types of nuclear fuel materials and compositions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NATURAL_URANIUM: + title: Natural Uranium + description: Uranium as found in nature (0.711% U-235) + aliases: + - Natural U + - Unat + - uranium atom + meaning: CHEBI:27214 annotations: - symbol: TW - ucum: TW - watts: 1e12 - HORSEPOWER: - description: Horsepower - meaning: QUDT:HP + u235_content: 0.711% + u238_content: 99.289% + enrichment_required: false + typical_use: PHWR, some research reactors + LOW_ENRICHED_URANIUM: + title: Low Enriched Uranium (LEU) + description: Uranium enriched to 0.7%-20% U-235 + aliases: + - LEU + annotations: + u235_content: 0.7-20% + proliferation_risk: low + typical_use: commercial power reactors + iaea_category: indirect use material + HIGH_ASSAY_LEU: + title: High-Assay Low Enriched Uranium (HALEU) + description: Uranium enriched to 5%-20% U-235 + aliases: + - HALEU + - LEU+ + annotations: + u235_content: 5-20% + typical_use: advanced reactors, SMRs + proliferation_risk: moderate + HIGHLY_ENRICHED_URANIUM: + title: Highly Enriched Uranium (HEU) + description: Uranium enriched to 20% or more U-235 + aliases: + - HEU + annotations: + u235_content: ≥20% + proliferation_risk: high + typical_use: research reactors, naval propulsion + iaea_category: direct use material + WEAPONS_GRADE_URANIUM: + title: Weapons-Grade Uranium + description: Uranium enriched to 90% or more U-235 + aliases: + - WGU + annotations: + u235_content: ≥90% + proliferation_risk: very high + typical_use: nuclear weapons, some naval reactors + REACTOR_GRADE_PLUTONIUM: + title: Reactor-Grade Plutonium + description: Plutonium with high Pu-240 content from spent fuel + aliases: + - RGPu + annotations: + pu239_content: <93% + pu240_content: '>7%' + source: spent nuclear fuel + typical_use: MOX fuel + WEAPONS_GRADE_PLUTONIUM: + title: Weapons-Grade Plutonium + description: Plutonium with low Pu-240 content + aliases: + - WGPu + annotations: + pu239_content: ≥93% + pu240_content: <7% + proliferation_risk: very high + MOX_FUEL: + title: Mixed Oxide Fuel + description: Mixture of plutonium and uranium oxides + aliases: + - MOX + - Mixed Oxide + annotations: + composition: UO2 + PuO2 + plutonium_content: 3-10% + typical_use: thermal reactors + recycling: enables plutonium recycling + THORIUM_FUEL: + title: Thorium-Based Fuel + description: Fuel containing thorium-232 as fertile material + aliases: + - Thorium fuel + - thorium + meaning: CHEBI:33385 + annotations: + fertile_isotope: Th-232 + fissile_product: U-233 + abundance: more abundant than uranium + proliferation_resistance: high + TRISO_FUEL: + title: Tri-structural Isotropic Fuel + description: Coated particle fuel with multiple containment layers + aliases: + - TRISO + annotations: + form: coated particles + containment_layers: 4 + meltdown_resistance: very high + typical_use: HTGR, some SMRs + LIQUID_FUEL: + title: Liquid Nuclear Fuel + description: Fuel dissolved in liquid medium + annotations: + phase: liquid + typical_use: molten salt reactors + reprocessing: online + METALLIC_FUEL: + title: Metallic Nuclear Fuel + description: Fuel in metallic form + annotations: + form: metal alloy + typical_use: fast reactors + thermal_conductivity: high + CARBIDE_FUEL: + title: Carbide Nuclear Fuel + description: Uranium or plutonium carbide fuel + annotations: + chemical_form: carbide + melting_point: very high + typical_use: advanced reactors + NITRIDE_FUEL: + title: Nitride Nuclear Fuel + description: Uranium or plutonium nitride fuel + annotations: + chemical_form: nitride + density: high + typical_use: fast reactors + is_a: NuclearFuelsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuels + UraniumEnrichmentLevelEnum: + title: Uranium Enrichment Level + description: Standard uranium-235 enrichment level classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NATURAL: + title: Natural Uranium + description: Natural uranium enrichment (0.711% U-235) + annotations: + u235_percentage: 0.711 + category: natural + separative_work: 0 + SLIGHTLY_ENRICHED: + title: Slightly Enriched Uranium + description: Minimal enrichment above natural levels + annotations: + u235_percentage: 0.8-2.0 + category: SEU + typical_use: some heavy water reactors + LOW_ENRICHED: + title: Low Enriched Uranium + description: Standard commercial reactor enrichment + annotations: + u235_percentage: 2.0-5.0 + category: LEU + typical_use: PWR, BWR commercial reactors + HIGH_ASSAY_LOW_ENRICHED: + title: High-Assay Low Enriched Uranium + description: Higher enrichment for advanced reactors + annotations: + u235_percentage: 5.0-20.0 + category: HALEU + typical_use: advanced reactors, SMRs + HIGHLY_ENRICHED: + title: Highly Enriched Uranium + description: High enrichment for research and naval reactors + annotations: + u235_percentage: 20.0-90.0 + category: HEU + typical_use: research reactors, naval propulsion + WEAPONS_GRADE: + title: Weapons-Grade Uranium + description: Very high enrichment for weapons + annotations: + u235_percentage: 90.0+ + category: WGU + proliferation_concern: extreme + is_a: NuclearFuelsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuels + FuelFormEnum: + title: Fuel Form + description: Physical forms of nuclear fuel + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + OXIDE_PELLETS: + title: Oxide Pellets + description: Ceramic uranium dioxide pellets + annotations: + chemical_form: UO2 + shape: cylindrical pellets + typical_use: PWR, BWR fuel rods + METAL_SLUGS: + title: Metal Slugs + description: Metallic uranium fuel elements + annotations: + chemical_form: metallic uranium + shape: cylindrical slugs + typical_use: production reactors + COATED_PARTICLES: + title: Coated Particles + description: Microspheres with protective coatings + annotations: + structure: TRISO or BISO coated + size: microscopic spheres + typical_use: HTGR + LIQUID_SOLUTION: + title: Liquid Solution + description: Fuel dissolved in liquid carrier + annotations: + phase: liquid + typical_use: molten salt reactors + DISPERSION_FUEL: + title: Dispersion Fuel + description: Fuel particles dispersed in matrix + annotations: + structure: particles in matrix + typical_use: research reactors + CERMET_FUEL: + title: Cermet Fuel + description: Ceramic-metal composite fuel + annotations: + structure: ceramic in metal matrix + typical_use: advanced reactors + PLATE_FUEL: + title: Plate Fuel + description: Flat plate fuel elements + annotations: + geometry: flat plates + typical_use: research reactors + ROD_FUEL: + title: Rod Fuel + description: Cylindrical fuel rods + annotations: + geometry: long cylinders + typical_use: commercial power reactors + is_a: NuclearFuelsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuels + FuelAssemblyTypeEnum: + title: Fuel Assembly Type + description: Types of fuel assembly configurations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PWR_ASSEMBLY: + title: PWR Fuel Assembly + description: Square array fuel assembly for PWR + annotations: + geometry: square array + rod_count: 264-289 typical + control_method: control rod clusters + BWR_ASSEMBLY: + title: BWR Fuel Assembly + description: Square array fuel assembly for BWR + annotations: + geometry: square array with channel + rod_count: 49-100 typical + control_method: control blades + CANDU_BUNDLE: + title: CANDU Fuel Bundle + description: Cylindrical fuel bundle for PHWR + annotations: + geometry: cylindrical bundle + rod_count: 28-43 typical + length: ~50 cm + RBMK_ASSEMBLY: + title: RBMK Fuel Assembly + description: Fuel assembly for RBMK reactors + annotations: + geometry: 18-rod bundle + length: ~3.5 m + control_method: control rods + AGR_ASSEMBLY: + title: AGR Fuel Assembly + description: Fuel stringer for AGR + annotations: + geometry: stacked pins + cladding: stainless steel + HTGR_BLOCK: + title: HTGR Fuel Block + description: Graphite block with TRISO fuel + annotations: + geometry: hexagonal or cylindrical blocks + fuel_form: TRISO particles + FAST_REACTOR_ASSEMBLY: + title: Fast Reactor Assembly + description: Fuel assembly for fast reactors + annotations: + geometry: hexagonal wrapper + coolant_flow: axial + is_a: NuclearFuelsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuels + FuelCycleStageEnum: + title: Fuel Cycle Stage + description: Stages in the nuclear fuel cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MINING: + title: Uranium Mining + description: Extraction of uranium ore from deposits + annotations: + process: mining and milling + product: uranium ore concentrate (yellowcake) + CONVERSION: + title: Conversion + description: Conversion of uranium concentrate to UF6 + annotations: + input: U3O8 yellowcake + output: uranium hexafluoride (UF6) + ENRICHMENT: + title: Enrichment + description: Increase of U-235 concentration + annotations: + input: natural UF6 + output: enriched UF6 + waste: depleted uranium tails + FUEL_FABRICATION: + title: Fuel Fabrication + description: Manufacturing of fuel assemblies + annotations: + input: enriched UF6 + output: fuel assemblies + process: pellet and rod manufacturing + REACTOR_OPERATION: + title: Reactor Operation + description: Power generation in nuclear reactor + annotations: + input: fresh fuel assemblies + output: electricity and spent fuel + duration: 12-24 months per cycle + INTERIM_STORAGE: + title: Interim Storage + description: Temporary storage of spent fuel + annotations: + purpose: cooling and decay + duration: 5-40+ years + location: reactor pools or dry casks + REPROCESSING: + title: Reprocessing + description: Chemical separation of spent fuel components + annotations: + input: spent nuclear fuel + output: uranium, plutonium, waste + status: practiced in some countries + DISPOSAL: + title: Disposal + description: Permanent disposal of nuclear waste + annotations: + method: geological repository + duration: permanent + status: under development globally + is_a: NuclearFuelsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuels + FissileIsotopeEnum: + title: Fissile Isotope + description: Fissile isotopes used in nuclear fuel + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + URANIUM_233: + title: Uranium-233 + description: Fissile isotope produced from thorium + aliases: + - U-233 + annotations: + mass_number: 233 + half_life: 159,200 years + thermal_fission: true + breeding_from: Th-232 + URANIUM_235: + title: Uranium-235 + description: Naturally occurring fissile uranium isotope + aliases: + - U-235 + annotations: + mass_number: 235 + half_life: 703,800,000 years + natural_abundance: 0.711% + thermal_fission: true + PLUTONIUM_239: + title: Plutonium-239 + description: Fissile plutonium isotope from U-238 breeding + aliases: + - Pu-239 + annotations: + mass_number: 239 + half_life: 24,110 years + thermal_fission: true + breeding_from: U-238 + PLUTONIUM_241: + title: Plutonium-241 + description: Fissile plutonium isotope with short half-life + aliases: + - Pu-241 + annotations: + mass_number: 241 + half_life: 14.3 years + thermal_fission: true + decay_product: Am-241 + is_a: NuclearFuelsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_fuels + NuclearOperationsSchemaEnum: + description: Schema-level enum for nuclear_operations in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_operations.yaml + ReactorOperatingStateEnum: + title: Reactor Operating State + description: Operational states of nuclear reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + STARTUP: + title: Startup + description: Reactor transitioning from shutdown to power operation + annotations: + neutron_level: increasing + control_rod_position: withdrawing + power_level: rising from zero + duration: hours to days + operator_attention: high + CRITICAL: + title: Critical + description: Reactor achieving self-sustaining chain reaction + annotations: + neutron_multiplication: k-effective = 1.0 + power_level: minimal but self-sustaining + control_rod_position: critical position + milestone: first criticality achievement + POWER_ESCALATION: + title: Power Escalation + description: Reactor increasing power toward full power operation + annotations: + power_level: increasing incrementally + testing: ongoing at each power level + duration: days to weeks + procedures: systematic power increases + FULL_POWER_OPERATION: + title: Full Power Operation + description: Reactor operating at rated thermal power + annotations: + power_level: 100% rated power + operation_mode: commercial electricity generation + duration: typically 12-24 months + fuel_burnup: accumulating + LOAD_FOLLOWING: + title: Load Following + description: Reactor adjusting power to match electrical demand + annotations: + power_level: variable based on demand + control_mode: automatic load following + flexibility: grid demand responsive + frequency: daily power variations + REDUCED_POWER: + title: Reduced Power Operation + description: Reactor operating below rated power + annotations: + power_level: <100% rated power + reasons: maintenance, grid demand, testing + control_rod_position: partially inserted + HOT_STANDBY: + title: Hot Standby + description: Reactor subcritical but at operating temperature + annotations: + criticality: subcritical + temperature: operating temperature maintained + pressure: operating pressure maintained + ready_time: rapid return to power possible + COLD_SHUTDOWN: + title: Cold Shutdown + description: Reactor subcritical and cooled below operating temperature + annotations: + criticality: subcritical with margin + temperature: <200°F (93°C) typically + refueling: possible in this state + maintenance: major maintenance possible + REFUELING: + title: Refueling + description: Reactor shut down for fuel replacement + annotations: + reactor_head: removed + fuel_handling: active fuel movement + criticality_control: strict procedures + duration: typically 30-60 days + REACTOR_TRIP: + title: Reactor Trip + description: Rapid automatic shutdown due to safety system actuation + annotations: + shutdown_speed: seconds + cause: safety system activation + control_rods: fully inserted rapidly + investigation: cause determination required + SCRAM: + title: Scram + description: Emergency rapid shutdown of reactor + annotations: + shutdown_type: emergency shutdown + control_rod_insertion: fastest possible + operator_action: manual or automatic + follow_up: immediate safety assessment + EMERGENCY_SHUTDOWN: + title: Emergency Shutdown + description: Shutdown due to emergency conditions + annotations: + urgency: immediate shutdown required + safety_systems: may be activated + investigation: extensive post-event analysis + recovery: detailed restart procedures + is_a: NuclearOperationsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_operations + MaintenanceTypeEnum: + title: Maintenance Type + description: Types of nuclear facility maintenance activities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PREVENTIVE_MAINTENANCE: + title: Preventive Maintenance + description: Scheduled maintenance to prevent equipment failure + annotations: + schedule: predetermined intervals + purpose: prevent failures + planning: extensive advance planning + outage_type: planned outage + CORRECTIVE_MAINTENANCE: + title: Corrective Maintenance + description: Maintenance to repair failed or degraded equipment + annotations: + trigger: equipment failure or degradation + urgency: varies by safety significance + planning: may be immediate + schedule: unplanned + PREDICTIVE_MAINTENANCE: + title: Predictive Maintenance + description: Maintenance based on condition monitoring + annotations: + basis: condition monitoring data + timing: based on predicted failure + efficiency: optimized maintenance timing + technology: condition monitoring systems + CONDITION_BASED_MAINTENANCE: + title: Condition-Based Maintenance + description: Maintenance triggered by equipment condition assessment + annotations: + assessment: continuous condition monitoring + trigger: condition degradation + optimization: resource optimization + safety: maintains safety margins + REFUELING_OUTAGE_MAINTENANCE: + title: Refueling Outage Maintenance + description: Major maintenance during scheduled refueling + annotations: + frequency: every 12-24 months + scope: major equipment inspection and repair + duration: 30-60 days typical + access: full plant access available + FORCED_OUTAGE_MAINTENANCE: + title: Forced Outage Maintenance + description: Unplanned maintenance due to equipment failure + annotations: + cause: unexpected equipment failure + urgency: immediate attention required + duration: variable + safety_significance: may affect safety systems + IN_SERVICE_INSPECTION: + title: In-Service Inspection + description: Required inspection of safety-related components + annotations: + regulatory_requirement: mandated by regulations + frequency: specified intervals (typically 10 years) + scope: pressure vessels, piping, supports + techniques: non-destructive testing + MODIFICATION_WORK: + title: Modification Work + description: Changes to plant design or configuration + annotations: + purpose: plant improvement or regulatory compliance + approval: requires design change approval + testing: extensive post-modification testing + documentation: comprehensive documentation updates + is_a: NuclearOperationsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_operations + LicensingStageEnum: + title: Licensing Stage + description: Stages in nuclear facility licensing process + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PRE_APPLICATION: + description: Pre-application consultation and preparation + CONSTRUCTION_PERMIT: + description: Construction permit application and review + OPERATING_LICENSE: + description: Operating license application and review + LICENSE_RENEWAL: + description: License renewal application and review + POWER_UPRATE: + description: Power uprate license amendment + DECOMMISSIONING_PLAN: + description: Decommissioning plan approval + LICENSE_TERMINATION: + description: License termination and site release + DESIGN_CERTIFICATION: + description: Standard design certification + EARLY_SITE_PERMIT: + description: Early site permit for future construction + COMBINED_LICENSE: + description: Combined construction and operating license + is_a: NuclearRegulatorySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_regulatory + FuelCycleOperationEnum: + title: Fuel Cycle Operation + description: Nuclear fuel cycle operational activities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + URANIUM_EXPLORATION: + title: Uranium Exploration + description: Search and evaluation of uranium deposits + annotations: + activities: geological surveys, drilling, sampling + purpose: locate economically viable deposits + methods: airborne surveys, ground exploration + URANIUM_EXTRACTION: + title: Uranium Extraction + description: Mining and extraction of uranium ore + annotations: + methods: open pit, underground, in-situ leaching + output: uranium ore + processing: crushing and grinding + URANIUM_MILLING: + title: Uranium Milling + description: Processing of uranium ore to produce yellowcake + annotations: + input: uranium ore + output: uranium concentrate (U3O8) + process: acid or alkaline leaching + URANIUM_CONVERSION: + title: Uranium Conversion + description: Conversion of yellowcake to uranium hexafluoride + annotations: + input: uranium concentrate (U3O8) + output: uranium hexafluoride (UF6) + purpose: prepare for enrichment + URANIUM_ENRICHMENT: + title: Uranium Enrichment + description: Increase U-235 concentration in uranium + annotations: + input: natural uranium (0.711% U-235) + output: enriched uranium (3-5% typical) + waste: depleted uranium tails + methods: gas centrifuge, gaseous diffusion + FUEL_FABRICATION: + title: Fuel Fabrication + description: Manufacturing of nuclear fuel assemblies + annotations: + input: enriched uranium + output: fuel assemblies + process: pellet production, rod assembly + REACTOR_FUEL_LOADING: + title: Reactor Fuel Loading + description: Installation of fresh fuel in reactor + annotations: + frequency: every 12-24 months + procedure: careful criticality control + configuration: specific loading pattern + REACTOR_OPERATION: + title: Reactor Operation + description: Power generation and fuel burnup + annotations: + duration: 12-24 months typical cycle + burnup: fuel depletion over time + output: electricity and fission products + SPENT_FUEL_DISCHARGE: + title: Spent Fuel Discharge + description: Removal of used fuel from reactor + annotations: + timing: end of fuel cycle + handling: underwater fuel handling + destination: spent fuel pool storage + SPENT_FUEL_STORAGE: + title: Spent Fuel Storage + description: Interim storage of discharged fuel + annotations: + cooling: decay heat removal + duration: 5-100+ years + methods: pools, dry casks + SPENT_FUEL_REPROCESSING: + title: Spent Fuel Reprocessing + description: Chemical separation of spent fuel components + annotations: + separation: uranium, plutonium, waste + recovery: recovers usable materials + waste: high-level waste production + WASTE_CONDITIONING: + title: Waste Conditioning + description: Preparation of waste for storage or disposal + annotations: + treatment: solidification, encapsulation + purpose: stable waste form + standards: waste acceptance criteria + WASTE_DISPOSAL: + title: Waste Disposal + description: Permanent disposal of nuclear waste + annotations: + method: geological repository + isolation: long-term containment + safety: protect public and environment + is_a: NuclearOperationsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_operations + ReactorControlModeEnum: + title: Reactor Control Mode + description: Reactor control and safety system operational modes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MANUAL_CONTROL: + title: Manual Control + description: Direct operator control of reactor systems + annotations: + operator_role: direct manual operation + automation: minimal automation + response_time: depends on operator + application: startup, shutdown, testing + AUTOMATIC_CONTROL: + title: Automatic Control + description: Automated reactor control systems + annotations: + automation: high level automation + operator_role: supervisory + response_time: rapid automatic response + application: normal power operation + REACTOR_PROTECTION_SYSTEM: + title: Reactor Protection System Active + description: Safety system monitoring for trip conditions + annotations: + function: automatic reactor trip on unsafe conditions + redundancy: multiple independent channels + response_time: milliseconds to seconds + priority: overrides operator actions + ENGINEERED_SAFEGUARDS: + title: Engineered Safeguards Active + description: Safety systems for accident mitigation + annotations: + function: mitigate consequences of accidents + activation: automatic on accident conditions + systems: emergency core cooling, containment + redundancy: multiple trains + EMERGENCY_OPERATING_PROCEDURES: + title: Emergency Operating Procedures + description: Operator actions for emergency conditions + annotations: + guidance: symptom-based procedures + training: extensive operator training + decision_making: structured approach + coordination: with emergency response + SEVERE_ACCIDENT_MANAGEMENT: + title: Severe Accident Management + description: Procedures for beyond design basis accidents + annotations: + scope: core damage mitigation + guidance: severe accident management guidelines + equipment: portable emergency equipment + coordination: multi-unit considerations + is_a: NuclearOperationsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_operations + OperationalProcedureEnum: + title: Operational Procedure + description: Standard nuclear facility operational procedures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + STARTUP_PROCEDURE: + title: Reactor Startup Procedure + description: Systematic procedure for bringing reactor to power + annotations: + phases: multiple phases with hold points + testing: system testing at each phase + authorization: management authorization required + duration: hours to days + SHUTDOWN_PROCEDURE: + title: Reactor Shutdown Procedure + description: Systematic procedure for shutting down reactor + annotations: + control_rod_insertion: gradual or rapid + cooling: controlled cooldown + systems: systematic system shutdown + verification: shutdown margin verification + REFUELING_PROCEDURE: + title: Refueling Procedure + description: Procedure for fuel handling and replacement + annotations: + criticality_control: strict criticality prevention + handling: underwater fuel handling + documentation: detailed records + verification: independent verification + SURVEILLANCE_TESTING: + title: Surveillance Testing + description: Regular testing of safety systems + annotations: + frequency: specified by technical specifications + scope: functionality verification + documentation: test result documentation + corrective_action: if performance degraded + MAINTENANCE_PROCEDURE: + title: Maintenance Procedure + description: Systematic approach to equipment maintenance + annotations: + work_control: work order control process + safety_tagging: equipment isolation + testing: post-maintenance testing + documentation: maintenance records + EMERGENCY_RESPONSE: + title: Emergency Response Procedure + description: Response to emergency conditions + annotations: + classification: event classification + notification: offsite notification + mitigation: protective action implementation + coordination: with offsite authorities + RADIOLOGICAL_PROTECTION: + title: Radiological Protection Procedure + description: Procedures for radiation protection + annotations: + monitoring: radiation monitoring + contamination_control: contamination prevention + dose_control: personnel dose limits + emergency: radiological emergency response + SECURITY_PROCEDURE: + title: Security Procedure + description: Physical security and access control procedures + annotations: + access_control: personnel access authorization + detection: intrusion detection systems + response: security force response + coordination: with law enforcement + is_a: NuclearOperationsSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_operations + NuclearRegulatorySchemaEnum: + description: Schema-level enum for nuclear_regulatory in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_regulatory.yaml + NuclearRegulatoryBodyEnum: + title: Nuclear Regulatory Body + description: Nuclear regulatory authorities and international organizations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + IAEA: + description: International Atomic Energy Agency + title: International Atomic Energy Agency + NRC: + description: US Nuclear Regulatory Commission + title: Nuclear Regulatory Commission (US) + ONR: + description: Office for Nuclear Regulation (UK) + title: Office for Nuclear Regulation (UK) + ASN: + description: Autorité de sûreté nucléaire (France) + title: Nuclear Safety Authority (France) + NISA: + description: Nuclear and Industrial Safety Agency (Japan) + title: Nuclear and Industrial Safety Agency (Japan) + CNSC: + description: Canadian Nuclear Safety Commission + title: Canadian Nuclear Safety Commission + STUK: + description: Radiation and Nuclear Safety Authority (Finland) + title: Radiation and Nuclear Safety Authority (Finland) + SKI: + description: Swedish Nuclear Power Inspectorate + title: Swedish Nuclear Power Inspectorate + ENSI: + description: Swiss Federal Nuclear Safety Inspectorate + title: Swiss Federal Nuclear Safety Inspectorate + ROSATOM: + description: State Atomic Energy Corporation (Russia) + title: State Atomic Energy Corporation (Russia) + CNNC: + description: China National Nuclear Corporation + title: China National Nuclear Corporation + KAERI: + description: Korea Atomic Energy Research Institute + title: Korea Atomic Energy Research Institute + AERB: + description: Atomic Energy Regulatory Board (India) + title: Atomic Energy Regulatory Board (India) + is_a: NuclearRegulatorySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_regulatory + RegulatoryFrameworkEnum: + title: Regulatory Framework + description: Nuclear regulatory frameworks and international conventions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NPT: + description: Nuclear Non-Proliferation Treaty + title: Nuclear Non-Proliferation Treaty + COMPREHENSIVE_SAFEGUARDS: + description: IAEA Comprehensive Safeguards Agreements + title: IAEA Comprehensive Safeguards Agreement + ADDITIONAL_PROTOCOL: + description: IAEA Additional Protocol + title: IAEA Additional Protocol + CONVENTION_NUCLEAR_SAFETY: + description: Convention on Nuclear Safety + title: Convention on Nuclear Safety + JOINT_CONVENTION: + description: Joint Convention on the Safety of Spent Fuel Management and Radioactive Waste + title: Joint Convention on Radioactive Waste Safety + PARIS_CONVENTION: + description: Paris Convention on Third Party Liability in the Field of Nuclear Energy + title: Paris Convention on Nuclear Liability + VIENNA_CONVENTION: + description: Vienna Convention on Civil Liability for Nuclear Damage + title: Vienna Convention on Nuclear Liability + CPPNM: + description: Convention on the Physical Protection of Nuclear Material + title: Convention on Physical Protection of Nuclear Material + ICSANT: + description: International Convention for the Suppression of Acts of Nuclear Terrorism + title: International Convention for Suppression of Nuclear Terrorism + SAFETY_STANDARDS: + description: IAEA Safety Standards Series + title: IAEA Safety Standards + SECURITY_SERIES: + description: IAEA Nuclear Security Series + title: IAEA Nuclear Security Series + is_a: NuclearRegulatorySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_regulatory + ComplianceStandardEnum: + title: Compliance Standard + description: Nuclear safety and security compliance standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ISO_14001: + description: Environmental Management Systems + title: ISO 14001 Environmental Management + ISO_9001: + description: Quality Management Systems + title: ISO 9001 Quality Management + ASME_NQA_1: + description: Quality Assurance Requirements for Nuclear Facility Applications + title: ASME NQA-1 Quality Assurance + IEEE_603: + description: IEEE Standard Criteria for Safety Systems for Nuclear Power Generating Stations + title: IEEE 603 Safety Systems Criteria + IEC_61513: + description: Nuclear power plants - Instrumentation and control systems + title: IEC 61513 I&C Systems + ANSI_N45_2: + description: Quality Assurance Program Requirements for Nuclear Power Plants + title: ANSI N45.2 Quality Assurance + NUREG_0800: + description: Standard Review Plan for the Review of Safety Analysis Reports + title: NUREG-0800 Standard Review Plan + IAEA_GSR: + description: IAEA General Safety Requirements + title: IAEA General Safety Requirements + IAEA_NSS: + description: IAEA Nuclear Security Series + title: IAEA Nuclear Security Series + WENRA_RL: + description: Western European Nuclear Regulators Association Reference Levels + title: WENRA Reference Levels + is_a: NuclearRegulatorySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_regulatory + InspectionTypeEnum: + title: Inspection Type + description: Types of nuclear regulatory inspections and assessments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ROUTINE_INSPECTION: + description: Regularly scheduled inspection activities + REACTIVE_INSPECTION: + description: Event-driven or follow-up inspections + TEAM_INSPECTION: + description: Multi-disciplinary team inspections + TRIENNIAL_INSPECTION: + description: Three-year cycle comprehensive inspections + CONSTRUCTION_INSPECTION: + description: Construction phase inspections + PRE_OPERATIONAL_TESTING: + description: Pre-operational testing and commissioning inspections + STARTUP_TESTING: + description: Initial startup and power ascension inspections + PERIODIC_SAFETY_REVIEW: + description: Comprehensive periodic safety reviews + INTEGRATED_INSPECTION: + description: Integrated inspection program + FORCE_ON_FORCE: + description: Security force-on-force exercises + EMERGENCY_PREPAREDNESS: + description: Emergency preparedness and response inspections + SPECIAL_INSPECTION: + description: Special inspections for significant events + VENDOR_INSPECTION: + description: Nuclear vendor and supplier inspections + CYBER_SECURITY: + description: Cybersecurity program inspections + DECOMMISSIONING_INSPECTION: + description: Decommissioning activities inspections + is_a: NuclearRegulatorySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_regulatory + NuclearSafetySchemaEnum: + description: Schema-level enum for nuclear_safety in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_safety.yaml + INESLevelEnum: + title: INES Level + description: International Nuclear and Radiological Event Scale (INES) levels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LEVEL_0: + title: Level 0 - Below Scale/Deviation + description: Events without safety significance + annotations: + scale_position: below scale + safety_significance: no safety significance + public_impact: none + examples: minor technical issues + LEVEL_1: + title: Level 1 - Anomaly + description: Anomaly beyond authorized operating regime annotations: - symbol: hp - ucum: '[HP]' - watts: 745.7 - BTU_PER_HOUR: - description: BTU per hour + scale_position: incidents + safety_significance: minor + public_impact: none + examples: minor contamination, minor safety system failure + LEVEL_2: + title: Level 2 - Incident + description: Incident with significant defenses remaining annotations: - symbol: BTU/h - ucum: '[Btu_IT]/h' - watts: 0.293 - is_a: EnergySchemaEnum + scale_position: incidents + safety_significance: minor + public_impact: none + radiation_dose: <10 mSv to workers + LEVEL_3: + title: Level 3 - Serious Incident + description: Serious incident with some defense degradation + annotations: + scale_position: incidents + safety_significance: minor + public_impact: very minor + radiation_dose: <100 mSv to workers + examples: near accident, serious contamination + LEVEL_4: + title: Level 4 - Accident with Local Consequences + description: Accident with minor off-site releases + annotations: + scale_position: accidents + safety_significance: moderate + public_impact: minor local impact + evacuation: not required + examples: partial core damage + LEVEL_5: + title: Level 5 - Accident with Wider Consequences + description: Accident with limited off-site releases + annotations: + scale_position: accidents + safety_significance: moderate to major + public_impact: limited wider impact + protective_actions: limited evacuation + examples: Three Mile Island (1979) + LEVEL_6: + title: Level 6 - Serious Accident + description: Serious accident with significant releases + annotations: + scale_position: accidents + safety_significance: major + public_impact: significant + protective_actions: extensive evacuation and countermeasures + LEVEL_7: + title: Level 7 - Major Accident + description: Major accident with widespread health and environmental effects + annotations: + scale_position: accidents + safety_significance: major + public_impact: widespread + examples: Chernobyl (1986), Fukushima (2011) + consequences: long-term environmental contamination + is_a: NuclearSafetySchemaEnum annotations: source_domain: energy - source_schema: energy - EnergyEfficiencyRating: - description: Energy efficiency ratings and standards + source_schema: nuclear_safety + EmergencyClassificationEnum: + title: Emergency Classification + description: Nuclear emergency action levels and classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NOTIFICATION_UNUSUAL_EVENT: + title: Notification of Unusual Event (NOUE) + description: Events that are in process or have occurred which indicate potential degradation + aliases: + - NOUE + - Unusual Event + annotations: + severity: lowest emergency level + off_site_response: notification only + public_protective_actions: none required + emergency_response: minimal activation + ALERT: + title: Alert + description: Events involving actual or potential substantial degradation of plant safety + annotations: + severity: second emergency level + off_site_response: notification and standby + public_protective_actions: none required, but preparation + emergency_response: partial activation + plant_status: substantial safety degradation possible + SITE_AREA_EMERGENCY: + title: Site Area Emergency (SAE) + description: Events with actual or likely major failures of plant protective systems + aliases: + - SAE + annotations: + severity: third emergency level + off_site_response: offsite centers activated + public_protective_actions: may be required near site + emergency_response: full activation + plant_status: major plant safety systems failure + GENERAL_EMERGENCY: + title: General Emergency + description: Events involving actual or imminent substantial core degradation + annotations: + severity: highest emergency level + off_site_response: full activation + public_protective_actions: implementation likely + emergency_response: maximum response + plant_status: core degradation or containment failure + is_a: NuclearSafetySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_safety + NuclearSecurityCategoryEnum: + title: Nuclear Security Category + description: IAEA nuclear material security categories (INFCIRC/225) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CATEGORY_I: + title: Category I Nuclear Material + description: Material that can be used directly to manufacture nuclear explosive devices + annotations: + direct_use: true + proliferation_risk: highest + protection_requirements: maximum + examples: HEU ≥20%, Pu ≥2kg, U-233 ≥2kg + physical_protection: multiple independent physical barriers + CATEGORY_II: + title: Category II Nuclear Material + description: Material requiring further processing to manufacture nuclear explosive devices + annotations: + direct_use: requires processing + proliferation_risk: moderate + protection_requirements: substantial + examples: HEU <20% but >5%, natural uranium >500kg + physical_protection: significant barriers required + CATEGORY_III: + title: Category III Nuclear Material + description: Material posing radiation hazard but minimal proliferation risk + annotations: + direct_use: false + proliferation_risk: low + protection_requirements: basic + examples: natural uranium 10-500kg, depleted uranium + physical_protection: basic measures sufficient + CATEGORY_IV: + title: Category IV Nuclear Material + description: Material with minimal security significance + annotations: + direct_use: false + proliferation_risk: minimal + protection_requirements: administrative + examples: small quantities of natural uranium + is_a: NuclearSafetySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_safety + SafetySystemClassEnum: + title: Safety System Class + description: Nuclear safety system classifications (based on IEEE and ASME standards) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CLASS_1E: + title: Class 1E Safety Systems + description: Safety systems essential to emergency reactor shutdown and core cooling + annotations: + safety_function: essential to safety + redundancy: required + independence: required + power_supply: independent emergency power + seismic_qualification: required + examples: reactor protection system, emergency core cooling + SAFETY_RELATED: + title: Safety-Related Systems + description: Systems important to safety but not classified as Class 1E + annotations: + safety_function: important to safety + quality_requirements: enhanced + testing_requirements: extensive + examples: some support systems, barriers + SAFETY_SIGNIFICANT: + title: Safety-Significant Systems + description: Systems with risk significance but not safety-related + annotations: + safety_function: risk-significant + quality_requirements: graded approach + risk_informed: classification based on risk assessment + NON_SAFETY_RELATED: + title: Non-Safety-Related Systems + description: Systems not required for nuclear safety functions + annotations: + safety_function: not required for safety + quality_requirements: commercial standards + failure_impact: minimal safety impact + is_a: NuclearSafetySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_safety + ReactorSafetyFunctionEnum: + title: Reactor Safety Function + description: Fundamental nuclear reactor safety functions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + REACTIVITY_CONTROL: + title: Reactivity Control + description: Control of nuclear chain reaction + annotations: + function: maintain reactor subcritical when required + systems: control rods, neutron absorbers + failure_consequence: criticality accident + defense_category: prevent accidents + HEAT_REMOVAL: + title: Heat Removal + description: Removal of decay heat from reactor core + annotations: + function: prevent fuel overheating + systems: cooling systems, heat exchangers + failure_consequence: core damage, meltdown + defense_category: mitigate consequences + CONTAINMENT_INTEGRITY: + title: Containment Integrity + description: Confinement of radioactive materials + annotations: + function: prevent radioactive release + systems: containment structure, isolation systems + failure_consequence: environmental contamination + defense_category: mitigate consequences + CORE_COOLING: + title: Core Cooling + description: Maintenance of adequate core cooling + annotations: + function: prevent fuel damage + systems: primary cooling, emergency cooling + failure_consequence: fuel damage + time_sensitivity: immediate to long-term + SHUTDOWN_CAPABILITY: + title: Shutdown Capability + description: Ability to shut down and maintain shutdown + annotations: + function: terminate power operation safely + systems: control systems, shutdown systems + time_requirement: rapid response capability + is_a: NuclearSafetySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_safety + DefenseInDepthLevelEnum: + title: Defense In Depth Level + description: Defense in depth barrier levels for nuclear safety + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - A_PLUS_PLUS_PLUS: - description: A+++ (highest efficiency) - annotations: - rank: 1 - region: EU - A_PLUS_PLUS: - description: A++ - annotations: - rank: 2 - region: EU - A_PLUS: - description: A+ + LEVEL_1: + title: Level 1 - Prevention of Abnormal Operation + description: Conservative design and high quality in construction and operation annotations: - rank: 3 - region: EU - A: - description: A + objective: prevent deviations from normal operation + approach: conservative design, quality assurance + examples: design margins, quality construction + LEVEL_2: + title: Level 2 - Control of Abnormal Operation + description: Control of abnormal operation and detection of failures annotations: - rank: 4 - region: EU - B: - description: B + objective: control abnormal operation and failures + approach: control systems, protection systems + examples: reactor protection systems, safety systems + LEVEL_3: + title: Level 3 - Control of Accidents Within Design Basis + description: Control of accidents to prevent progression to severe conditions annotations: - rank: 5 - region: EU - C: - description: C + objective: control design basis accidents + approach: engineered safety features + examples: emergency core cooling, containment systems + LEVEL_4: + title: Level 4 - Control of Severe Plant Conditions + description: Control of severe accidents including prevention of core melt progression annotations: - rank: 6 - region: EU - D: - description: D + objective: control severe accidents + approach: severe accident management + examples: cavity flooding, filtered venting + LEVEL_5: + title: Level 5 - Mitigation of Radiological Consequences + description: Mitigation of off-site radiological consequences annotations: - rank: 7 - region: EU - E: - description: E + objective: protect public and environment + approach: emergency planning and response + examples: evacuation plans, protective actions + is_a: NuclearSafetySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_safety + RadiationProtectionZoneEnum: + title: Radiation Protection Zone + description: Radiation protection zone classifications for nuclear facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + EXCLUSION_AREA: + title: Exclusion Area + description: Area under control of reactor operator with restricted access + annotations: + control: reactor operator + public_access: restricted + size: typically few hundred meters radius + purpose: immediate accident response control + LOW_POPULATION_ZONE: + title: Low Population Zone (LPZ) + description: Area with low population density surrounding exclusion area + annotations: + population_density: low + evacuation: feasible if needed + size: typically few kilometers radius + dose_limit: design basis for accident consequences + EMERGENCY_PLANNING_ZONE: + title: Emergency Planning Zone (EPZ) + description: Area for which emergency planning is conducted + annotations: + planning_required: comprehensive emergency plans + size: typically 10-mile (16 km) radius + protective_actions: evacuation and sheltering plans + INGESTION_PATHWAY_ZONE: + title: Ingestion Pathway Zone + description: Area for controlling food and water contamination + annotations: + contamination_control: food and water supplies + size: typically 50-mile (80 km) radius + monitoring: food chain monitoring required + CONTROLLED_AREA: + title: Controlled Area + description: Area within facility boundary with access control + annotations: + access_control: personnel monitoring required + radiation_monitoring: continuous monitoring + training_required: radiation safety training + SUPERVISED_AREA: + title: Supervised Area + description: Area with potential for radiation exposure but lower than controlled + annotations: + monitoring: periodic monitoring + access_control: limited restrictions + training_required: basic radiation awareness + is_a: NuclearSafetySchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_safety + NuclearWasteSchemaEnum: + description: Schema-level enum for nuclear_waste in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/nuclear_waste.yaml + IAEAWasteClassificationEnum: + title: IAEA Waste Classification + description: IAEA General Safety Requirements radioactive waste classification scheme + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + EXEMPT_WASTE: + title: Exempt Waste (EW) + description: Waste with negligible radioactivity requiring no regulatory control + aliases: + - EW + annotations: + regulatory_control: none required + clearance: can be cleared from regulatory control + disposal: as ordinary waste + activity_level: negligible + VERY_SHORT_LIVED_WASTE: + title: Very Short-Lived Waste (VSLW) + description: Waste stored for decay to exempt levels within few years + aliases: + - VSLW + annotations: + storage_period: up to few years + decay_strategy: storage for decay + clearance: after decay period + typical_sources: medical, research isotopes + VERY_LOW_LEVEL_WASTE: + title: Very Low Level Waste (VLLW) + description: Waste requiring limited containment and isolation + aliases: + - VLLW + annotations: + containment_requirement: limited + disposal: near-surface landfill-type + activity_level: very low but above exempt + isolation_period: limited + LOW_LEVEL_WASTE: + title: Low Level Waste (LLW) + description: Waste requiring containment for up to hundreds of years + aliases: + - LLW + annotations: + containment_period: up to few hundred years + disposal: near-surface disposal + activity_level: low + heat_generation: negligible + INTERMEDIATE_LEVEL_WASTE: + title: Intermediate Level Waste (ILW) + description: Waste requiring containment for thousands of years + aliases: + - ILW + annotations: + containment_period: up to thousands of years + disposal: geological disposal + activity_level: intermediate + heat_generation: low (<2 kW/m³) + shielding: required + HIGH_LEVEL_WASTE: + title: High Level Waste (HLW) + description: Waste requiring containment for thousands to hundreds of thousands of years + aliases: + - HLW + annotations: + containment_period: thousands to hundreds of thousands of years + disposal: geological disposal + activity_level: high + heat_generation: significant (>2 kW/m³) + cooling: required + shielding: heavy shielding required + is_a: NuclearWasteSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_waste + NRCWasteClassEnum: + title: NRC Waste Class + description: US NRC 10 CFR 61 low-level radioactive waste classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CLASS_A: + title: Class A Low-Level Waste + description: Lowest radioactivity waste suitable for shallow land burial + annotations: + disposal_method: shallow land burial + segregation_requirements: minimal + waste_form_requirements: none + typical_sources: medical, industrial, power plants + concentration_limits: lowest of three classes + CLASS_B: + title: Class B Low-Level Waste + description: Intermediate radioactivity requiring waste form stability + annotations: + disposal_method: shallow land burial + segregation_requirements: from Class A + waste_form_requirements: structural stability + institutional_control: 100 years minimum + concentration_limits: intermediate + CLASS_C: + title: Class C Low-Level Waste + description: Highest concentration suitable for shallow land burial + annotations: + disposal_method: shallow land burial + segregation_requirements: enhanced + waste_form_requirements: structural stability + institutional_control: 100 years minimum + intruder_barriers: required + concentration_limits: highest for shallow burial + GREATER_THAN_CLASS_C: + title: Greater Than Class C Waste (GTCC) + description: Waste exceeding Class C limits, generally unsuitable for shallow burial + aliases: + - GTCC + annotations: + disposal_method: case-by-case evaluation + shallow_burial: generally not acceptable + deep_disposal: may be required + nrc_evaluation: required + concentration_limits: exceeds Class C + is_a: NuclearWasteSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_waste + WasteHeatGenerationEnum: + title: Waste Heat Generation + description: Heat generation categories for radioactive waste + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NEGLIGIBLE_HEAT: + title: Negligible Heat Generation + description: Waste generating negligible heat + annotations: + heat_output: <0.1 kW/m³ + cooling_required: false + thermal_consideration: minimal + LOW_HEAT: + title: Low Heat Generation + description: Waste generating low but measurable heat + annotations: + heat_output: 0.1-2 kW/m³ + cooling_required: minimal + thermal_consideration: some design consideration + HIGH_HEAT: + title: High Heat Generation + description: Waste generating significant heat requiring thermal management + annotations: + heat_output: '>2 kW/m³' + cooling_required: true + thermal_consideration: major design factor + typical_waste: spent nuclear fuel, HLW glass + is_a: NuclearWasteSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_waste + WasteHalfLifeCategoryEnum: + title: Waste Half Life Category + description: Half-life categories for radioactive waste classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + VERY_SHORT_LIVED: + title: Very Short-Lived + description: Radionuclides with very short half-lives + annotations: + half_life_range: seconds to days + decay_strategy: storage for decay + typical_examples: medical isotopes, some activation products + SHORT_LIVED: + title: Short-Lived + description: Radionuclides with short half-lives + annotations: + half_life_range: <30 years + containment_period: hundreds of years + decay_significance: significant over containment period + LONG_LIVED: + title: Long-Lived + description: Radionuclides with long half-lives + annotations: + half_life_range: '>30 years' + containment_period: thousands to millions of years + decay_significance: minimal over human timescales + examples: actinides, some fission products + is_a: NuclearWasteSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_waste + WasteDisposalMethodEnum: + title: Waste Disposal Method + description: Methods for radioactive waste disposal + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CLEARANCE: + title: Clearance for Unrestricted Use + description: Release from regulatory control as ordinary waste + annotations: + regulatory_oversight: none after clearance + waste_category: exempt waste + disposal_location: conventional facilities + DECAY_STORAGE: + title: Decay Storage + description: Storage for radioactive decay to exempt levels + annotations: + storage_duration: typically <10 years + waste_category: very short-lived waste + final_disposal: as ordinary waste after decay + NEAR_SURFACE_DISPOSAL: + title: Near-Surface Disposal + description: Disposal in engineered near-surface facilities + annotations: + depth: typically <30 meters + waste_categories: VLLW, LLW, some ILW + institutional_control: 100-300 years + barriers: engineered barriers + GEOLOGICAL_DISPOSAL: + title: Geological Disposal + description: Deep underground disposal in stable geological formations + annotations: + depth: typically >300 meters + waste_categories: HLW, long-lived ILW, spent fuel + containment_period: thousands to millions of years + barriers: multiple barriers including geology + BOREHOLE_DISPOSAL: + title: Borehole Disposal + description: Disposal in deep boreholes + annotations: + depth: 1-5 kilometers + waste_categories: disused sealed sources, some HLW + isolation: extreme depth isolation + TRANSMUTATION: + title: Transmutation + description: Nuclear transformation to shorter-lived or stable isotopes + annotations: + method: accelerator-driven systems or fast reactors + waste_categories: long-lived actinides + status: research and development + is_a: NuclearWasteSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_waste + WasteSourceEnum: + title: Waste Source + description: Sources of radioactive waste generation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NUCLEAR_POWER_PLANTS: + title: Nuclear Power Plants + description: Waste from commercial nuclear power generation + annotations: + waste_types: spent fuel, operational waste, decommissioning waste + volume_fraction: largest single source + waste_classes: all classes including HLW + MEDICAL_APPLICATIONS: + title: Medical Applications + description: Waste from nuclear medicine and radiotherapy + annotations: + waste_types: short-lived medical isotopes, sealed sources + typical_classification: Class A, VSLW + decay_strategy: often storage for decay + INDUSTRIAL_APPLICATIONS: + title: Industrial Applications + description: Waste from industrial use of radioactive materials + annotations: + applications: gauging, radiography, sterilization + waste_types: sealed sources, contaminated equipment + typical_classification: Class A and B + RESEARCH_FACILITIES: + title: Research Facilities + description: Waste from research reactors and laboratories + annotations: + waste_types: activation products, contaminated materials + typical_classification: Class A, B, and C + fuel_type: often HEU spent fuel + NUCLEAR_WEAPONS_PROGRAM: + title: Nuclear Weapons Program + description: Waste from defense nuclear activities + annotations: + waste_types: TRU waste, HLW, contaminated equipment + legacy_waste: significant volumes from past activities + classification: all classes including TRU + DECOMMISSIONING: + title: Facility Decommissioning + description: Waste from dismantling nuclear facilities + annotations: + waste_types: activated concrete, contaminated metal + volume: large volumes of VLLW and LLW + activity_level: generally low level + URANIUM_MINING: + title: Uranium Mining and Milling + description: Waste from uranium extraction and processing + annotations: + waste_types: tailings, contaminated equipment + volume: very large volumes + activity_level: naturally occurring radioactivity + FUEL_CYCLE_FACILITIES: + title: Fuel Cycle Facilities + description: Waste from fuel fabrication, enrichment, and reprocessing + annotations: + waste_types: contaminated equipment, process waste + classification: variable depending on process + uranium_content: often contains enriched uranium + is_a: NuclearWasteSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_waste + TransuranicWasteCategoryEnum: + title: Transuranic Waste Category + description: Transuranic waste classifications (US system) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CONTACT_HANDLED_TRU: + title: Contact-Handled Transuranic Waste + description: TRU waste with surface dose rate ≤200 mrem/hr + aliases: + - CH-TRU + annotations: + dose_rate: ≤200 mrem/hr at surface + handling: direct contact possible with protection + disposal: geological repository (WIPP) + plutonium_content: '>100 nCi/g' + REMOTE_HANDLED_TRU: + title: Remote-Handled Transuranic Waste + description: TRU waste with surface dose rate >200 mrem/hr + aliases: + - RH-TRU + annotations: + dose_rate: '>200 mrem/hr at surface' + handling: remote handling required + disposal: geological repository with additional shielding + plutonium_content: '>100 nCi/g' + TRU_MIXED_WASTE: + title: TRU Mixed Waste + description: TRU waste also containing hazardous chemical components + annotations: + regulation: both radiological and chemical hazard regulations + treatment: may require chemical treatment before disposal + disposal: geological repository after treatment + complexity: dual regulatory framework + is_a: NuclearWasteSchemaEnum + annotations: + source_domain: energy + source_schema: nuclear_waste + ReactorTypesSchemaEnum: + description: Schema-level enum for reactor_types in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/nuclear/reactor_types.yaml + ReactorTypeEnum: + title: Reactor Type + description: Nuclear reactor types based on design and operational characteristics + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PWR: + title: Pressurized Water Reactor + description: Most common reactor type using light water under pressure + aliases: + - Pressurized Water Reactor + annotations: + coolant: light water + moderator: light water + pressure: high + steam_generation: indirect + worldwide_count: ~300 + fuel_enrichment: 3-5% + BWR: + title: Boiling Water Reactor + description: Light water reactor where water boils directly in core + aliases: + - Boiling Water Reactor + annotations: + coolant: light water + moderator: light water + pressure: medium + steam_generation: direct + worldwide_count: ~60 + fuel_enrichment: 3-5% + PHWR: + title: Pressurized Heavy Water Reactor + description: Heavy water moderated and cooled reactor (CANDU type) + aliases: + - CANDU + - Pressurized Heavy Water Reactor + annotations: + coolant: heavy water + moderator: heavy water + pressure: high + steam_generation: indirect + worldwide_count: ~47 + fuel_enrichment: natural uranium + LWGR: + title: Light Water Graphite Reactor + description: Graphite moderated, light water cooled reactor (RBMK type) + aliases: + - RBMK + - Light Water Graphite Reactor + annotations: + coolant: light water + moderator: graphite + pressure: medium + steam_generation: direct + worldwide_count: ~10 + fuel_enrichment: 1.8-2.4% + AGR: + title: Advanced Gas-Cooled Reactor + description: Graphite moderated, CO2 gas cooled reactor + aliases: + - Advanced Gas-Cooled Reactor + annotations: + coolant: carbon dioxide + moderator: graphite + pressure: high + steam_generation: indirect + worldwide_count: ~8 + fuel_enrichment: 2.5-3.5% + GCR: + title: Gas-Cooled Reactor + description: Early gas-cooled reactor design (Magnox type) + aliases: + - Magnox + - Gas-Cooled Reactor + annotations: + coolant: carbon dioxide + moderator: graphite + pressure: low + fuel_enrichment: natural uranium + FBR: + title: Fast Breeder Reactor + description: Fast neutron reactor that breeds fissile material + aliases: + - Fast Breeder Reactor + - Liquid Metal Fast Breeder Reactor + annotations: + coolant: liquid metal + moderator: none + neutron_spectrum: fast + worldwide_count: ~2 + fuel_enrichment: 15-20% + HTGR: + title: High Temperature Gas-Cooled Reactor + description: Helium-cooled reactor with TRISO fuel + aliases: + - High Temperature Gas-Cooled Reactor + annotations: + coolant: helium + moderator: graphite + temperature: very high + fuel_type: TRISO + MSR: + title: Molten Salt Reactor + description: Reactor using molten salt as coolant and/or fuel + aliases: + - Molten Salt Reactor + annotations: + coolant: molten salt + fuel_form: liquid + generation: IV + SMR: + title: Small Modular Reactor + description: Small reactors designed for modular construction + aliases: + - Small Modular Reactor + annotations: + power_output: <300 MWe + modularity: high + generation: III+/IV + VHTR: + title: Very High Temperature Reactor + description: Generation IV reactor for very high temperature applications + aliases: + - Very High Temperature Reactor + annotations: + temperature: '>950°C' + generation: IV + coolant: helium + SFR: + title: Sodium-Cooled Fast Reactor + description: Fast reactor cooled by liquid sodium + aliases: + - Sodium-Cooled Fast Reactor + annotations: + coolant: liquid sodium + neutron_spectrum: fast + generation: IV + LFR: + title: Lead-Cooled Fast Reactor + description: Fast reactor cooled by liquid lead or lead-bismuth + aliases: + - Lead-Cooled Fast Reactor + annotations: + coolant: liquid lead + neutron_spectrum: fast + generation: IV + GFR: + title: Gas-Cooled Fast Reactor + description: Fast reactor with gas cooling + aliases: + - Gas-Cooled Fast Reactor + annotations: + coolant: helium + neutron_spectrum: fast + generation: IV + SCWR: + title: Supercritical Water-Cooled Reactor + description: Reactor using supercritical water as coolant + aliases: + - Supercritical Water-Cooled Reactor + annotations: + coolant: supercritical water + generation: IV + is_a: ReactorTypesSchemaEnum + annotations: + source_domain: energy + source_schema: reactor_types + ReactorGenerationEnum: + title: Reactor Generation + description: Nuclear reactor generational classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GENERATION_I: + title: Generation I + description: Early commercial reactors (1950s-1960s) + annotations: + period: 1950s-1960s + status: retired + examples: Shippingport, Dresden-1 + GENERATION_II: + title: Generation II + description: Current operating commercial reactors + annotations: + period: 1970s-1990s + status: operating + examples: PWR, BWR, CANDU + design_life: 40 years + GENERATION_III: + title: Generation III + description: Advanced reactors with enhanced safety + annotations: + period: 1990s-2010s + status: some operating + improvements: passive safety, standardization + examples: AP1000, EPR, ABWR + GENERATION_III_PLUS: + title: Generation III+ + description: Evolutionary improvements to Generation III + annotations: + period: 2000s-present + status: deployment + improvements: enhanced passive safety + examples: AP1000, APR1400 + GENERATION_IV: + title: Generation IV + description: Next generation advanced reactor concepts + annotations: + period: 2030s and beyond + status: development + goals: sustainability, economics, safety, proliferation resistance + examples: VHTR, SFR, LFR, GFR, SCWR, MSR + is_a: ReactorTypesSchemaEnum + annotations: + source_domain: energy + source_schema: reactor_types + ReactorCoolantEnum: + title: Reactor Coolant + description: Primary coolant types used in nuclear reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LIGHT_WATER: + title: Light Water (H2O) + description: Ordinary water as primary coolant + annotations: + chemical_formula: H2O + density: 1.0 g/cm³ + neutron_absorption: moderate + HEAVY_WATER: + title: Heavy Water (D2O) + description: Deuterium oxide as primary coolant + annotations: + chemical_formula: D2O + density: 1.1 g/cm³ + neutron_absorption: low + CARBON_DIOXIDE: + title: Carbon Dioxide + description: CO2 gas as primary coolant + annotations: + chemical_formula: CO2 + phase: gas + pressure: high + HELIUM: + title: Helium + description: Helium gas as primary coolant + annotations: + chemical_formula: He + phase: gas + neutron_absorption: very low + temperature_capability: very high + LIQUID_SODIUM: + title: Liquid Sodium + description: Molten sodium metal as coolant + annotations: + chemical_formula: Na + phase: liquid + melting_point: 98°C + neutron_absorption: low + LIQUID_LEAD: + title: Liquid Lead + description: Molten lead or lead-bismuth as coolant + annotations: + chemical_formula: Pb + phase: liquid + melting_point: 327°C + neutron_absorption: low + MOLTEN_SALT: + title: Molten Salt + description: Molten fluoride or chloride salts annotations: - rank: 8 - region: EU - F: - description: F + phase: liquid + temperature_capability: very high + neutron_absorption: variable + SUPERCRITICAL_WATER: + title: Supercritical Water + description: Water above critical point annotations: - rank: 9 - region: EU - G: - description: G (lowest efficiency) + chemical_formula: H2O + pressure: '>221 bar' + temperature: '>374°C' + is_a: ReactorTypesSchemaEnum + annotations: + source_domain: energy + source_schema: reactor_types + ReactorModeratorEnum: + title: Reactor Moderator + description: Neutron moderator types used in nuclear reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LIGHT_WATER: + title: Light Water (H2O) + description: Ordinary water as neutron moderator + annotations: + chemical_formula: H2O + moderation_effectiveness: good + neutron_absorption: moderate + HEAVY_WATER: + title: Heavy Water (D2O) + description: Deuterium oxide as neutron moderator + annotations: + chemical_formula: D2O + moderation_effectiveness: excellent + neutron_absorption: very low + GRAPHITE: + title: Graphite + description: Carbon graphite as neutron moderator annotations: - rank: 10 - region: EU - ENERGY_STAR: - description: Energy Star certified + chemical_formula: C + moderation_effectiveness: good + neutron_absorption: low + temperature_resistance: high + BERYLLIUM: + title: Beryllium + description: Beryllium metal as neutron moderator annotations: - region: US - ENERGY_STAR_MOST_EFFICIENT: - description: Energy Star Most Efficient + chemical_formula: Be + moderation_effectiveness: good + neutron_absorption: very low + NONE: + title: No Moderator + description: Fast reactors with no neutron moderation annotations: - region: US - is_a: EnergySchemaEnum + neutron_spectrum: fast + moderation: none + is_a: ReactorTypesSchemaEnum annotations: source_domain: energy - source_schema: energy - BuildingEnergyStandard: - description: Building energy efficiency standards and certifications - permissible_values: - PASSIVE_HOUSE: - description: Passive House (Passivhaus) standard - LEED_PLATINUM: - description: LEED Platinum certification - LEED_GOLD: - description: LEED Gold certification - LEED_SILVER: - description: LEED Silver certification - LEED_CERTIFIED: - description: LEED Certified - BREEAM_OUTSTANDING: - description: BREEAM Outstanding - BREEAM_EXCELLENT: - description: BREEAM Excellent - BREEAM_VERY_GOOD: - description: BREEAM Very Good - BREEAM_GOOD: - description: BREEAM Good - BREEAM_PASS: - description: BREEAM Pass - NET_ZERO: - description: Net Zero Energy Building - ENERGY_POSITIVE: - description: Energy Positive Building - ZERO_CARBON: - description: Zero Carbon Building - is_a: EnergySchemaEnum + source_schema: reactor_types + ReactorNeutronSpectrumEnum: + title: Reactor Neutron Spectrum + description: Neutron energy spectrum classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + THERMAL: + title: Thermal Neutron Spectrum + description: Low energy neutrons in thermal equilibrium + annotations: + energy_range: <1 eV + temperature_equivalent: room temperature + fission_probability: high for U-235 + EPITHERMAL: + title: Epithermal Neutron Spectrum + description: Intermediate energy neutrons + annotations: + energy_range: 1 eV - 1 keV + temperature_equivalent: elevated + FAST: + title: Fast Neutron Spectrum + description: High energy neutrons from fission + annotations: + energy_range: '>1 keV' + moderation: minimal or none + breeding_capability: high + is_a: ReactorTypesSchemaEnum annotations: source_domain: energy - source_schema: energy - GridType: - description: Types of electrical grid systems - permissible_values: - MAIN_GRID: - description: Main utility grid - MICROGRID: - description: Microgrid - OFF_GRID: - description: Off-grid/standalone - SMART_GRID: - description: Smart grid - MINI_GRID: - description: Mini-grid - VIRTUAL_POWER_PLANT: - description: Virtual power plant - is_a: EnergySchemaEnum + source_schema: reactor_types + ReactorSizeCategoryEnum: + title: Reactor Size Category + description: Nuclear reactor size classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LARGE: + title: Large Reactor + description: Traditional large-scale commercial reactors + annotations: + power_output: '>700 MWe' + construction: custom on-site + MEDIUM: + title: Medium Reactor + description: Mid-scale reactors + annotations: + power_output: 300-700 MWe + construction: semi-modular + SMALL: + title: Small Reactor + description: Small modular reactors + annotations: + power_output: 50-300 MWe + construction: modular + transport: potentially transportable + MICRO: + title: Micro Reactor + description: Very small reactors for remote applications + annotations: + power_output: <50 MWe + construction: factory-built + transport: transportable + RESEARCH: + title: Research Reactor + description: Small reactors for research and isotope production + annotations: + power_output: <100 MWt + primary_use: research, isotopes, training + is_a: ReactorTypesSchemaEnum annotations: source_domain: energy - source_schema: energy - EnergyStorageType: - description: Types of energy storage systems - permissible_values: - LITHIUM_ION_BATTERY: - description: Lithium-ion battery + source_schema: reactor_types + BioenergySchemaEnum: + description: Schema-level enum for bioenergy in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/renewable/bioenergy.yaml + BiomassFeedstockType: + title: Biomass Feedstock Type + description: Types of biomass materials used as feedstocks for bioenergy production. Includes dedicated energy crops, + agricultural residues, forest residues, and waste streams. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.energy.gov/eere/bioenergy/feedstock-technologies + - https://www.energy.gov/eere/bioenergy/biomass-resources + permissible_values: + CORN_STOVER: + title: Corn Stover + description: Agricultural residue consisting of leaves, stalks, and cobs remaining after corn grain harvest. + aliases: + - Corn Residue + annotations: + category: agricultural_residue + lignocellulosic: true + WHEAT_STRAW: + title: Wheat Straw + description: Agricultural residue remaining after wheat grain harvest. + annotations: + category: agricultural_residue + lignocellulosic: true + RICE_STRAW: + title: Rice Straw + description: Agricultural residue remaining after rice grain harvest. + annotations: + category: agricultural_residue + lignocellulosic: true + SWITCHGRASS: + title: Switchgrass + description: Perennial warm-season grass native to North America, cultivated as dedicated energy crop for cellulosic + biofuel production. + related_mappings: + - AGRO:00000325 + annotations: + category: energy_crop + lignocellulosic: true + perennial: true + MISCANTHUS: + title: Miscanthus + description: High-yielding perennial grass cultivated as dedicated energy crop. + aliases: + - Elephant Grass + annotations: + category: energy_crop + lignocellulosic: true + perennial: true + ENERGY_CANE: + title: Energy Cane + description: High-fiber sugarcane varieties bred for biomass production rather than sugar content. + annotations: + category: energy_crop + lignocellulosic: true + SWEET_SORGHUM: + title: Sweet Sorghum + description: Sorghum variety with high sugar content in stalks, suitable for both sugar and lignocellulosic conversion. + annotations: + category: energy_crop + sugar_crop: true + POPLAR: + title: Poplar + description: Fast-growing hardwood tree cultivated as short-rotation woody crop for biomass. + aliases: + - Hybrid Poplar + annotations: + category: woody_crop + lignocellulosic: true + WILLOW: + title: Willow + description: Fast-growing shrub cultivated as short-rotation woody crop. + aliases: + - Shrub Willow + annotations: + category: woody_crop + lignocellulosic: true + FOREST_RESIDUE: + title: Forest Residue + description: Biomass from forest operations including logging residues, thinning material, and salvage timber. + aliases: + - Logging Residue + related_mappings: + - AGRO:00000546 + broad_mappings: + - sweet:matrBiomass/Biomass annotations: - category: electrochemical - LEAD_ACID_BATTERY: - description: Lead-acid battery + category: forestry_residue + lignocellulosic: true + WOOD_PROCESSING_RESIDUE: + title: Wood Processing Residue + description: Byproducts from wood processing including sawdust, bark, shavings, and wood chips. + aliases: + - Mill Residue annotations: - category: electrochemical - FLOW_BATTERY: - description: Flow battery (e.g., vanadium redox) + category: processing_residue + lignocellulosic: true + MUNICIPAL_SOLID_WASTE: + title: Municipal Solid Waste (Organic Fraction) + description: Organic portion of municipal solid waste suitable for bioenergy conversion. + aliases: + - MSW + related_mappings: + - ENVO:00002273 annotations: - category: electrochemical - SOLID_STATE_BATTERY: - description: Solid-state battery + category: waste + FOOD_WASTE: + title: Food Waste + description: Waste food from residential, commercial, and industrial sources. annotations: - category: electrochemical - SODIUM_ION_BATTERY: - description: Sodium-ion battery + category: wet_waste + ANIMAL_MANURE: + title: Animal Manure + description: Livestock waste including cattle, swine, and poultry manure. + related_mappings: + - ENVO:00003031 + annotations: + category: wet_waste + biogas_suitable: true + ALGAE: + title: Algae + description: Microalgae or macroalgae cultivated for lipid or carbohydrate content for biofuel production. + aliases: + - Microalgae + annotations: + category: aquatic_biomass + lipid_rich: true + USED_COOKING_OIL: + title: Used Cooking Oil + description: Waste vegetable oils from food preparation. + aliases: + - UCO + - Waste Vegetable Oil + annotations: + category: waste + lipid_rich: true + SOYBEAN_OIL: + title: Soybean Oil + description: Vegetable oil from soybean seeds, used for biodiesel. + meaning: CHEBI:166975 + annotations: + category: oil_crop + lipid_rich: true + CORN_GRAIN: + title: Corn Grain + description: Corn kernels used for starch-based ethanol production. + annotations: + category: grain + starch_crop: true + SUGARCANE: + title: Sugarcane + description: Sugar-rich crop used for first-generation ethanol production. + annotations: + category: sugar_crop + is_a: BioenergySchemaEnum + annotations: + source_domain: energy + source_schema: bioenergy + BiofuelType: + title: Biofuel Type + description: Types of fuels produced from biomass feedstocks. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.energy.gov/eere/bioenergy/full-text-glossary + permissible_values: + ETHANOL: + title: Ethanol + description: Alcohol biofuel (C2H5OH) produced by fermentation of sugars or starches, or from cellulosic biomass. + meaning: CHEBI:16236 + aliases: + - Fuel Ethanol + - Bioethanol + close_mappings: + - sweet:matrEnergy/Ethanol annotations: - category: electrochemical - PUMPED_HYDRO: - description: Pumped hydroelectric storage + chemical_formula: C2H5OH + BIODIESEL: + title: Biodiesel + description: Fatty acid methyl esters (FAME) produced by transesterification of vegetable oils or animal fats. + aliases: + - FAME + close_mappings: + - MESH:D056804 + - sweet:matrEnergy/Biodiesel annotations: - category: mechanical - COMPRESSED_AIR: - description: Compressed air energy storage (CAES) + production_method: transesterification + RENEWABLE_DIESEL: + title: Renewable Diesel + description: Hydrocarbon diesel produced by hydrotreating lipids. Chemically identical to petroleum diesel. + aliases: + - Green Diesel + - HVO + - Hydrotreated Vegetable Oil annotations: - category: mechanical - FLYWHEEL: - description: Flywheel energy storage + drop_in_fuel: true + SUSTAINABLE_AVIATION_FUEL: + title: Sustainable Aviation Fuel (SAF) + description: Jet fuel produced from biomass or waste, meeting aviation fuel specifications. + aliases: + - SAF + - Biojet annotations: - category: mechanical - GRAVITY_STORAGE: - description: Gravity-based storage + drop_in_fuel: true + BIOGAS: + title: Biogas + description: Gaseous mixture of methane and CO2 produced by anaerobic digestion of organic matter. + aliases: + - Raw Biogas annotations: - category: mechanical - MOLTEN_SALT: - description: Molten salt thermal storage + methane_content_percent: 50-70 + BIOMETHANE: + title: Biomethane + description: Purified biogas upgraded to natural gas quality (>95% methane). + aliases: + - Renewable Natural Gas + - RNG + broad_mappings: + - sweet:matrOrganicCompound/Methane annotations: - category: thermal - ICE_STORAGE: - description: Ice thermal storage + methane_content_percent: 95+ + pipeline_quality: true + BIO_OIL: + title: Bio-Oil + description: Liquid intermediate produced by pyrolysis or hydrothermal liquefaction of biomass. + aliases: + - Pyrolysis Oil annotations: - category: thermal - PHASE_CHANGE: - description: Phase change materials + intermediate: true + SYNGAS: + title: Syngas (Bio-Based) + description: Synthesis gas (CO + H2) produced by gasification of biomass. + aliases: + - Synthesis Gas + - gasification + close_mappings: + - CHMO:0001501 + - sweet:matrEnergy/Syngas annotations: - category: thermal - HYDROGEN_STORAGE: - description: Hydrogen storage + intermediate: true + BUTANOL: + title: butan-1-ol + description: Four-carbon alcohol biofuel with higher energy density than ethanol. + meaning: CHEBI:28885 + aliases: + - Biobutanol + annotations: + chemical_formula: C4H9OH + METHANOL: + title: Biomethanol + description: Methanol produced from biomass-derived syngas. + meaning: CHEBI:17790 + annotations: + chemical_formula: CH3OH + DIMETHYL_ETHER: + title: Bio-DME + description: Dimethyl ether produced from biomass, usable as diesel substitute. + aliases: + - DME + meaning: CHEBI:28887 + is_a: BioenergySchemaEnum + annotations: + source_domain: energy + source_schema: bioenergy + BiofuelGeneration: + title: Biofuel Generation + description: Classification of biofuels by feedstock source and technology generation. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FIRST_GENERATION: + title: First Generation Biofuel + description: Biofuels produced from food crops (sugar, starch, vegetable oils) using conventional conversion technologies. + aliases: + - 1G Biofuel + - Conventional Biofuel + annotations: + feedstock: food_crops + examples: corn_ethanol,soy_biodiesel + SECOND_GENERATION: + title: Second Generation Biofuel + description: Biofuels produced from lignocellulosic biomass (non-food) using advanced conversion technologies. + aliases: + - 2G Biofuel + - Cellulosic Biofuel + - Advanced Biofuel + annotations: + feedstock: lignocellulosic + examples: cellulosic_ethanol,wood_diesel + THIRD_GENERATION: + title: Third Generation Biofuel + description: Biofuels produced from algae or other photosynthetic microorganisms. + aliases: + - 3G Biofuel + - Algal Biofuel + annotations: + feedstock: algae + FOURTH_GENERATION: + title: Fourth Generation Biofuel + description: Biofuels from genetically engineered organisms designed for carbon capture and enhanced fuel production. + aliases: + - 4G Biofuel + annotations: + feedstock: engineered_organisms + carbon_negative: true + is_a: BioenergySchemaEnum + annotations: + source_domain: energy + source_schema: bioenergy + BioconversionProcess: + title: Bioconversion Process + description: Processes for converting biomass feedstocks into biofuels and bioproducts. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FERMENTATION: + title: Fermentation + description: Biological conversion of sugars to alcohols using yeast or bacteria. + annotations: + category: biochemical + products: ethanol,butanol + ANAEROBIC_DIGESTION: + title: Anaerobic Digestion + description: Biological breakdown of organic matter by microorganisms in the absence of oxygen, producing biogas. + annotations: + category: biochemical + products: biogas + TRANSESTERIFICATION: + title: Transesterification + description: Chemical reaction of triglycerides with alcohol to produce fatty acid esters (biodiesel) and glycerol. annotations: category: chemical - SYNTHETIC_FUEL: - description: Synthetic fuel storage + products: biodiesel + HYDROTREATING: + title: Hydrotreating/Hydroprocessing + description: Catalytic reaction of lipids with hydrogen to produce hydrocarbon fuels. + aliases: + - Hydroprocessing + annotations: + category: thermochemical + products: renewable_diesel,SAF + PYROLYSIS: + title: Pyrolysis + description: Thermal decomposition of biomass in the absence of oxygen to produce bio-oil, syngas, and biochar. + annotations: + category: thermochemical + temperature_c: 400-600 + products: bio_oil,syngas,biochar + GASIFICATION: + title: Gasification + description: High-temperature conversion of carbonaceous materials to syngas using controlled oxygen and/or steam. + meaning: CHMO:0001501 + annotations: + category: thermochemical + temperature_c: 700-1500 + products: syngas + HYDROTHERMAL_LIQUEFACTION: + title: Hydrothermal Liquefaction (HTL) + description: Conversion of wet biomass to bio-crude using high temperature and pressure water. + aliases: + - HTL + annotations: + category: thermochemical + temperature_c: 250-400 + pressure_bar: 100-200 + wet_feedstock: true + ENZYMATIC_HYDROLYSIS: + title: Enzymatic Hydrolysis + description: Breakdown of cellulose and hemicellulose to fermentable sugars using enzymes. + annotations: + category: biochemical + pretreatment_step: true + ACID_HYDROLYSIS: + title: Acid Hydrolysis + description: Chemical breakdown of cellulose to sugars using dilute or concentrated acid. annotations: category: chemical - SUPERCAPACITOR: - description: Supercapacitor + pretreatment_step: true + FISCHER_TROPSCH: + title: Fischer-Tropsch Synthesis + description: Catalytic conversion of syngas to liquid hydrocarbons. + aliases: + - FT Synthesis annotations: - category: electrical - SUPERCONDUCTING: - description: Superconducting magnetic energy storage (SMES) + category: thermochemical + feedstock: syngas + products: FT_diesel,FT_jet + ALCOHOL_TO_JET: + title: Alcohol-to-Jet (ATJ) + description: Conversion of alcohols (ethanol, isobutanol) to jet fuel through dehydration, oligomerization, and hydrogenation. + aliases: + - ATJ annotations: - category: electrical - is_a: EnergySchemaEnum + category: chemical + products: SAF + is_a: BioenergySchemaEnum annotations: source_domain: energy - source_schema: energy - EmissionScope: - description: Greenhouse gas emission scopes (GHG Protocol) + source_schema: bioenergy + GeothermalSchemaEnum: + description: Schema-level enum for geothermal in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/renewable/geothermal.yaml + GeothermalSystemType: + title: Geothermal System Type + description: Types of geothermal energy systems, including conventional hydrothermal and enhanced/engineered geothermal + systems. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.energy.gov/eere/geothermal/enhanced-geothermal-systems + - https://gdr.openei.org/ permissible_values: - SCOPE_1: - description: Direct emissions from owned or controlled sources + HYDROTHERMAL: + title: Conventional Hydrothermal System + description: Naturally occurring geothermal system with heat, fluid, and permeability sufficient for energy extraction + without stimulation. + broad_mappings: + - sweet:phenEnergy/Geothermal + annotations: + conventional: true + ENHANCED_GEOTHERMAL_SYSTEM: + title: Enhanced Geothermal System (EGS) + description: Engineered reservoirs created to extract heat from low permeability geothermal resources through stimulation + methods. + aliases: + - EGS + - Engineered Geothermal System + annotations: + requires_stimulation: true + ADVANCED_GEOTHERMAL_SYSTEM: + title: Advanced Geothermal System (AGS) + description: Closed-loop geothermal systems that circulate working fluid through wellbores to extract heat conductively + without reservoir stimulation. + aliases: + - AGS + - Closed-Loop Geothermal + annotations: + closed_loop: true + HOT_DRY_ROCK: + title: Hot Dry Rock (HDR) + description: Geothermal system targeting hot basement rock lacking natural fluid or permeability, requiring artificial + reservoir creation. + aliases: + - HDR + GEOPRESSURED: + title: Geopressured System + description: Deep sedimentary formations with abnormally high fluid pressure containing hot brine and dissolved methane. + annotations: + methane_recovery: true + SUPERCRITICAL: + title: Supercritical Geothermal System + description: Very high temperature systems (>374C) where water exists above its critical point, offering higher energy + density. + annotations: + temperature_min_c: 374 + GROUND_SOURCE_HEAT_PUMP: + title: Ground Source Heat Pump (GSHP) + description: Shallow geothermal system using stable ground temperatures for heating and cooling buildings. + aliases: + - GSHP + - Geothermal Heat Pump + annotations: + direct_use: true + is_a: GeothermalSchemaEnum + annotations: + source_domain: energy + source_schema: geothermal + GeothermalReservoirType: + title: Geothermal Reservoir Type + description: Classification of geothermal reservoirs by geological setting and characteristics. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + VOLCANIC: + title: Volcanic Reservoir + description: Reservoir associated with volcanic activity, typically in active volcanic regions with magma heat sources. + related_mappings: + - ENVO:00000247 + broad_mappings: + - sweet:realmLandVolcanic/VolcanicField + SEDIMENTARY: + title: Sedimentary Basin Reservoir + description: Reservoir in sedimentary formations with elevated temperatures due to depth or regional heat flow. + broad_mappings: + - sweet:realmGeolBasin/SedimentaryBasin + FRACTURED_BASEMENT: + title: Fractured Basement Reservoir + description: Reservoir in fractured crystalline basement rocks, typically granitic or metamorphic. + aliases: + - Hot Fractured Rock + FAULT_CONTROLLED: + title: Fault-Controlled Reservoir + description: Reservoir where fluid flow is controlled by fault systems providing permeability pathways. + MAGMATIC: + title: Magmatic/Near-Magmatic Reservoir + description: Very high temperature reservoir near or in contact with magma bodies or recent intrusions. + related_mappings: + - sweet:matrRockIgneous/Magma + CONDUCTION_DOMINATED: + title: Conduction-Dominated Reservoir + description: Low permeability reservoir where heat transfer is primarily through conduction rather than convection. + is_a: GeothermalSchemaEnum + annotations: + source_domain: energy + source_schema: geothermal + GeothermalWellType: + title: Geothermal Well Type + description: Types of wells used in geothermal energy development and production. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PRODUCTION_WELL: + title: Production Well + description: Well used to extract geothermal fluids or steam from the reservoir. + INJECTION_WELL: + title: Injection Well + description: Well used to return cooled geothermal fluids to the reservoir to maintain pressure and sustainability. + aliases: + - Reinjection Well + EXPLORATION_WELL: + title: Exploration Well + description: Well drilled to evaluate geothermal resource characteristics. + aliases: + - Wildcat Well + OBSERVATION_WELL: + title: Observation/Monitoring Well + description: Well used to monitor reservoir conditions and pressure. + aliases: + - Monitoring Well + SLIM_HOLE: + title: Slim Hole + description: Smaller diameter well used for initial exploration and temperature gradient measurement. + DIRECTIONAL_WELL: + title: Directional/Deviated Well + description: Well drilled at an angle to access reservoir from offset surface location or increase reservoir contact. + is_a: GeothermalSchemaEnum + annotations: + source_domain: energy + source_schema: geothermal + GeothermalApplication: + title: Geothermal Application + description: Applications and uses of geothermal energy. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ELECTRICITY_GENERATION: + title: Electricity Generation + description: Use of geothermal resources for power generation through steam turbines or binary cycle plants. + close_mappings: + - ENVO:2000034 + - sweet:humanTechEnergy/ElectricalGeneration + DIRECT_USE_HEATING: + title: Direct Use Heating + description: Direct use of geothermal heat for space heating, district heating, or industrial processes. + GREENHOUSE_HEATING: + title: Greenhouse Heating + description: Use of geothermal heat for agricultural greenhouses. + AQUACULTURE: + title: Aquaculture Heating + description: Use of geothermal heat for fish farming and aquaculture. + INDUSTRIAL_PROCESS_HEAT: + title: Industrial Process Heat + description: Use of geothermal heat for industrial manufacturing processes. + FOOD_PROCESSING: + title: Food Processing + description: Use of geothermal heat for food drying, pasteurization, and processing. + BATHING_RECREATION: + title: Bathing and Recreation + description: Use of geothermal waters for spas, pools, and recreation. + LITHIUM_EXTRACTION: + title: Lithium Extraction + description: Extraction of lithium and other minerals from geothermal brines as a co-product of energy production. + annotations: + co_production: true + is_a: GeothermalSchemaEnum + annotations: + source_domain: energy + source_schema: geothermal + GeothermalResourceTemperature: + title: Geothermal Resource Temperature Classification + description: Classification of geothermal resources by temperature range. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LOW_TEMPERATURE: + title: Low Temperature Resource + description: Geothermal resource below 90C, suitable for direct use applications. + annotations: + temperature_max_c: 90 + MODERATE_TEMPERATURE: + title: Moderate Temperature Resource + description: Geothermal resource 90-150C, suitable for binary power generation. + annotations: + temperature_min_c: 90 + temperature_max_c: 150 + HIGH_TEMPERATURE: + title: High Temperature Resource + description: Geothermal resource above 150C, suitable for flash steam power generation. + annotations: + temperature_min_c: 150 + SUPERCRITICAL: + title: Supercritical Resource + description: Very high temperature resource above 374C where water exists in supercritical state. + annotations: + temperature_min_c: 374 + is_a: GeothermalSchemaEnum + annotations: + source_domain: energy + source_schema: geothermal + HydrogenSchemaEnum: + description: Schema-level enum for hydrogen in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/renewable/hydrogen.yaml + HydrogenType: + title: Hydrogen Type (Color Classification) + description: Color-coded classification of hydrogen based on production method and carbon intensity. This informal industry + taxonomy differentiates hydrogen by its carbon footprint and energy source. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.energy.gov/eere/fuelcells/hydrogen-production + - https://www.nationalgrid.com/stories/energy-explained/hydrogen-colour-spectrum + permissible_values: + GREEN_HYDROGEN: + title: Green Hydrogen + description: Hydrogen produced via electrolysis powered by renewable energy sources (solar, wind, hydro). Zero carbon + emissions during production. + aliases: + - Renewable Hydrogen + broad_mappings: + - sweet:matrElement/Hydrogen + annotations: + production_method: electrolysis + energy_source: renewable + carbon_intensity: zero + BLUE_HYDROGEN: + title: Blue Hydrogen + description: Hydrogen produced from natural gas via steam methane reforming (SMR) with carbon capture and storage + (CCS). Low carbon intensity. + annotations: + production_method: steam_methane_reforming + energy_source: natural_gas + carbon_intensity: low + requires_ccs: true + GREY_HYDROGEN: + title: Grey Hydrogen + description: Hydrogen produced from natural gas via steam methane reforming without carbon capture. Most common production + method currently. + aliases: + - Gray Hydrogen + annotations: + production_method: steam_methane_reforming + energy_source: natural_gas + carbon_intensity: high + co2_per_kg_h2: 9-12 + BROWN_HYDROGEN: + title: Brown Hydrogen + description: Hydrogen produced from brown coal (lignite) gasification without carbon capture. High carbon intensity. + annotations: + production_method: coal_gasification + energy_source: lignite + carbon_intensity: very_high + BLACK_HYDROGEN: + title: Black Hydrogen + description: Hydrogen produced from black coal (bituminous) gasification without carbon capture. High carbon intensity. + annotations: + production_method: coal_gasification + energy_source: bituminous_coal + carbon_intensity: very_high + PINK_HYDROGEN: + title: Pink Hydrogen + description: Hydrogen produced via electrolysis powered by nuclear energy. Zero carbon emissions during production. + aliases: + - Purple Hydrogen + - Red Hydrogen + annotations: + production_method: electrolysis + energy_source: nuclear + carbon_intensity: zero + TURQUOISE_HYDROGEN: + title: Turquoise Hydrogen + description: Hydrogen produced via methane pyrolysis, producing solid carbon instead of CO2. Lower carbon intensity + than grey hydrogen. + annotations: + production_method: methane_pyrolysis + energy_source: natural_gas + carbon_intensity: low + byproduct: solid_carbon + WHITE_HYDROGEN: + title: White Hydrogen + description: Naturally occurring geological hydrogen found in underground deposits. Zero production emissions. + aliases: + - Natural Hydrogen + - Geological Hydrogen + - Gold Hydrogen + annotations: + production_method: geological_extraction + energy_source: natural + carbon_intensity: zero + YELLOW_HYDROGEN: + title: Yellow Hydrogen + description: Hydrogen produced via electrolysis powered by solar energy specifically. A subset of green hydrogen. + annotations: + production_method: electrolysis + energy_source: solar + carbon_intensity: zero + ORANGE_HYDROGEN: + title: Orange Hydrogen + description: Hydrogen produced from plastic waste gasification or pyrolysis. Emerging technology addressing both energy + and waste challenges. + annotations: + production_method: waste_gasification + energy_source: plastic_waste + carbon_intensity: varies + is_a: HydrogenSchemaEnum + annotations: + source_domain: energy + source_schema: hydrogen + HydrogenProductionMethod: + title: Hydrogen Production Method + description: Methods and processes for producing hydrogen. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.energy.gov/eere/fuelcells/hydrogen-production + permissible_values: + STEAM_METHANE_REFORMING: + title: Steam Methane Reforming (SMR) + description: High temperature steam reacts with methane to produce hydrogen, carbon monoxide, and carbon dioxide. + aliases: + - SMR + annotations: + feedstock: natural_gas + temperature_c: 700-1000 + dominant_method: true + AUTOTHERMAL_REFORMING: + title: Autothermal Reforming (ATR) + description: Combines steam reforming and partial oxidation using oxygen and steam to produce hydrogen from hydrocarbons. + aliases: + - ATR + PARTIAL_OXIDATION: + title: Partial Oxidation (POX) + description: Exothermic process reacting hydrocarbons with limited oxygen to produce hydrogen and carbon monoxide. + aliases: + - POX + COAL_GASIFICATION: + title: gasification + description: Conversion of coal to syngas (hydrogen and carbon monoxide) using high temperature and steam. + meaning: CHMO:0001501 + WATER_ELECTROLYSIS: + title: Water Electrolysis + description: Splitting water into hydrogen and oxygen using electrical current. Can be powered by various energy sources. + aliases: + - Electrolysis + close_mappings: + - sweet:procChemical/Electrolysis + ALKALINE_ELECTROLYSIS: + title: Alkaline Electrolysis (AEL) + description: Electrolysis using alkaline solution (typically KOH) as electrolyte. Mature commercial technology. + aliases: + - AEL + annotations: + electrolyte: alkaline + maturity: commercial + PEM_ELECTROLYSIS: + title: PEM Electrolysis + description: Proton Exchange Membrane electrolysis using solid polymer electrolyte. Higher efficiency, faster response. + aliases: + - PEMEC + - Polymer Electrolyte Membrane Electrolysis + annotations: + electrolyte: polymer_membrane + maturity: commercial + SOLID_OXIDE_ELECTROLYSIS: + title: Solid Oxide Electrolysis (SOEC) + description: High temperature electrolysis using solid ceramic electrolyte. Higher efficiency when waste heat is available. + aliases: + - SOEC + annotations: + electrolyte: solid_oxide + temperature_c: 700-850 + maturity: emerging + METHANE_PYROLYSIS: + title: Methane Pyrolysis + description: Thermal decomposition of methane into hydrogen and solid carbon without oxygen. Produces no direct CO2. + aliases: + - Thermal Cracking + annotations: + feedstock: natural_gas + byproduct: solid_carbon + BIOMASS_GASIFICATION: + title: Biomass Gasification + description: Thermochemical conversion of biomass to hydrogen-rich syngas at high temperatures. + narrow_mappings: + - sweet:procPhysical/Gasification annotations: - ghg_protocol: Scope 1 - SCOPE_2: - description: Indirect emissions from purchased energy + feedstock: biomass + renewable: true + BIOLOGICAL_PRODUCTION: + title: Biological Hydrogen Production + description: Production of hydrogen by microorganisms through photosynthesis, fermentation, or other biological processes. + aliases: + - Biohydrogen annotations: - ghg_protocol: Scope 2 - SCOPE_3: - description: All other indirect emissions in value chain + renewable: true + maturity: research + THERMOCHEMICAL_WATER_SPLITTING: + title: Thermochemical Water Splitting + description: Using high temperatures from concentrated solar or nuclear to drive chemical cycles that split water. annotations: - ghg_protocol: Scope 3 - SCOPE_3_UPSTREAM: - description: Upstream Scope 3 emissions + temperature_c: 500-2000 + maturity: research + PHOTOELECTROCHEMICAL: + title: Photoelectrochemical Water Splitting + description: Direct conversion of sunlight to hydrogen using specialized semiconductor materials in contact with water. + aliases: + - PEC annotations: - ghg_protocol: Scope 3 - SCOPE_3_DOWNSTREAM: - description: Downstream Scope 3 emissions + maturity: research + is_a: HydrogenSchemaEnum + annotations: + source_domain: energy + source_schema: hydrogen + HydrogenStorageMethod: + title: Hydrogen Storage Method + description: Methods for storing hydrogen for later use or transport. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + COMPRESSED_GAS: + title: Compressed Gas Storage + description: Storage of hydrogen as compressed gas at high pressure (350-700 bar) in pressure vessels. + aliases: + - CGH2 + annotations: + pressure_bar: 350-700 + maturity: commercial + LIQUID_HYDROGEN: + title: Liquid Hydrogen Storage + description: Storage of hydrogen in liquid form at cryogenic temperatures (-253C). Higher energy density but requires + insulation. + aliases: + - LH2 + annotations: + temperature_c: -253 + maturity: commercial + METAL_HYDRIDE: + title: Metal Hydride Storage + description: Storage of hydrogen absorbed into metal alloys forming metal hydrides. Safer but heavier than compressed + gas. + annotations: + maturity: commercial + CHEMICAL_HYDRIDE: + title: Chemical Hydride Storage + description: Storage as chemical compounds (ammonia, methanol, LOHC) that release hydrogen when processed. + aliases: + - LOHC + - Liquid Organic Hydrogen Carrier + UNDERGROUND_STORAGE: + title: Underground Storage + description: Large-scale storage in salt caverns, depleted gas fields, or aquifers for grid-scale applications. + aliases: + - Geological Storage + annotations: + scale: utility + CRYO_COMPRESSED: + title: Cryo-Compressed Storage + description: Hybrid approach combining cryogenic cooling with high pressure for improved density. + aliases: + - CcH2 + annotations: + maturity: emerging + is_a: HydrogenSchemaEnum + annotations: + source_domain: energy + source_schema: hydrogen + HydrogenApplication: + title: Hydrogen Application + description: End-use applications for hydrogen. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FUEL_CELL_VEHICLE: + title: Fuel Cell Electric Vehicle + description: Use of hydrogen in fuel cells for transportation (cars, trucks, buses). + aliases: + - FCEV + FUEL_CELL_STATIONARY: + title: Stationary Fuel Cell + description: Use of hydrogen in stationary fuel cells for power generation. + INDUSTRIAL_FEEDSTOCK: + title: Industrial Feedstock + description: Use of hydrogen as chemical feedstock for ammonia production, petroleum refining, and chemical synthesis. + STEEL_PRODUCTION: + title: Steel Production (Direct Reduction) + description: Use of hydrogen to reduce iron ore in steelmaking, replacing coal. + aliases: + - Green Steel + AMMONIA_SYNTHESIS: + title: Ammonia Synthesis + description: Use of hydrogen with nitrogen to produce ammonia for fertilizers. + related_mappings: + - sweet:matrCompound/Ammonia + METHANOL_SYNTHESIS: + title: Methanol Synthesis + description: Use of hydrogen with CO2 to produce methanol. + related_mappings: + - sweet:matrOrganicCompound/Methanol + POWER_TO_GAS: + title: Power-to-Gas + description: Conversion of excess renewable electricity to hydrogen for grid balancing and energy storage. + aliases: + - P2G + BLENDING_NATURAL_GAS: + title: Natural Gas Blending + description: Blending hydrogen into natural gas pipelines for decarbonization of heating. + SYNTHETIC_FUELS: + title: Synthetic Fuel Production + description: Use of hydrogen with captured CO2 to produce synthetic hydrocarbons (e-fuels, SAF). + aliases: + - E-Fuels + - Power-to-Liquid + is_a: HydrogenSchemaEnum + annotations: + source_domain: energy + source_schema: hydrogen + SubsurfaceEnergySchemaEnum: + description: Schema-level enum for subsurface_energy in energy + is_a: EnergyDomainEnum + abstract: true + annotations: + source_file: energy/subsurface_energy.yaml + SubsurfaceEnergyResourceType: + title: Subsurface Energy Resource Type + description: Types of subsurface energy resources including geothermal, hydrocarbon, and other geological energy assets + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GEOTHERMAL_RESERVOIR: + description: Natural subsurface reservoir containing hot water or steam suitable for geothermal energy extraction + broad_mappings: + - ENVO:2000034 + annotations: + temperature_range: 90-350 C + resource_type: renewable + ENHANCED_GEOTHERMAL_SYSTEM: + description: Engineered subsurface reservoir created by hydraulic stimulation of hot dry rock for geothermal energy + annotations: + abbreviation: EGS + resource_type: renewable + OIL_RESERVOIR: + title: oil reservoir + description: Subsurface formation containing fluid hydrocarbons in porous or fractured rock + meaning: ENVO:00002185 + NATURAL_GAS_RESERVOIR: + description: Subsurface formation containing natural gas trapped in porous or fractured rock + annotations: + resource_type: fossil fuel + COALBED_METHANE: + description: Methane gas adsorbed in coal seams that can be extracted as an energy resource + annotations: + abbreviation: CBM + resource_type: fossil fuel + GAS_HYDRATE: + title: methane clathrate + description: Crystalline ice-like structures containing methane trapped in water molecule cages, found in ocean sediments + and permafrost regions + meaning: ENVO:01000851 + HOT_DRY_ROCK: + description: Deep crystalline basement rock with high temperature but low natural permeability, targeted for enhanced + geothermal systems + annotations: + typical_depth: '>3 km' + temperature: '>150 C' + SEDIMENTARY_BASIN: + description: Large-scale geological depression filled with sedimentary rocks that may contain energy resources + close_mappings: + - ENVO:01000275 annotations: - ghg_protocol: Scope 3 - is_a: EnergySchemaEnum + resource_potential: hydrocarbons, geothermal, CO2 storage + VOLCANIC_SYSTEM: + title: volcanic field + description: Volcanic geological system with high geothermal gradients suitable for energy extraction + meaning: ENVO:00000354 + is_a: SubsurfaceEnergySchemaEnum annotations: source_domain: energy - source_schema: energy - CarbonIntensity: - description: Carbon intensity levels for energy sources - permissible_values: - ZERO_CARBON: - description: Zero carbon emissions + source_schema: subsurface_energy + SubsurfaceStorageType: + title: Subsurface Storage Type + description: Types of subsurface energy and material storage technologies utilizing geological formations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CARBON_CAPTURE_AND_STORAGE: + title: carbon capture and storage + description: Capture of CO2 from industrial sources and injection into deep geological formations for permanent storage + close_mappings: + - OEO:00010141 + related_mappings: + - ENVO:04000017 annotations: - gCO2_per_kWh: 0 - VERY_LOW_CARBON: - description: Very low carbon (< 50 gCO2/kWh) + abbreviation: CCS + target_formations: saline aquifers, depleted reservoirs + HYDROGEN_STORAGE: + title: underground hydrogen storage object + description: Underground storage of hydrogen gas in geological formations such as salt caverns or depleted reservoirs + close_mappings: + - OEO:00000429 annotations: - gCO2_per_kWh: 0-50 - LOW_CARBON: - description: Low carbon (50-200 gCO2/kWh) + formations: salt caverns, depleted gas fields, aquifers + COMPRESSED_AIR_ENERGY_STORAGE: + title: compressed-air energy storage unit + description: Storage of compressed air in underground caverns for later electricity generation + close_mappings: + - OEO:00020249 annotations: - gCO2_per_kWh: 50-200 - MEDIUM_CARBON: - description: Medium carbon (200-500 gCO2/kWh) + abbreviation: CAES + formations: salt caverns, hard rock caverns + NATURAL_GAS_STORAGE: + description: Underground storage of natural gas in geological formations for seasonal demand management annotations: - gCO2_per_kWh: 200-500 - HIGH_CARBON: - description: High carbon (500-1000 gCO2/kWh) + formations: depleted reservoirs, aquifers, salt caverns + THERMAL_ENERGY_STORAGE: + title: thermal energy storage object + description: Storage of thermal energy in subsurface formations for heating and cooling applications + close_mappings: + - OEO:00020365 annotations: - gCO2_per_kWh: 500-1000 - VERY_HIGH_CARBON: - description: Very high carbon (> 1000 gCO2/kWh) + types: aquifer thermal energy storage, borehole thermal energy storage + NUCLEAR_WASTE_REPOSITORY: + description: Deep geological repository for permanent disposal of high-level nuclear waste annotations: - gCO2_per_kWh: 1000+ - is_a: EnergySchemaEnum - annotations: - source_domain: energy - source_schema: energy - ElectricityMarket: - description: Types of electricity markets and pricing - permissible_values: - SPOT_MARKET: - description: Spot market/real-time pricing - DAY_AHEAD: - description: Day-ahead market - INTRADAY: - description: Intraday market - FUTURES: - description: Futures market - CAPACITY_MARKET: - description: Capacity market - ANCILLARY_SERVICES: - description: Ancillary services market - BILATERAL: - description: Bilateral contracts - FEED_IN_TARIFF: - description: Feed-in tariff - NET_METERING: - description: Net metering - POWER_PURCHASE_AGREEMENT: - description: Power purchase agreement (PPA) - is_a: EnergySchemaEnum + formations: crystalline rock, clay, salt + depth: '>300 m' + is_a: SubsurfaceEnergySchemaEnum annotations: source_domain: energy - source_schema: energy - FossilFuelsSchemaEnum: - description: Schema-level enum for fossil_fuels in energy - is_a: EnergyDomainEnum - abstract: true - annotations: - source_file: energy/fossil_fuels.yaml - FossilFuelTypeEnum: - description: Types of fossil fuels used for energy generation - permissible_values: - COAL: - description: Coal - title: Coal - meaning: ENVO:02000091 - NATURAL_GAS: - description: Natural gas - title: Natural Gas - meaning: ENVO:01000552 - PETROLEUM: - description: Petroleum - title: Petroleum - meaning: ENVO:00002984 - is_a: FossilFuelsSchemaEnum + source_schema: subsurface_energy + ReservoirCharacterizationMethodType: + title: Reservoir Characterization Method Type + description: Methods and techniques used to characterize subsurface reservoirs for energy extraction and storage applications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + WELL_TEST_ANALYSIS: + description: Analysis of pressure and flow rate data from well tests to determine reservoir properties + annotations: + parameters: permeability, skin factor, reservoir boundaries + SEISMIC_INTERPRETATION: + description: Interpretation of seismic survey data to map subsurface geological structures and properties + annotations: + types: 2D seismic, 3D seismic, 4D time-lapse + CORE_ANALYSIS: + description: Laboratory analysis of rock core samples to determine petrophysical and geomechanical properties + annotations: + measurements: porosity, permeability, saturation, mechanical strength + WIRELINE_LOGGING: + description: Measurement of formation properties using instruments lowered into a wellbore on a wireline + annotations: + logs: gamma ray, resistivity, neutron, density, sonic + TRACER_TEST: + description: Injection and monitoring of chemical or radioactive tracers to characterize fluid flow paths + annotations: + purpose: flow path identification, residence time distribution + PRESSURE_TRANSIENT_ANALYSIS: + description: Analysis of pressure changes over time during well operations to infer reservoir characteristics + annotations: + tests: drawdown, buildup, interference + PRODUCTION_HISTORY_MATCHING: + description: Calibration of reservoir simulation models by matching historical production data + annotations: + approach: inverse modeling, parameter estimation + GEOSTATISTICAL_MODELING: + description: Statistical methods for spatial interpolation and uncertainty quantification of reservoir properties + annotations: + methods: kriging, sequential Gaussian simulation, multiple-point statistics + is_a: SubsurfaceEnergySchemaEnum annotations: source_domain: energy - source_schema: fossil_fuels + source_schema: subsurface_energy EnvironmentalHealthDomainEnum: description: Domain-level enum for environmental_health value sets is_a: ValueSetEnum abstract: true + CarcinogenicitySchemaEnum: + description: Schema-level enum for carcinogenicity in environmental_health + is_a: EnvironmentalHealthDomainEnum + abstract: true + annotations: + source_file: environmental_health/carcinogenicity.yaml + IARCCarcinogenicityGroup: + title: IARC Carcinogenicity Group + description: International Agency for Research on Cancer (IARC) classification groups for carcinogenic hazard to humans. + IARC evaluates the strength of evidence that an agent can cause cancer in humans. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.iarc.who.int + publishers: https://www.iarc.who.int + source: https://monographs.iarc.who.int/agents-classified-by-the-iarc/ + source_domain: environmental_health + source_schema: carcinogenicity + permissible_values: + GROUP_1: + title: Carcinogenic to humans + description: Sufficient evidence of carcinogenicity in humans. The agent is carcinogenic to humans. + annotations: + evidence_level: sufficient in humans + examples: asbestos, benzene, tobacco smoking, ionizing radiation + GROUP_2A: + title: Probably carcinogenic to humans + description: Limited evidence of carcinogenicity in humans and sufficient evidence in experimental animals. The agent + is probably carcinogenic to humans. + annotations: + evidence_level: limited in humans, sufficient in animals + examples: red meat, night shift work, glyphosate + GROUP_2B: + title: Possibly carcinogenic to humans + description: Limited evidence of carcinogenicity in humans and less than sufficient evidence in experimental animals. + The agent is possibly carcinogenic to humans. + annotations: + evidence_level: limited in humans or animals + examples: coffee, pickled vegetables, gasoline engine exhaust + GROUP_3: + title: Not classifiable as to carcinogenicity + description: Inadequate evidence of carcinogenicity in humans and inadequate or limited evidence in experimental animals. + The agent is not classifiable as to its carcinogenicity to humans. + annotations: + evidence_level: inadequate + examples: caffeine, cholesterol, saccharin + is_a: CarcinogenicitySchemaEnum + EPAIRISCarcinogenicityGroup: + title: EPA IRIS Carcinogenicity Group + description: U.S. Environmental Protection Agency Integrated Risk Information System (IRIS) weight-of-evidence descriptors + for carcinogenicity. These classifications characterize the extent to which available data support the hypothesis that + an agent causes cancer in humans. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.epa.gov + publishers: https://www.epa.gov/iris + source: https://www.epa.gov/iris + source_domain: environmental_health + source_schema: carcinogenicity + permissible_values: + CARCINOGENIC_TO_HUMANS: + title: Carcinogenic to Humans + description: Strong evidence of human carcinogenicity. This descriptor is appropriate when there is convincing epidemiologic + evidence of a causal association between human exposure and cancer. + annotations: + legacy_group: A + evidence: convincing epidemiologic evidence + LIKELY_CARCINOGENIC: + title: Likely to Be Carcinogenic to Humans + description: Evidence is adequate to demonstrate carcinogenic potential to humans but does not reach the weight of + evidence for Carcinogenic to Humans. + annotations: + legacy_group: B1/B2 + evidence: adequate evidence + SUGGESTIVE_EVIDENCE: + title: Suggestive Evidence of Carcinogenic Potential + description: Evidence is suggestive of carcinogenicity but not sufficient to assess human carcinogenic potential. + annotations: + legacy_group: C + evidence: suggestive but not sufficient + INADEQUATE_INFORMATION: + title: Inadequate Information to Assess Carcinogenic Potential + description: Available data are inadequate for an assessment of human carcinogenic potential. + annotations: + legacy_group: D + evidence: inadequate data + NOT_LIKELY_CARCINOGENIC: + title: Not Likely to Be Carcinogenic to Humans + description: Available data are considered robust for deciding that there is no basis for human hazard concern. + annotations: + legacy_group: E + evidence: robust evidence of no hazard + GROUP_A: + title: Group A - Human Carcinogen (Legacy) + description: Legacy EPA classification. Sufficient evidence from epidemiologic studies to support a causal association + between exposure and cancer. + annotations: + status: legacy + superseded_by: CARCINOGENIC_TO_HUMANS + GROUP_B1: + title: Group B1 - Probable Human Carcinogen (Legacy) + description: Legacy EPA classification. Limited evidence of carcinogenicity from epidemiologic studies. + annotations: + status: legacy + superseded_by: LIKELY_CARCINOGENIC + GROUP_B2: + title: Group B2 - Probable Human Carcinogen (Legacy) + description: Legacy EPA classification. Sufficient evidence from animal studies and inadequate evidence from epidemiologic + studies. + annotations: + status: legacy + superseded_by: LIKELY_CARCINOGENIC + GROUP_C: + title: Group C - Possible Human Carcinogen (Legacy) + description: Legacy EPA classification. Limited evidence of carcinogenicity in animals in the absence of human data. + annotations: + status: legacy + superseded_by: SUGGESTIVE_EVIDENCE + GROUP_D: + title: Group D - Not Classifiable (Legacy) + description: Legacy EPA classification. Inadequate human and animal evidence of carcinogenicity or no data available. + annotations: + status: legacy + superseded_by: INADEQUATE_INFORMATION + GROUP_E: + title: Group E - Evidence of Non-Carcinogenicity (Legacy) + description: Legacy EPA classification. No evidence of carcinogenicity in at least two adequate animal tests or in + adequate epidemiologic and animal studies. + annotations: + status: legacy + superseded_by: NOT_LIKELY_CARCINOGENIC + is_a: CarcinogenicitySchemaEnum + NTPCarcinogenicityGroup: + title: NTP Carcinogenicity Group + description: U.S. National Toxicology Program (NTP) Report on Carcinogens classifications. The NTP identifies and discusses + agents, substances, mixtures, or exposure circumstances that may pose a carcinogenic hazard to human health. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://ntp.niehs.nih.gov + publishers: https://ntp.niehs.nih.gov + source: https://ntp.niehs.nih.gov/go/roc + source_domain: environmental_health + source_schema: carcinogenicity + permissible_values: + KNOWN_CARCINOGEN: + title: Known To Be Human Carcinogen + description: There is sufficient evidence of carcinogenicity from studies in humans, which indicates a causal relationship + between exposure to the agent and human cancer. + annotations: + abbreviation: K + evidence: sufficient human evidence + examples: arsenic, asbestos, benzene, vinyl chloride + RAHC: + title: Reasonably Anticipated To Be Human Carcinogen + description: There is limited evidence of carcinogenicity from studies in humans, which indicates that causal interpretation + is credible but alternative explanations cannot be ruled out, OR there is sufficient evidence of carcinogenicity + from studies in experimental animals. + annotations: + abbreviation: RAHC + evidence: limited human or sufficient animal evidence + examples: lead compounds, styrene, trichloroethylene + is_a: CarcinogenicitySchemaEnum ExposuresSchemaEnum: description: Schema-level enum for exposures in environmental_health is_a: EnvironmentalHealthDomainEnum @@ -18189,7 +34491,14 @@ enums: annotations: source_file: environmental_health/exposures.yaml AirPollutantEnum: + title: Air Pollutant description: Common air pollutants and air quality indicators + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PM2_5: description: Fine particulate matter with diameter less than 2.5 micrometers @@ -18238,7 +34547,14 @@ enums: source_domain: environmental_health source_schema: exposures PesticideTypeEnum: + title: Pesticide Type description: Categories of pesticides by target organism or chemical class + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HERBICIDE: description: Chemical used to kill unwanted plants @@ -18280,7 +34596,14 @@ enums: source_domain: environmental_health source_schema: exposures HeavyMetalEnum: + title: Heavy Metal description: Heavy metals of environmental health concern + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEAD: description: Lead (Pb) @@ -18323,16 +34646,27 @@ enums: source_domain: environmental_health source_schema: exposures ExposureRouteEnum: + title: Exposure Route description: Routes by which exposure to environmental agents occurs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INHALATION: description: Exposure through breathing meaning: NCIT:C38284 title: Nasal Route of Administration + related_mappings: + - ExO:0000057 INGESTION: description: Exposure through eating or drinking meaning: NCIT:C38288 title: Oral Route of Administration + related_mappings: + - ExO:0000056 DERMAL: description: Exposure through skin contact meaning: NCIT:C38675 @@ -18341,14 +34675,61 @@ enums: description: Exposure through injection meaning: NCIT:C38276 title: Intravenous Route of Administration + related_mappings: + - ExO:0000060 TRANSPLACENTAL: description: Exposure through placental transfer meaning: NCIT:C38307 title: Transplacental Route of Administration + related_mappings: + - ExO:0000159 OCULAR: description: Exposure through the eyes meaning: NCIT:C38287 title: Ophthalmic Route of Administration + ABSORPTION: + description: Exposure through absorption (dermal or other surface) + meaning: ExO:0000058 + GASTROINTESTINAL_TRACT: + description: Exposure through the gastrointestinal tract + meaning: ExO:0000165 + title: gastrointestinal tract route + GAVAGE: + description: Direct administration into the stomach + meaning: ExO:0000166 + title: gavage route + AMBIENT_ENVIRONMENT: + description: Exposure through contact with stressors in the ambient surroundings + meaning: ExO:0000160 + title: ambient environment route + AMBIENT_AQUATIC: + description: Exposure through ambient aquatic environment + meaning: ExO:0000161 + title: ambient acquatic environment route + AMBIENT_TERRESTRIAL: + description: Exposure through ambient terrestrial environment + meaning: ExO:0000162 + title: ambient terrestrial environment route + PASSIVE_INHALATION: + description: Passive inhalation of ambient environment stressors + meaning: ExO:0000163 + title: passive inhalation of the ambient environment route + ACTIVE_INHALATION: + description: Purposeful breathing or inhaling of stressor + meaning: ExO:0000164 + title: active inhalation route + SUBCUTANEOUS: + description: Exposure through subcutaneous tissue + related_mappings: + - ExO:0000061 + INTRAMUSCULAR: + description: Exposure through muscle tissue + related_mappings: + - ExO:0000062 + INTRAVASCULAR: + description: Exposure through blood vessels + related_mappings: + - ExO:0000063 MULTIPLE_ROUTES: description: Exposure through multiple pathways is_a: ExposuresSchemaEnum @@ -18356,16 +34737,25 @@ enums: source_domain: environmental_health source_schema: exposures ExposureSourceEnum: + title: Exposure Source description: Common sources of environmental exposures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AMBIENT_AIR: description: Outdoor air pollution related_mappings: - ENVO:01000676 + - ExO:0000020 INDOOR_AIR: description: Indoor air pollution related_mappings: - ENVO:01000676 + - ExO:0000019 DRINKING_WATER: description: Contaminated drinking water related_mappings: @@ -18383,6 +34773,8 @@ enums: description: Workplace exposure meaning: ENVO:03501332 title: occupational environment + related_mappings: + - ExO:0000093 CONSUMER_PRODUCTS: description: Household and consumer products related_mappings: @@ -18420,7 +34812,14 @@ enums: source_domain: environmental_health source_schema: exposures WaterContaminantEnum: + title: Water Contaminant description: Common water contaminants + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEAD: description: Lead contamination @@ -18471,7 +34870,14 @@ enums: source_domain: environmental_health source_schema: exposures EndocrineDisruptorEnum: + title: Endocrine Disruptor description: Common endocrine disrupting chemicals + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BPA: description: Bisphenol A @@ -18512,7 +34918,14 @@ enums: source_domain: environmental_health source_schema: exposures ExposureDurationEnum: + title: Exposure Duration description: Duration categories for environmental exposures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACUTE: description: Single or short-term exposure (hours to days) @@ -18534,6 +34947,989 @@ enums: annotations: source_domain: environmental_health source_schema: exposures + SmokingStatusEnum: + title: Smoking Status + description: Tobacco and nicotine consumption status + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CURRENT_SMOKER: + description: Person who is currently smoking tobacco + meaning: ExO:0000115 + FORMER_SMOKER: + description: Person who has smoked at least 100 cigarettes in their life but is not currently smoking + meaning: ExO:0000116 + NEVER_SMOKER: + description: Person who has smoked less than 100 cigarettes in their life + meaning: ExO:0000117 + NON_SMOKER: + description: Person who is not currently smoking + meaning: ExO:0000118 + is_a: ExposuresSchemaEnum + annotations: + source_domain: environmental_health + source_schema: exposures + ExposureStressorTypeEnum: + title: Exposure Stressor Type + description: Types of exposure stressors by their origin or nature + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BIOLOGICAL_AGENT: + description: Agent of biological origin (e.g., bacteria, viruses, allergens) + meaning: ExO:0000005 + CHEMICAL_AGENT: + description: Agent of chemical origin (e.g., toxins, pollutants) + meaning: ExO:0000006 + PHYSICAL_AGENT: + description: Physical source of energy that may cause injury (e.g., radiation, noise, temperature extremes) + meaning: ExO:0000008 + PSYCHOSOCIAL_AGENT: + description: Agent that interferes with psychological development or social interaction + meaning: ExO:0000009 + BIOMECHANICAL_AGENT: + description: Mechanical agent applied to biological systems (e.g., repetitive motion, physical strain) + meaning: ExO:0000011 + ECOLOGICAL_PERTURBATION: + description: Disruption to ecological systems (e.g., habitat degradation, climate change) + meaning: ExO:0000007 + is_a: ExposuresSchemaEnum + annotations: + source_domain: environmental_health + source_schema: exposures + ExposureTransportPathEnum: + title: Exposure Transport Path + description: Transport medium through which exposure stressor reaches the recipient + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AIR_TRANSPORT_PATH: + description: Transport path allowing stressor to interact with recipient via air + meaning: ExO:0000010 + WATER_TRANSPORT_PATH: + description: Transport path involving interaction with stressor via water + meaning: ExO:0000028 + SOIL_TRANSPORT_PATH: + description: Transport path involving interaction with stressor via soil + meaning: ExO:0000029 + is_a: ExposuresSchemaEnum + annotations: + source_domain: environmental_health + source_schema: exposures + ExposureFrequencyEnum: + title: Exposure Frequency + description: Temporal pattern of exposure occurrence + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + INTERMITTENT: + description: Exposure occurring at irregular intervals or periodically + meaning: ExO:0000052 + CONTINUOUS: + description: Exposure occurring without interruption + meaning: ExO:0000053 + is_a: ExposuresSchemaEnum + annotations: + source_domain: environmental_health + source_schema: exposures + StudyPopulationEnum: + title: Study Population + description: Specific population groups commonly studied in exposure research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CHILDREN: + description: Human children (pediatric population) + meaning: ExO:0000119 + FETUSES: + description: Human fetuses (prenatal population) + meaning: ExO:0000122 + INFANTS_OR_NEWBORNS: + description: Human infants and newborns + meaning: ExO:0000123 + PREGNANT_FEMALES: + description: Human females who are pregnant + meaning: ExO:0000126 + MOTHERS: + description: Human mothers + meaning: ExO:0000125 + MILITARY_PERSONNEL: + description: Active military personnel + meaning: ExO:0000124 + VETERANS: + description: Military veterans + meaning: ExO:0000130 + WORKERS: + description: Occupational workers + meaning: ExO:0000131 + CONTROLS: + description: Control group participants without the disease or phenotype of interest + meaning: ExO:0000121 + title: controls for disease or phenotype + is_a: ExposuresSchemaEnum + annotations: + source_domain: environmental_health + source_schema: exposures + HHEARExposureAssessedEnum: + title: HHEAR Study Environmental Exposures Assessed + description: Categories of environmental exposures assessed in Human Health Exposure Analysis Resource (HHEAR) studies. + Based on the HHEAR value set HHEARVS:00008 (Study Environmental Exposures Assessed). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AIR_POLLUTANT: + title: exposure to air pollution + description: Airborne pollutants including particulate matter and gaseous contaminants + meaning: ECTO:8000036 + ALKYL_PHOSPHATE_PESTICIDE_METABOLITE: + title: exposure to pesticide + description: Metabolites of organophosphate pesticides + meaning: ECTO:0000530 + related_mappings: + - CHEBI:25703 + ALLERGEN: + title: exposure to allergen + description: Substances that can cause allergic reactions + meaning: ECTO:0000726 + exact_mappings: + - NCIT:C62651 + ARSENIC_SPECIES: + title: exposure to arsenic + description: Various forms of arsenic compounds + meaning: ECTO:9000032 + BROMINATED_FLAME_RETARDANT: + title: exposure to brominated flame retardant + description: Organobromine compounds used as flame retardants + meaning: ECTO:9002162 + exact_mappings: + - CHEBI:172368 + BUILT_ENVIRONMENT: + title: Built Environment + description: Human-made surroundings including buildings and infrastructure + meaning: ExO:0000048 + ENVIRONMENTAL_PHENOL: + title: exposure to phenol + description: Phenolic compounds in the environment + meaning: ECTO:9000071 + exact_mappings: + - CHEBI:15882 + FOOD_PACKAGING: + title: Food Packaging + description: Materials used to package food products + meaning: FOODON:03490100 + MERCURY_SPECIES: + title: exposure to mercury + description: Various forms of mercury compounds + meaning: ECTO:0001571 + METAL: + title: exposure to heavy metal + description: Metallic elements and compounds + meaning: ECTO:9002163 + ORGANOCHLORINE_COMPOUND: + title: exposure to organochlorine compound + description: Organic compounds containing chlorine + meaning: ECTO:0001152 + exact_mappings: + - CHEBI:36683 + ORGANOPHOSPHORUS_FLAME_RETARDANT: + title: exposure to organophosphorus compound + description: Organophosphorus compounds used as flame retardants + meaning: ECTO:9000284 + PARABEN: + title: exposure to paraben + description: 4-hydroxybenzoate esters used as preservatives + meaning: ECTO:9000930 + exact_mappings: + - CHEBI:85122 + PERFLUOROALKYL_AND_POLYFLUOROALKYL_SUBSTANCE: + title: exposure to perfluoroalkyl substance + description: PFAS compounds including PFOA and PFOS + meaning: ECTO:9002160 + aliases: + - PFAS + exact_mappings: + - CHEBI:172397 + PESTICIDE: + title: exposure to pesticide + description: Substances used to control pests + meaning: ECTO:0000530 + exact_mappings: + - CHEBI:25944 + PHTHALATE: + title: exposure to phthalate + description: Phthalic acid esters used as plasticizers + meaning: ECTO:9000522 + exact_mappings: + - CHEBI:26092 + POLYBROMINATED_DIPHENYL_ETHER: + title: exposure to polybromodiphenyl ether + description: Brominated aromatic ethers used as flame retardants + meaning: ECTO:9001619 + aliases: + - PBDE + exact_mappings: + - CHEBI:134094 + TOBACCO_METABOLITE: + title: exposure to tobacco + description: Metabolites of tobacco and nicotine + meaning: ECTO:0100013 + TOBACCO_SMOKE_EXPOSURE: + title: exposure to tobacco smoking + description: Exposure to primary or secondhand tobacco smoke + meaning: ECTO:6000029 + VOLATILE_ORGANIC_COMPOUND: + title: exposure to volatile organic compound + description: Organic compounds with high vapor pressure + meaning: ECTO:9001621 + aliases: + - VOC + exact_mappings: + - CHEBI:134179 + WEATHER: + title: exposure to weather + description: Atmospheric conditions and weather-related exposures + meaning: ECTO:1000020 + exact_mappings: + - NCIT:C170964 + is_a: ExposuresSchemaEnum + annotations: + source_domain: environmental_health + source_schema: exposures + GbEdohSchemaEnum: + description: Schema-level enum for gb_edoh in environmental_health + is_a: EnvironmentalHealthDomainEnum + abstract: true + annotations: + source_file: environmental_health/gb_edoh.yaml + ExtremeWeatherEventEnum: + title: Extreme Weather Event + description: Types of extreme weather events relevant to health outcomes and environmental epidemiology. Used for characterizing + weather-related health impacts in the NIH Health and Extreme Weather (HEW) program. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH classification + source_domain: environmental_health + source_schema: gb_edoh + permissible_values: + HEAT_WAVE: + title: Heat wave + description: Prolonged period of excessively hot weather relative to the expected conditions for a given area. Associated + with increased mortality, heat stroke, and cardiovascular events. + annotations: + health_impacts: heat stroke, cardiovascular events, mortality + nws_threshold: 2+ days of heat index >= 105F + COLD_WAVE: + title: Cold wave + description: Prolonged period of excessively cold weather relative to the expected conditions for a given area. Associated + with hypothermia and cardiovascular events. + annotations: + health_impacts: hypothermia, cardiovascular events, frostbite + WILDFIRE: + title: wildfire + description: Uncontrolled fire in vegetated areas producing smoke containing particulate matter and hazardous air + pollutants. Major source of PM2.5 exposure. + meaning: ENVO:01000787 + annotations: + health_impacts: respiratory illness, cardiovascular events, mental health + exposure_agent: PM2.5, CO, VOCs + FOREST_FIRE: + title: forest fire + description: Wildfire occurring primarily in forested areas, producing dense smoke plumes that can travel long distances. + meaning: ENVO:01000791 + is_a: WILDFIRE + TROPICAL_STORM: + title: tropical storm + description: Atmospheric storm originating over tropical waters with organized circulation and sustained winds 39-73 + mph. Precursor to hurricanes. + meaning: ENVO:01001296 + annotations: + health_impacts: injuries, drowning, displacement, mental health + HURRICANE: + title: Hurricane/Typhoon/Cyclone + description: Intense tropical cyclone with sustained winds of 74 mph or greater. Called hurricane (Atlantic/E. Pacific), + typhoon (W. Pacific), or cyclone (Indian Ocean). + annotations: + saffir_simpson: Category 1-5 + health_impacts: traumatic injuries, drowning, displacement, infectious disease + related: ENVO:01001297 + TORNADO: + title: tornado + description: Violently rotating column of air extending from a thunderstorm to the ground. Characterized by extreme + winds and path of destruction. + meaning: ENVO:01001482 + annotations: + ef_scale: EF0-EF5 + health_impacts: traumatic injuries, death, mental health + FLOOD: + title: flood + description: Unusual accumulation of water above ground caused by high tide, heavy rain, melting snow, or dam failure. + meaning: ENVO:01000710 + annotations: + health_impacts: drowning, waterborne disease, injuries, displacement + RIVERINE_FLOOD: + title: riverine flood + description: Flood occurring when river flow exceeds channel capacity, typically developing over hours to days. + meaning: ENVO:01000712 + is_a: FLOOD + COASTAL_FLOOD: + title: coastal flood + description: Flood caused by storm surge, high tides, or sea level rise affecting coastal areas. + meaning: ENVO:01000711 + is_a: FLOOD + FLASH_FLOOD: + title: flash flood + description: Rapid flooding of low-lying areas within 6 hours of heavy rainfall or dam failure. Particularly dangerous + due to sudden onset. + meaning: ENVO:01000713 + is_a: FLOOD + DROUGHT: + title: drought + description: Extended period of deficient precipitation resulting in water shortage. Affects water quality, food security, + and mental health. + meaning: ENVO:1000745 + annotations: + health_impacts: water quality, food insecurity, mental health + indices: PDSI, SPI, USDM + BLIZZARD: + title: blizzard + description: Severe snowstorm with sustained winds >= 35 mph and reduced visibility for 3+ hours. Creates dangerous + travel conditions and cold exposure risk. + meaning: ENVO:01000903 + annotations: + health_impacts: hypothermia, injuries, carbon monoxide poisoning + WINTER_STORM: + title: Winter storm + description: Storm producing significant snow, ice, or sleet. Includes ice storms, nor'easters, and lake-effect snow + events. + annotations: + health_impacts: injuries, hypothermia, carbon monoxide poisoning + SEVERE_THUNDERSTORM: + title: convective storm + description: Thunderstorm producing hail >= 1 inch, wind gusts >= 58 mph, or a tornado. Source of lightning, flash + flooding, and wind damage. + meaning: ENVO:01001294 + annotations: + health_impacts: lightning injuries, wind injuries, flash flooding + DUST_STORM: + title: Dust storm + description: Meteorological event with strong winds lifting large amounts of sand and dust into the atmosphere. Reduces + visibility and air quality. + annotations: + health_impacts: respiratory illness, traffic accidents + related: haboob, sandstorm + EXTREME_PRECIPITATION: + title: Extreme precipitation + description: Precipitation event exceeding historical norms for intensity or duration. Often precedes flooding events. + annotations: + health_impacts: flooding, infrastructure damage + STORM_SURGE: + title: storm surge + description: Abnormal rise in sea level during a storm, caused by wind pushing water toward shore. Major cause of + hurricane-related deaths. + meaning: ENVO:01000714 + annotations: + health_impacts: drowning, injuries + LANDSLIDE: + title: Landslide + description: Mass movement of rock, debris, or earth down a slope. Often triggered by extreme precipitation or earthquakes. + annotations: + health_impacts: traumatic injuries, burial, displacement + AIR_QUALITY_EVENT: + title: Air quality event + description: Period of degraded air quality due to pollution accumulation, typically during temperature inversions + or stagnant air conditions. + annotations: + health_impacts: respiratory illness, cardiovascular events + indices: AQI, PM2.5, ozone + is_a: GbEdohSchemaEnum + ExposureAgentCategoryEnum: + title: Exposure Agent Category + description: Categories of environmental exposure agents for GB-EDoH classification. Used to categorize the type of environmental + factor being measured and modeled in geospatial exposure assessments. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH metadata + source_domain: environmental_health + source_schema: gb_edoh + permissible_values: + CRITERIA_AIR_POLLUTANT: + title: Criteria air pollutant + description: 'EPA-regulated criteria air pollutants under the Clean Air Act: PM2.5, PM10, O3, NO2, SO2, CO, and Pb.' + annotations: + examples: PM2.5, PM10, O3, NO2, SO2, CO, Pb + regulatory: EPA NAAQS + HAZARDOUS_AIR_POLLUTANT: + title: Hazardous air pollutant + description: EPA-designated hazardous air pollutants (HAPs) known to cause cancer or other serious health effects. + annotations: + examples: benzene, formaldehyde, acetaldehyde + regulatory: EPA HAPs list (187 pollutants) + WILDFIRE_SMOKE: + title: Wildfire smoke + description: Smoke from wildfires containing PM2.5, CO, VOCs, and other combustion products. Distinct from anthropogenic + air pollution. + annotations: + components: PM2.5, CO, VOCs, PAHs + WATER_CONTAMINANT: + title: Water contaminant + description: Chemical, biological, or physical contaminants in drinking water or recreational water bodies. + annotations: + examples: lead, arsenic, nitrates, PFAS, pathogens + SOIL_CONTAMINANT: + title: Soil contaminant + description: Chemical contaminants in soil that may affect health through direct contact, ingestion, or vapor intrusion. + annotations: + examples: lead, arsenic, petroleum, pesticides + RADIONUCLIDE: + title: Radionuclide + description: Naturally occurring or anthropogenic radioactive materials in the environment, including radon gas. + annotations: + examples: radon-222, uranium, radium + EXTREME_HEAT: + title: Extreme heat + description: Ambient heat exposure characterized by temperature, heat index, or other thermal comfort metrics. + annotations: + metrics: temperature, heat index, WBGT, apparent temperature + EXTREME_COLD: + title: Extreme cold + description: Ambient cold exposure characterized by temperature or wind chill. + annotations: + metrics: temperature, wind chill + UV_RADIATION: + title: UV radiation + description: Solar ultraviolet radiation exposure, particularly UVB relevant to skin cancer and vitamin D synthesis. + annotations: + metrics: UV index, erythemal UV dose + NOISE: + title: Environmental noise + description: Ambient noise from traffic, airports, industry, and other sources. Associated with cardiovascular and + mental health effects. + annotations: + metrics: Lden, Lnight, LAeq + LIGHT_POLLUTION: + title: Light pollution + description: Artificial light at night from urban and industrial sources. Associated with circadian disruption. + annotations: + metrics: radiance, sky brightness + ALLERGEN: + title: Aeroallergen + description: Airborne allergens including pollen, mold spores, and other biological particles triggering allergic + responses. + annotations: + examples: tree pollen, grass pollen, ragweed, mold spores + VECTOR_HABITAT: + title: Vector habitat suitability + description: Environmental conditions favoring disease vector populations (mosquitoes, ticks) based on climate and + land use. + annotations: + vectors: Aedes mosquitoes, Ixodes ticks + diseases: dengue, Zika, Lyme disease + GREEN_SPACE: + title: Green space + description: Access to and amount of vegetated areas including parks, forests, and urban greenery. Associated with + mental and physical health benefits. + annotations: + metrics: NDVI, park access, tree canopy cover + BLUE_SPACE: + title: Blue space + description: Access to and proximity to water bodies including lakes, rivers, and coastal areas. + annotations: + metrics: distance to water, water body area + BUILT_ENVIRONMENT: + title: Built environment + description: Characteristics of the human-made environment including walkability, food access, and housing quality. + annotations: + metrics: walkability score, food desert index, housing age + SOCIOECONOMIC_DEPRIVATION: + title: Socioeconomic deprivation + description: Area-level measures of socioeconomic disadvantage that modify or mediate environmental health effects. + annotations: + indices: ADI, NDI, SVI + is_a: GbEdohSchemaEnum + TemporalAggregationEnum: + title: Temporal Aggregation Method + description: Methods used to aggregate environmental exposure data over time. Critical metadata for GB-EDoH to ensure + comparability across studies and integration with health outcome data. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH temporal metadata + source_domain: environmental_health + source_schema: gb_edoh + permissible_values: + INSTANTANEOUS: + title: Instantaneous + description: Single point-in-time measurement without temporal aggregation. + annotations: + example: hourly sensor reading + HOURLY_MEAN: + title: Hourly mean + description: Arithmetic mean of measurements within a 1-hour window. + annotations: + window: 1 hour + DAILY_MEAN: + title: Daily mean (24-hour average) + description: Arithmetic mean of measurements over a 24-hour period. Standard for many EPA air quality standards. + annotations: + window: 24 hours + regulatory: EPA PM2.5 24-hour standard + DAILY_MAX: + title: Daily maximum + description: Maximum value recorded during a 24-hour period. + annotations: + window: 24 hours + DAILY_MIN: + title: Daily minimum + description: Minimum value recorded during a 24-hour period. + annotations: + window: 24 hours + DAILY_MAX_8HR: + title: Daily maximum 8-hour average + description: Maximum of rolling 8-hour averages within a day. Standard metric for ozone exposure assessment. + annotations: + window: 8-hour rolling within 24 hours + regulatory: EPA ozone standard + WEEKLY_MEAN: + title: Weekly mean + description: Arithmetic mean of daily values over a 7-day period. + annotations: + window: 7 days + MONTHLY_MEAN: + title: Monthly mean + description: Arithmetic mean of daily values over a calendar month. + annotations: + window: calendar month + QUARTERLY_MEAN: + title: Quarterly mean + description: Arithmetic mean of daily values over a 3-month period. + annotations: + window: 3 months + ANNUAL_MEAN: + title: Annual mean + description: Arithmetic mean of daily values over a calendar year. Standard for EPA PM2.5 annual standard. + annotations: + window: calendar year + regulatory: EPA PM2.5 annual standard + CUMULATIVE: + title: Cumulative + description: Sum of exposure values over a defined period, representing total dose. + annotations: + example: cumulative UV dose, total precipitation + DAYS_ABOVE_THRESHOLD: + title: Days above threshold + description: Count of days exceeding a specified threshold value within a period. + annotations: + example: days with AQI > 100 + PERCENTILE: + title: Percentile + description: Specified percentile of distribution (e.g., 98th percentile of daily values). Captures extreme exposure + events. + annotations: + example: 98th percentile of daily PM2.5 + MOVING_AVERAGE: + title: Moving average + description: Rolling average over a specified window (e.g., 7-day moving average). Smooths short-term variability. + annotations: + example: 7-day rolling average + TRIMESTER_MEAN: + title: Trimester mean + description: Mean exposure during a pregnancy trimester. Used in birth outcomes research. + annotations: + window: ~13 weeks + use_case: perinatal epidemiology + HEATING_SEASON_MEAN: + title: Heating season mean + description: Mean during heating season (typically Oct-Mar in Northern Hemisphere). Relevant for indoor air quality. + annotations: + window: heating season + COOLING_SEASON_MEAN: + title: Cooling season mean + description: Mean during cooling season (typically May-Sep in Northern Hemisphere). Relevant for heat exposure and + ozone. + annotations: + window: cooling season + is_a: GbEdohSchemaEnum + SpatialResolutionEnum: + title: Spatial Resolution + description: Geographic units and spatial resolutions used for GB-EDoH exposure estimates. Critical metadata for understanding + exposure misclassification and supporting OMOP geocoding requirements. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH spatial metadata + source_domain: environmental_health + source_schema: gb_edoh + permissible_values: + POINT_LOCATION: + title: Point location (lat/lon) + description: Exact geographic coordinates. Highest spatial precision but may require privacy protection measures. + annotations: + precision: exact coordinates + privacy: requires protection + ADDRESS_GEOCODED: + title: Geocoded address + description: Address geocoded to rooftop or parcel level. Standard for linking patient data to environmental exposures. + annotations: + precision: parcel level + use_case: patient-level exposure + CENSUS_BLOCK: + title: Census block + description: US Census block, the smallest geographic unit. Typically contains 600-3000 people. + annotations: + typical_population: 600-3000 + country: US + CENSUS_BLOCK_GROUP: + title: Census block group + description: US Census block group, a cluster of blocks. Standard unit for many socioeconomic and environmental datasets. + annotations: + typical_population: 600-3000 + country: US + CENSUS_TRACT: + title: Census tract + description: US Census tract, designed to be relatively homogeneous in population characteristics. Common for health + research. + annotations: + typical_population: 2500-8000 + country: US + ZIP_CODE: + title: ZIP code + description: US Postal Service ZIP code. Common in administrative health data but boundaries change and may cross + jurisdictions. + annotations: + typical_population: varies widely + country: US + limitations: unstable boundaries + ZCTA: + title: ZIP Code Tabulation Area + description: Census Bureau generalization of ZIP codes with stable boundaries. Preferred over ZIP codes for research. + annotations: + country: US + advantage: stable boundaries + COUNTY: + title: County/Parish + description: County or parish level. Used for many public health surveillance systems and vital statistics. + annotations: + country: US + use_case: vital statistics, surveillance + STATE: + title: State/Territory + description: State or territory level. Coarsest common administrative unit. + annotations: + country: US + GRID_1KM: + title: 1 km grid cell + description: 1 kilometer resolution grid. Common for satellite-derived and modeled air quality data. + annotations: + resolution: 1 km + example: EPA downscaler output + GRID_4KM: + title: 4 km grid cell + description: 4 kilometer resolution grid. Common for weather and some air quality models. + annotations: + resolution: 4 km + example: HRRR weather model + GRID_12KM: + title: 12 km grid cell + description: 12 kilometer resolution grid. Standard CMAQ model output resolution. + annotations: + resolution: 12 km + example: EPA CMAQ output + GRID_36KM: + title: 36 km grid cell + description: 36 kilometer resolution grid. Coarse model output. + annotations: + resolution: 36 km + HUC8: + title: HUC-8 watershed + description: 8-digit Hydrologic Unit Code watershed. Medium-sized watershed for water quality assessment. + annotations: + typical_area: 700 sq mi + use_case: water quality + HUC12: + title: HUC-12 subwatershed + description: 12-digit Hydrologic Unit Code subwatershed. Finest watershed unit. + annotations: + typical_area: 40 sq mi + use_case: local water quality + AIRSHED: + title: Airshed + description: Geographic area defined by air pollution transport patterns. May cross administrative boundaries. + annotations: + example: South Coast Air Basin + BUFFER_500M: + title: 500 meter buffer + description: Circular buffer of 500 meters around a point. Common for traffic-related air pollution exposure. + annotations: + radius: 500 m + use_case: TRAP exposure + BUFFER_1KM: + title: 1 kilometer buffer + description: Circular buffer of 1 kilometer around a point. + annotations: + radius: 1 km + BUFFER_5KM: + title: 5 kilometer buffer + description: Circular buffer of 5 kilometers around a point. + annotations: + radius: 5 km + CUSTOM_POLYGON: + title: Custom polygon + description: User-defined geographic area. Requires specification of boundary source. + annotations: + example: school district, hospital service area + is_a: GbEdohSchemaEnum + RadionuclidesSchemaEnum: + description: Schema-level enum for radionuclides in environmental_health + is_a: EnvironmentalHealthDomainEnum + abstract: true + annotations: + source_file: environmental_health/radionuclides.yaml + RadionuclideEnum: + title: Radionuclide + description: Radioactive elements and isotopes commonly measured in environmental health studies, including naturally + occurring radioactive materials (NORM) and anthropogenic radionuclides. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + RADON_222: + title: radon-222 atom + description: Radioactive noble gas produced by decay of radium-226. Major contributor to natural background radiation + and indoor air quality concern. + meaning: CHEBI:33492 + annotations: + symbol: Rn-222 + half_life: 3.82 days + decay_mode: alpha + parent: Ra-226 + health_concern: lung cancer risk from inhalation + URANIUM_238: + title: Uranium-238 + description: Most abundant uranium isotope, primordial radionuclide. Parent of the uranium decay series. + annotations: + symbol: U-238 + half_life: 4.47 billion years + decay_mode: alpha + abundance: 99.3% + URANIUM_235: + title: Uranium-235 + description: Fissile uranium isotope used in nuclear reactors and weapons. + annotations: + symbol: U-235 + half_life: 704 million years + decay_mode: alpha + abundance: 0.7% + THORIUM_232: + title: Thorium-232 + description: Primordial radionuclide, parent of the thorium decay series. Found in soil, rocks, and building materials. + annotations: + symbol: Th-232 + half_life: 14 billion years + decay_mode: alpha + RADIUM_226: + title: Radium-226 + description: Radioactive alkaline earth metal in the uranium decay series. Historically significant in medicine and + industry. + meaning: CHEBI:80504 + annotations: + symbol: Ra-226 + half_life: 1600 years + decay_mode: alpha + daughter: Rn-222 + RADIUM_228: + title: Radium-228 + description: Radioactive isotope in the thorium decay series. + meaning: CHEBI:80505 + annotations: + symbol: Ra-228 + half_life: 5.75 years + decay_mode: beta + POTASSIUM_40: + title: Potassium-40 + description: Primordial radionuclide, naturally occurring in all potassium. Major contributor to internal dose from + dietary intake. + annotations: + symbol: K-40 + half_life: 1.25 billion years + decay_mode: beta, electron capture + abundance: 0.012% of natural potassium + CESIUM_137: + title: caesium-137 + description: Anthropogenic radionuclide from nuclear fission. Environmental contaminant from nuclear weapons testing + and accidents. + meaning: CHEBI:196959 + annotations: + symbol: Cs-137 + half_life: 30.17 years + decay_mode: beta + source: nuclear fission + STRONTIUM_90: + title: Strontium Sr-90 + description: Anthropogenic radionuclide from nuclear fission. Bone-seeking due to chemical similarity to calcium. + meaning: NCIT:C29776 + annotations: + symbol: Sr-90 + half_life: 28.8 years + decay_mode: beta + health_concern: bone cancer, leukemia + IODINE_131: + title: Iodine I-131 + description: Radioactive iodine isotope from nuclear fission. Concentrates in thyroid gland. Used medically and released + in nuclear accidents. + meaning: NCIT:C1639 + annotations: + symbol: I-131 + half_life: 8.02 days + decay_mode: beta + health_concern: thyroid cancer + PLUTONIUM_239: + title: Plutonium-239 + description: Transuranic element produced in nuclear reactors. Highly toxic alpha emitter with very long half-life. + meaning: NCIT:C29774 + annotations: + symbol: Pu-239 + half_life: 24100 years + decay_mode: alpha + source: nuclear reactors + AMERICIUM_241: + title: Americium-241 + description: Transuranic element, alpha emitter. Used in smoke detectors. + annotations: + symbol: Am-241 + half_life: 432 years + decay_mode: alpha + use: smoke detectors + TRITIUM: + title: tritium atom + description: Radioactive hydrogen isotope. Produced naturally and in nuclear reactors. Weak beta emitter. + meaning: CHEBI:29238 + annotations: + symbol: H-3 + half_life: 12.3 years + decay_mode: beta (weak) + CARBON_14: + title: carbon-14 atom + description: Cosmogenic radionuclide used in radiocarbon dating. Produced by cosmic ray interactions in atmosphere. + meaning: CHEBI:36927 + annotations: + symbol: C-14 + half_life: 5730 years + decay_mode: beta + use: radiocarbon dating + LEAD_210: + title: Lead-210 + description: Radioactive lead isotope in uranium decay series. Used as environmental tracer for sedimentation dating. + annotations: + symbol: Pb-210 + half_life: 22.3 years + decay_mode: beta + use: sediment dating + POLONIUM_210: + title: polonium-210 atom + description: Highly radioactive alpha emitter in uranium decay series. Found in tobacco smoke. + meaning: CHEBI:37340 + annotations: + symbol: Po-210 + half_life: 138 days + decay_mode: alpha + health_concern: lung cancer from tobacco + is_a: RadionuclidesSchemaEnum + annotations: + source_domain: environmental_health + source_schema: radionuclides + NORMEnum: + title: Naturally Occurring Radioactive Material + description: Naturally occurring radioactive materials (NORM) found in the environment. These are primordial radionuclides + and their decay products. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + acronym: NORM + source_domain: environmental_health + source_schema: radionuclides + permissible_values: + URANIUM_SERIES: + title: Uranium-238 decay series + description: The uranium decay series starting from U-238 and ending with stable Pb-206. Includes Ra-226, Rn-222, + Po-210, and other isotopes. + annotations: + parent: U-238 + end_product: Pb-206 + key_members: Ra-226, Rn-222, Po-210, Pb-210 + THORIUM_SERIES: + title: Thorium-232 decay series + description: The thorium decay series starting from Th-232 and ending with stable Pb-208. Includes Ra-228, Rn-220 + (thoron), and other isotopes. + annotations: + parent: Th-232 + end_product: Pb-208 + key_members: Ra-228, Rn-220, Pb-212 + ACTINIUM_SERIES: + title: Actinium (Uranium-235) decay series + description: The actinium decay series starting from U-235 and ending with stable Pb-207. + annotations: + parent: U-235 + end_product: Pb-207 + POTASSIUM_40_PRIMORDIAL: + title: Potassium-40 + description: Primordial radionuclide present in all potassium-bearing minerals and biological tissues. + annotations: + type: primordial + ubiquity: present in all potassium + is_a: RadionuclidesSchemaEnum GeographyDomainEnum: description: Domain-level enum for geography value sets is_a: ValueSetEnum @@ -18545,7 +35941,14 @@ enums: annotations: source_file: geography/geographic_codes.yaml CountryCodeISO2Enum: + title: Country Code ISO2 description: ISO 3166-1 alpha-2 country codes (2-letter codes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: US: description: United States of America @@ -18802,7 +36205,14 @@ enums: source_domain: geography source_schema: geographic_codes CountryCodeISO3Enum: + title: Country Code ISO3 description: ISO 3166-1 alpha-3 country codes (3-letter codes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: USA: description: United States of America @@ -18959,7 +36369,14 @@ enums: source_domain: geography source_schema: geographic_codes USStateCodeEnum: + title: US State Code description: United States state and territory codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AL: description: Alabama @@ -19078,7 +36495,14 @@ enums: source_domain: geography source_schema: geographic_codes CanadianProvinceCodeEnum: + title: Canadian Province Code description: Canadian province and territory codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AB: description: Alberta @@ -19111,7 +36535,14 @@ enums: source_domain: geography source_schema: geographic_codes CompassDirection: + title: Compass Direction description: Cardinal and intercardinal compass directions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NORTH: description: North (0°/360°) @@ -19198,7 +36629,14 @@ enums: source_domain: geography source_schema: geographic_codes RelativeDirection: + title: Relative Direction description: Relative directional terms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FORWARD: description: Forward/Ahead @@ -19246,7 +36684,14 @@ enums: source_domain: geography source_schema: geographic_codes WindDirection: + title: Wind Direction description: Wind direction nomenclature (named for where wind comes FROM) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NORTHERLY: description: Wind from the north @@ -19297,7 +36742,14 @@ enums: source_domain: geography source_schema: geographic_codes ContinentEnum: + title: Continent description: Continental regions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AFRICA: description: Africa @@ -19318,7 +36770,14 @@ enums: source_domain: geography source_schema: geographic_codes UNRegionEnum: + title: UN Region description: United Nations regional classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EASTERN_AFRICA: description: Eastern Africa @@ -19369,7 +36828,14 @@ enums: source_domain: geography source_schema: geographic_codes LanguageCodeISO639_1Enum: + title: Language Code ISO639_1 description: ISO 639-1 two-letter language codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EN: description: English @@ -19436,7 +36902,14 @@ enums: source_domain: geography source_schema: geographic_codes TimeZoneEnum: + title: Time Zone description: Common time zones + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: UTC: description: Coordinated Universal Time @@ -19487,7 +36960,14 @@ enums: source_domain: geography source_schema: geographic_codes CurrencyCodeISO4217Enum: + title: Currency Code ISO4217 description: ISO 4217 currency codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: USD: description: United States Dollar @@ -19568,7 +37048,14 @@ enums: annotations: source_file: health/vaccination.yaml VaccinationStatusEnum: + title: Vaccination Status description: The vaccination status of an individual + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VACCINATED: description: A status indicating that an individual has received a vaccination @@ -19596,7 +37083,14 @@ enums: source_domain: health source_schema: vaccination VaccinationPeriodicityEnum: + title: Vaccination Periodicity description: The periodicity or frequency of vaccination + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE_DOSE: description: A vaccination regimen requiring only one dose @@ -19621,7 +37115,14 @@ enums: source_domain: health source_schema: vaccination VaccineCategoryEnum: + title: Vaccine Category description: The broad category or type of vaccine + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIVE_ATTENUATED_VACCINE: description: A vaccine made from microbes that have been weakened in the laboratory @@ -19657,6 +37158,83 @@ enums: description: Domain-level enum for industry value sets is_a: ValueSetEnum abstract: true + ConstructionSchemaEnum: + description: Schema-level enum for construction in industry + is_a: IndustryDomainEnum + abstract: true + annotations: + source_file: industry/construction.yaml + BuildingSystemType: + title: Building System Type + description: Types of building systems for mechanical, electrical, and structural infrastructure + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + HVAC: + description: Heating, ventilation, and air conditioning systems for climate control + close_mappings: + - brick:HVAC_System + ELECTRICAL: + description: Electrical power distribution and wiring systems within the building + PLUMBING: + description: Water supply, drainage, and sewage systems + STRUCTURAL: + description: Load-bearing structural framework including foundations, columns, beams, and slabs + BUILDING_ENVELOPE: + description: Exterior enclosure system including walls, roof, windows, and insulation + meaning: ENVO:01000470 + FIRE_PROTECTION: + description: Fire detection, suppression, and alarm systems + close_mappings: + - brick:Fire_Safety_System + LIGHTING: + description: Interior and exterior lighting systems including controls and fixtures + close_mappings: + - brick:Lighting_System + BUILDING_AUTOMATION: + description: Integrated control systems for monitoring and managing building operations + RENEWABLE_ENERGY_INTEGRATION: + description: On-site renewable energy generation systems such as solar panels and wind turbines + is_a: ConstructionSchemaEnum + annotations: + source_domain: industry + source_schema: construction + BuildingEnergyPerformanceLevel: + title: Building Energy Performance Level + description: Energy performance certification levels and standards for buildings + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NET_ZERO_ENERGY: + description: Building that produces as much energy as it consumes on an annual basis + NET_POSITIVE_ENERGY: + description: Building that produces more energy than it consumes on an annual basis + PASSIVE_HOUSE: + description: Building meeting Passive House Institute standards for ultra-low energy consumption + LEED_CERTIFIED: + description: LEED Certified rating (40-49 points) from the U.S. Green Building Council + LEED_SILVER: + description: LEED Silver rating (50-59 points) from the U.S. Green Building Council + LEED_GOLD: + description: LEED Gold rating (60-79 points) from the U.S. Green Building Council + LEED_PLATINUM: + description: LEED Platinum rating (80+ points) from the U.S. Green Building Council + ENERGY_STAR_CERTIFIED: + description: EPA Energy Star certification for buildings performing in top 25% of energy efficiency + CODE_MINIMUM: + description: Building meeting minimum energy code requirements without additional certification + is_a: ConstructionSchemaEnum + annotations: + source_domain: industry + source_schema: construction ExtractiveIndustrySchemaEnum: description: Schema-level enum for extractive_industry in industry is_a: IndustryDomainEnum @@ -19664,7 +37242,14 @@ enums: annotations: source_file: industry/extractive_industry.yaml ExtractiveIndustryFacilityTypeEnum: + title: Extractive Industry Facility Type description: Types of extractive industry facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MINING_FACILITY: description: A facility where mineral resources are extracted @@ -19680,7 +37265,14 @@ enums: source_domain: industry source_schema: extractive_industry ExtractiveIndustryProductTypeEnum: + title: Extractive Industry Product Type description: Types of products extracted from extractive industry facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MINERAL: description: A solid inorganic substance @@ -19711,7 +37303,14 @@ enums: source_domain: industry source_schema: extractive_industry MiningMethodEnum: + title: Mining Method description: Methods used for extracting minerals from the earth + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: UNDERGROUND: description: Extraction occurs beneath the earth's surface @@ -19730,7 +37329,14 @@ enums: source_domain: industry source_schema: extractive_industry WellTypeEnum: + title: Well Type description: Types of wells used for extracting fluid resources + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: OIL: description: A well that primarily extracts crude oil @@ -19748,6 +37354,93 @@ enums: annotations: source_domain: industry source_schema: extractive_industry + ManufacturingSchemaEnum: + description: Schema-level enum for manufacturing in industry + is_a: IndustryDomainEnum + abstract: true + annotations: + source_file: industry/manufacturing.yaml + ManufacturingProcessType: + title: Manufacturing Process Type + description: Types of manufacturing processes including additive, subtractive, and formative methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ADDITIVE_MANUFACTURING: + description: Manufacturing by adding material layer by layer to build a three-dimensional object + SUBTRACTIVE_MANUFACTURING: + description: Manufacturing by removing material from a solid block to create a desired shape + FORMATIVE_MANUFACTURING: + description: Manufacturing by reshaping material through mechanical forces without significant addition or removal + CASTING: + description: Pouring molten material into a mold and allowing it to solidify + FORGING: + description: Shaping metal using compressive forces applied by hammering, pressing, or rolling + WELDING: + description: Joining materials by applying heat, pressure, or both to fuse them together + MACHINING: + description: Removing material from a workpiece using cutting tools to achieve a desired geometry + INJECTION_MOLDING: + title: injection moulding + description: Forcing molten material into a mold cavity where it cools and hardens + meaning: CHMO:0001430 + EXTRUSION: + description: Forcing material through a die to create objects with a fixed cross-sectional profile + meaning: CHMO:0001613 + POWDER_METALLURGY: + description: Forming metal parts from compacted and sintered metal powders + broad_mappings: + - CHMO:0001701 + CHEMICAL_VAPOR_DEPOSITION: + title: chemical vapour deposition + description: Depositing thin films by exposing a substrate to volatile precursors that react on the surface + meaning: CHMO:0001314 + PHYSICAL_VAPOR_DEPOSITION: + title: physical vapour deposition + description: Depositing thin films by condensing vaporized material onto a substrate surface + meaning: CHMO:0001356 + ELECTROFORMING: + description: Producing metal parts by electrodeposition of metal onto a mandrel or pattern + broad_mappings: + - CHMO:0001331 + is_a: ManufacturingSchemaEnum + annotations: + source_domain: industry + source_schema: manufacturing + SmartManufacturingTechnologyType: + title: Smart Manufacturing Technology Type + description: Types of digital and intelligent technologies used in modern manufacturing environments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + DIGITAL_TWIN: + description: Virtual replica of a physical asset or process used for simulation and optimization + INDUSTRIAL_IOT: + description: Network of interconnected sensors and devices in industrial settings for data collection and control + PREDICTIVE_MAINTENANCE: + description: Using data analytics and machine learning to predict equipment failures before they occur + COMPUTER_VISION_INSPECTION: + description: Automated visual inspection of manufactured parts using computer vision and image analysis + ROBOTIC_ASSEMBLY: + description: Automated assembly of components using programmable robotic systems + AUTOMATED_QUALITY_CONTROL: + description: Automated systems for monitoring and ensuring product quality during manufacturing + SUPPLY_CHAIN_OPTIMIZATION: + description: Data-driven optimization of supply chain logistics and inventory management + PROCESS_SIMULATION: + description: Computer-based simulation of manufacturing processes for design and optimization + is_a: ManufacturingSchemaEnum + annotations: + source_domain: industry + source_schema: manufacturing MiningSchemaEnum: description: Schema-level enum for mining in industry is_a: IndustryDomainEnum @@ -19755,7 +37448,14 @@ enums: annotations: source_file: industry/mining.yaml MiningType: + title: Mining Type description: Types of mining operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: OPEN_PIT: description: Open-pit mining @@ -19850,7 +37550,14 @@ enums: source_domain: industry source_schema: mining MineralCategory: + title: Mineral Category description: Categories of minerals and materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRECIOUS_METALS: description: Precious metals @@ -19898,11 +37605,18 @@ enums: source_domain: industry source_schema: mining CriticalMineral: + title: Critical Mineral description: 'Critical minerals essential for economic and national security, particularly for clean energy, defense, and technology applications. Based on US Geological Survey and EU critical raw materials lists.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LITHIUM: description: Lithium (Li) - essential for batteries @@ -20264,7 +37978,14 @@ enums: source_domain: industry source_schema: mining CommonMineral: + title: Common Mineral description: Common minerals extracted through mining + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GOLD: description: Gold (Au) @@ -20400,7 +38121,14 @@ enums: source_domain: industry source_schema: mining MiningEquipment: + title: Mining Equipment description: Types of mining equipment + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DRILL_RIG: description: Drilling rig @@ -20471,7 +38199,14 @@ enums: source_domain: industry source_schema: mining OreGrade: + title: Ore Grade description: Classification of ore grades + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HIGH_GRADE: description: High-grade ore @@ -20504,7 +38239,14 @@ enums: source_domain: industry source_schema: mining MiningPhase: + title: Mining Phase description: Phases of mining operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EXPLORATION: description: Exploration phase @@ -20539,7 +38281,14 @@ enums: source_domain: industry source_schema: mining MiningHazard: + title: Mining Hazard description: Mining-related hazards and risks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CAVE_IN: description: Cave-in/roof collapse @@ -20590,7 +38339,14 @@ enums: source_domain: industry source_schema: mining EnvironmentalImpact: + title: Environmental Impact description: Environmental impacts of mining + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HABITAT_DESTRUCTION: description: Habitat destruction @@ -20642,7 +38398,14 @@ enums: annotations: source_file: industry/safety_colors.yaml SafetyColorEnum: + title: Safety Color description: ANSI/ISO standard safety colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SAFETY_RED: description: Safety red - danger, stop, prohibition @@ -20714,7 +38477,14 @@ enums: source_domain: industry source_schema: safety_colors TrafficLightColorEnum: + title: Traffic Light Color description: Traffic signal colors (international) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED: description: Red - stop @@ -20756,7 +38526,14 @@ enums: source_domain: industry source_schema: safety_colors HazmatColorEnum: + title: Hazmat Color description: Hazardous materials placarding colors (DOT/UN) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ORANGE: description: Orange - explosives (Class 1) @@ -20811,7 +38588,14 @@ enums: source_domain: industry source_schema: safety_colors FireSafetyColorEnum: + title: Fire Safety Color description: Fire safety equipment and signage colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FIRE_RED: description: Fire red - fire equipment @@ -20845,7 +38629,14 @@ enums: source_domain: industry source_schema: safety_colors MaritimeSignalColorEnum: + title: Maritime Signal Color description: Maritime signal and navigation colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PORT_RED: description: Port (left) red light @@ -20890,7 +38681,14 @@ enums: source_domain: industry source_schema: safety_colors AviationLightColorEnum: + title: Aviation Light Color description: Aviation lighting colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED_BEACON: description: Red obstruction light @@ -20944,7 +38742,14 @@ enums: source_domain: industry source_schema: safety_colors ElectricalWireColorEnum: + title: Electrical Wire Color description: Electrical wire color codes (US/International) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLACK_HOT: description: Black - hot/live wire (US) @@ -20998,12 +38803,1366 @@ enums: description: Gray - neutral wire (alternative) meaning: HEX:808080 annotations: - function: neutral - region: some installations - is_a: SafetyColorsSchemaEnum + function: neutral + region: some installations + is_a: SafetyColorsSchemaEnum + annotations: + source_domain: industry + source_schema: safety_colors + UnconventionalResourcesSchemaEnum: + description: Schema-level enum for unconventional_resources in industry + is_a: IndustryDomainEnum + abstract: true + annotations: + source_file: industry/unconventional_resources.yaml + UnconventionalMineralResourceType: + title: Unconventional Mineral Resource Type + description: Types of unconventional mineral resources including industrial waste streams, mining residues, and brines + that contain recoverable critical minerals and metals + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MINE_TAILINGS: + title: mine tailing + description: Materials remaining after separating the valuable fraction from the uneconomic fraction of an ore + meaning: ENVO:00000003 + WASTE_ROCK: + description: Rock removed during mining that does not contain sufficient mineral of interest for processing + annotations: + source: surface and underground mining + ACID_MINE_DRAINAGE: + title: acid mine drainage + description: Acidic water outflow from mines containing dissolved metals and sulfuric acid + meaning: ENVO:00001997 + COAL_COMBUSTION_RESIDUALS: + title: coal ash + description: Residual materials from combustion of coal in power plants, including fly ash, bottom ash, and boiler + slag + meaning: ENVO:02000127 + RED_MUD: + description: Alkaline residue generated during alumina extraction from bauxite ore via the Bayer process + annotations: + composition: iron oxides, alumina, silica, rare earth elements + source: alumina refining + PHOSPHOGYPSUM: + description: Gypsum byproduct from phosphoric acid production containing trace radioactive elements and rare earth + elements + annotations: + composition: calcium sulfate dihydrate with trace REE + source: phosphate fertilizer production + SLAG: + title: boiler slag + description: Glassy material formed as a byproduct of smelting and refining metal ores + meaning: ENVO:02000130 + FLY_ASH: + title: fly ash + description: Fine powdery material composed mostly of silica collected from flue gases during coal combustion + meaning: ENVO:02000128 + ELECTRONIC_WASTE: + description: Discarded electronic devices and components containing recoverable precious and critical metals + annotations: + metals: gold, silver, platinum, copper, rare earth elements + SPENT_CATALYSTS: + description: Used industrial catalysts containing recoverable platinum group metals and other valuable elements + annotations: + metals: platinum, palladium, rhodium, rhenium + source: petroleum refining, chemical manufacturing + GEOTHERMAL_BRINE: + title: brine + description: Hot saline water from geothermal systems containing dissolved lithium, rare earth elements, and other + minerals + meaning: ENVO:00003044 + OIL_FIELD_BRINE: + description: Saline water produced during oil and gas extraction containing dissolved minerals including lithium and + boron + broad_mappings: + - ENVO:00003044 + annotations: + minerals: lithium, bromine, boron, iodine + source: oil and gas production + is_a: UnconventionalResourcesSchemaEnum + annotations: + source_domain: industry + source_schema: unconventional_resources + BioextractionMethodType: + title: Bioextraction Method Type + description: Biological methods for extracting metals and minerals from unconventional resources using microorganisms + or plants + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + HEAP_BIOLEACHING: + description: Biological leaching of metals from crushed ore stacked in heaps irrigated with acidic microbial solutions + broad_mappings: + - CHMO:0001681 + annotations: + organisms: Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans + scale: industrial + STIRRED_TANK_BIOLEACHING: + description: Biological leaching of metals in agitated tank reactors with controlled conditions + broad_mappings: + - CHMO:0001681 + annotations: + organisms: Acidithiobacillus, Leptospirillum + scale: industrial, pilot + IN_SITU_BIOLEACHING: + description: Biological leaching of metals directly in the ore body without excavation + broad_mappings: + - CHMO:0001681 + annotations: + advantage: minimal surface disturbance + application: low-grade deposits + PHYTOMINING: + description: Use of hyperaccumulator plants to extract metals from soil or mining waste for recovery + annotations: + organisms: Alyssum, Thlaspi, Pteris + metals: nickel, zinc, thallium + BIOSORPTION: + description: Passive binding of metal ions to the surface of biological materials such as microbial biomass + annotations: + mechanism: surface complexation, ion exchange + materials: dead biomass, algae, fungi + BIOACCUMULATION: + description: Active uptake and intracellular concentration of metals by living organisms + annotations: + mechanism: metabolically driven intracellular uptake + organisms: bacteria, fungi, algae + BIOPRECIPITATION: + description: Microbially mediated precipitation of metals as insoluble compounds such as sulfides or phosphates + broad_mappings: + - CHMO:0001688 + annotations: + mechanism: sulfate reduction, phosphate release + products: metal sulfides, metal phosphates + BIOFLOTATION: + description: Use of microorganisms or biosurfactants to selectively separate mineral particles by flotation + annotations: + mechanism: selective surface modification + organisms: Mycobacterium, Bacillus + is_a: UnconventionalResourcesSchemaEnum + annotations: + source_domain: industry + source_schema: unconventional_resources + TailingCharacterizationType: + title: Tailing Characterization Type + description: Types of measurements and analyses used to characterize mine tailings and other mineral processing residues + for resource recovery potential + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PARTICLE_SIZE_DISTRIBUTION: + description: Measurement of the distribution of particle sizes in tailing material + title: granulometry + meaning: CHMO:0002119 + annotations: + methods: sieve analysis, laser diffraction, sedimentation + MINERALOGICAL_COMPOSITION: + description: Determination of mineral phases present in tailing material using diffraction and spectroscopic methods + annotations: + methods: XRD, SEM-EDS, QEMSCAN, MLA + ACID_GENERATING_POTENTIAL: + description: Assessment of the potential for tailings to generate acid drainage through sulfide oxidation + annotations: + tests: acid-base accounting, NAG test, kinetic testing + METAL_CONTENT: + description: Quantitative analysis of metal and element concentrations in tailing material + close_mappings: + - CHMO:0001075 + annotations: + methods: ICP-MS, ICP-OES, XRF + MOISTURE_CONTENT: + description: Measurement of water content in tailing material affecting stability and handling + annotations: + methods: gravimetric, nuclear moisture gauge + GEOTECHNICAL_STABILITY: + description: Assessment of the mechanical and physical stability of tailing storage facilities + annotations: + parameters: shear strength, consolidation, liquefaction potential + ENVIRONMENTAL_RISK_CLASSIFICATION: + description: Classification of environmental risk based on contaminant mobility, toxicity, and exposure pathways + annotations: + frameworks: TCLP, WET, environmental impact assessment + is_a: UnconventionalResourcesSchemaEnum + annotations: + source_domain: industry + source_schema: unconventional_resources + LabAutomationDomainEnum: + description: Domain-level enum for lab_automation value sets + is_a: ValueSetEnum + abstract: true + AutonomousLabsSchemaEnum: + description: Schema-level enum for autonomous_labs in lab_automation + is_a: LabAutomationDomainEnum + abstract: true + annotations: + source_file: lab_automation/autonomous_labs.yaml + AutonomousLabComponentType: + title: Autonomous Lab Component Type + description: Types of hardware and software components that comprise an AI-driven autonomous laboratory system + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ROBOTIC_SAMPLE_HANDLER: + description: Robotic system for automated sample manipulation, transfer, and preparation + close_mappings: + - OBI:0400112 + annotations: + function: sample handling and transfer + AUTOMATED_SYNTHESIZER: + description: Automated system for chemical or biological synthesis operations + broad_mappings: + - NCIT:C50206 + annotations: + function: automated synthesis + HIGH_THROUGHPUT_SCREENING_PLATFORM: + title: high throughput screening + description: Integrated platform for rapid screening of large numbers of samples or conditions + meaning: BAO:0010074 + AUTOMATED_CHARACTERIZATION_INSTRUMENT: + description: Instrument for automated measurement and characterization of samples + annotations: + examples: automated XRD, SEM, spectroscopy + AI_EXPERIMENT_PLANNER: + description: AI-based software system that designs and plans experiments based on prior data and objectives + annotations: + function: experiment planning and design + DATA_MANAGEMENT_SYSTEM: + description: System for automated collection, storage, and management of experimental data + close_mappings: + - NCIT:C48209 + annotations: + function: data management and integration + SAFETY_MONITORING_SYSTEM: + description: System for real-time monitoring of laboratory safety conditions and automated hazard response + annotations: + function: safety monitoring and emergency response + SAMPLE_STORAGE_SYSTEM: + description: Automated storage and retrieval system for laboratory samples + annotations: + function: sample storage and inventory management + is_a: AutonomousLabsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: autonomous_labs + ExperimentalDesignMethodType: + title: Experimental Design Method Type + description: Computational and statistical methods used for experimental design in autonomous laboratory workflows + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BAYESIAN_OPTIMIZATION: + description: Probabilistic model-based optimization using Bayesian inference to guide experimental selection + annotations: + approach: surrogate model with acquisition function + ACTIVE_LEARNING: + description: Machine learning approach that iteratively selects the most informative experiments to perform + annotations: + approach: query-based learning from unlabeled data + REINFORCEMENT_LEARNING: + description: Machine learning approach where an agent learns optimal experimental strategies through trial and reward + annotations: + approach: reward-based sequential decision making + EVOLUTIONARY_ALGORITHM: + description: Optimization method inspired by biological evolution using mutation, crossover, and selection + annotations: + approach: population-based metaheuristic + RANDOM_SEARCH: + description: Experimental design using random sampling of the parameter space + annotations: + approach: random sampling + GRID_SEARCH: + description: Systematic exploration of parameter space using a regular grid of experimental conditions + annotations: + approach: exhaustive grid evaluation + LATIN_HYPERCUBE_SAMPLING: + description: Statistical sampling method that ensures even coverage of each parameter dimension + annotations: + approach: stratified random sampling + DESIGN_OF_EXPERIMENTS: + description: Classical statistical methods for planning experiments including factorial and response surface designs + annotations: + approaches: full factorial, fractional factorial, Box-Behnken, central composite + MULTI_OBJECTIVE_OPTIMIZATION: + description: Optimization approach that simultaneously considers multiple competing objectives + annotations: + approach: Pareto-optimal solution search + is_a: AutonomousLabsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: autonomous_labs + LabAutomationWorkflowType: + title: Lab Automation Workflow Type + description: Types of automated workflows implemented in autonomous laboratory systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CLOSED_LOOP_OPTIMIZATION: + description: Workflow where experimental results are automatically fed back to guide subsequent experiments + annotations: + characteristic: feedback-driven iterative optimization + HIGH_THROUGHPUT_SCREENING: + title: High Throughput Screening + description: Workflow for rapid parallel evaluation of many samples or conditions + meaning: NCIT:C18472 + related_mappings: + - BAO:0010074 + annotations: + characteristic: massively parallel evaluation + AUTOMATED_SYNTHESIS: + description: Workflow for automated execution of chemical or biological synthesis procedures + annotations: + characteristic: automated reaction execution + AUTONOMOUS_CHARACTERIZATION: + description: Workflow for automated sample characterization using multiple analytical techniques + annotations: + characteristic: multi-modal automated measurement + SELF_DRIVING_EXPERIMENTATION: + description: Fully autonomous workflow combining AI-driven planning, execution, and analysis without human intervention + annotations: + characteristic: end-to-end autonomous operation + ROBOTIC_SAMPLE_PREPARATION: + description: Workflow for automated preparation of samples for analysis or further processing + broad_mappings: + - OBI:0000073 + annotations: + characteristic: automated sample handling and preparation + is_a: AutonomousLabsSchemaEnum annotations: - source_domain: industry - source_schema: safety_colors + source_domain: lab_automation + source_schema: autonomous_labs + DevicesSchemaEnum: + description: Schema-level enum for devices in lab_automation + is_a: LabAutomationDomainEnum + abstract: true + annotations: + source_file: lab_automation/devices.yaml + LaboratoryDeviceTypeEnum: + title: Laboratory Device Type + description: Types of automated laboratory devices and equipment + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LIQUID_HANDLER: + description: A device that is used for automated liquid transfer and handling + meaning: OBI:0400112 + title: liquid handler + LIQUID_EXTRACTION_ROBOT: + description: A liquid handling device that provides automatic liquid extraction + meaning: OBI:0001097 + title: liquid extraction robot + CENTRIFUGE: + description: A device with a rapidly rotating container that applies centrifugal force to its contents + meaning: OBI:0400106 + title: centrifuge + MICROCENTRIFUGE: + description: A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has + a small footprint + meaning: OBI:0001100 + title: microcentrifuge + INCUBATOR: + description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled + meaning: OBI:0000136 + title: incubator + INCUBATOR_SHAKER: + description: An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures) + meaning: OBI:0001076 + title: incubator shaker + MICROPLATE_READER: + description: A measurement device that detects biological, chemical or physical events of samples in microtiter plates + meaning: OBI:0001058 + title: microplate reader + ELISA_MICROPLATE_READER: + description: A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA) + meaning: OBI:0001059 + title: ELISA microplate reader + MULTIMODE_MICROPLATE_READER: + description: A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence + meaning: OBI:0001090 + title: multimode microplate reader + MICROPLATE_WASHER: + description: A device that is used to wash immunoassays in microwell strips and plates with professional accuracy + meaning: OBI:0001113 + title: microplate washer + ELISA_MICROPLATE_WASHER: + description: A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA) + meaning: OBI:0001115 + title: ELISA microplate washer + MULTICHANNEL_PIPETTE: + description: A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications + meaning: OBI:0001118 + title: multichannel pipette + ROBOTIC_ARM: + description: A programmable mechanical arm used in laboratory automation + meaning: SNOMED:82830000 + title: robotic arm + THERMAL_CYCLER: + description: A laboratory apparatus used to amplify DNA segments via the polymerase chain reaction + title: thermal cycler + COLONY_PICKER: + description: An automated device for selecting and transferring individual bacterial or yeast colonies + title: colony picker + BARCODE_READER: + description: A device that reads barcode labels on laboratory samples and containers + title: barcode reader + PLATE_HANDLER: + description: An automated device designed to transfer microplates between workstations and lab instruments + title: plate handler + DISPENSER: + description: A device for automated dispensing of reagents or samples + title: dispenser + is_a: DevicesSchemaEnum + annotations: + source_domain: lab_automation + source_schema: devices + RoboticArmTypeEnum: + title: Robotic Arm Type + description: Types of robotic arms used in laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FLEXIBLE_CHANNEL_ARM: + description: Robotic arm with flexible channels for disposable tip handling and liquid handling + title: flexible channel arm + annotations: + abbreviation: FCA + MULTI_CHANNEL_ARM: + description: Robotic arm used for high-throughput pipetting with 96 or 384 channels + title: multi-channel arm + annotations: + abbreviation: MCA + ROBOTIC_GRIPPER_ARM: + description: Robotic arm used to pick and transfer objects within the working area, equipped with dedicated gripper + fingers + title: robotic gripper arm + annotations: + abbreviation: RGA + SINGLE_PROBE_ARM: + description: Robotic arm with a single probe for individual sample handling + title: single probe arm + is_a: DevicesSchemaEnum + annotations: + source_domain: lab_automation + source_schema: devices + LabwareSchemaEnum: + description: Schema-level enum for labware in lab_automation + is_a: LabAutomationDomainEnum + abstract: true + annotations: + source_file: lab_automation/labware.yaml + MicroplateFormatEnum: + title: Microplate Format + description: Standard microplate well configurations following ANSI/SLAS standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + WELL_6: + description: Microplate with 6 wells + title: 6-well plate + WELL_12: + description: Microplate with 12 wells + title: 12-well plate + WELL_24: + description: Microplate with 24 wells + title: 24-well plate + WELL_48: + description: Microplate with 48 wells + title: 48-well plate + WELL_96: + description: Microplate with 96 wells arranged in 8 rows of 12 columns with 9mm well-to-well spacing + meaning: MSIO:0000162 + title: 96-well microplate + annotations: + well_spacing: 9mm + standard: ANSI/SLAS 4-2004 + WELL_384: + description: Microplate with 384 wells with 4.5mm well-to-well spacing + title: 384-well plate + annotations: + well_spacing: 4.5mm + standard: ANSI/SLAS 4-2004 + WELL_1536: + description: Microplate with 1536 wells with 2.25mm well-to-well spacing + title: 1536-well plate + annotations: + well_spacing: 2.25mm + standard: ANSI/SLAS 4-2004 + is_a: LabwareSchemaEnum + annotations: + source_domain: lab_automation + source_schema: labware + ContainerTypeEnum: + title: Container Type + description: Types of laboratory containers and labware + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + MICROPLATE: + description: A flat dish with multiple individual wells that are arrayed in a standardized number, size, and arrangement + meaning: NCIT:C43377 + exact_mappings: + - BAO:0000508 + title: microplate + DEEP_WELL_PLATE: + description: A microplate with deeper wells for increased sample volume capacity + title: deep well plate + PCR_PLATE: + description: A microplate specifically designed for PCR thermal cycling applications + title: PCR plate + TUBE_RACK: + description: A rack designed to hold multiple laboratory tubes + title: tube rack + MICROTUBE: + description: Small laboratory tube with volume capacity from 0.2 ml to 2.0 ml + title: microtube + annotations: + volume_range: 0.2-2.0 ml + SCREW_CAP_TUBE: + description: Laboratory tube with screw cap closure + title: screw cap tube + SNAP_CAP_TUBE: + description: Laboratory tube with snap cap closure + title: snap cap tube + RESERVOIR: + description: Container for holding bulk reagents for dispensing + title: reservoir + PIPETTE_TIP_BOX: + description: Container for storing pipette tips in organized racks + title: pipette tip box + SPIN_COLUMN: + description: A chromatography column which is suitable for putting it into a centrifuge + meaning: OBI:0000570 + title: spin column + MICROPLATE_WELL: + description: Any of the individual wells on a microwell plate + meaning: NCIT:C128793 + title: microplate well + is_a: LabwareSchemaEnum + annotations: + source_domain: lab_automation + source_schema: labware + PlateMaterialEnum: + title: Plate Material + description: Material composition of laboratory microplates + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + POLYSTYRENE: + description: Plates made from polystyrene, the most common material for standard applications + title: polystyrene + POLYPROPYLENE: + description: Plates made from polypropylene for chemical resistance + title: polypropylene + GLASS: + description: Plates with glass inserts for samples not suitable for plastic containers + title: glass + is_a: LabwareSchemaEnum + annotations: + source_domain: lab_automation + source_schema: labware + PlateCoatingEnum: + title: Plate Coating + description: Surface treatment of microplates + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + COATED: + description: A microplate whose surface has been treated, for instance by covalently attaching proteins to favor cell + growth + meaning: MSIO:0000164 + title: coated microplate + UNCOATED: + description: A microplate whose surface has not received any treatment and is uniquely made of polymer + meaning: MSIO:0000170 + title: uncoated microplate + TISSUE_CULTURE_TREATED: + description: Surface treatment to enhance cell attachment and growth + title: tissue culture treated + PROTEIN_BINDING: + description: Surface treatment optimized for protein binding assays + title: protein binding + is_a: LabwareSchemaEnum + annotations: + source_domain: lab_automation + source_schema: labware + OperationsSchemaEnum: + description: Schema-level enum for operations in lab_automation + is_a: LabAutomationDomainEnum + abstract: true + annotations: + source_file: lab_automation/operations.yaml + LiquidHandlingOperationEnum: + title: Liquid Handling Operation + description: Operations for automated liquid handling in laboratory automation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PICK_UP_TIPS: + description: Operation to pick up pipette tips from a tip rack + title: pick up tips + ASPIRATE: + description: Operation to draw liquid into pipette tips + title: aspirate + DISPENSE: + description: Operation to dispense liquid from pipette tips + title: dispense + RETURN_TIPS: + description: Operation to return pipette tips to a tip rack + title: return tips + DROP_TIPS: + description: Operation to drop or discard pipette tips + title: drop tips + TRANSFER: + description: Combined operation to aspirate from source and dispense to destination + title: transfer + PIPETTING: + description: A procedure or technique by which the size of the three dimensional space occupied by a liquid substance + is ascertained using a pipette + meaning: MMO:0000392 + title: pipette method + MIXING: + description: Operation to mix liquids by repeated aspiration and dispensing + title: mixing + ALIQUOTING: + description: Operation to distribute a sample into multiple equal portions + title: aliquoting + SERIAL_DILUTION: + description: Operation to create a series of dilutions of a substance in solution + title: serial dilution + PLATE_STAMPING: + description: Operation to transfer samples from one plate to another in the same well pattern + title: plate stamping + ACOUSTIC_TRANSFER: + description: Acoustic liquid handling that uses acoustics to fly individual droplets from a source container to a + destination + title: acoustic transfer + MOUTH_PIPETTING: + description: A method of using the researcher's mouth to apply small negative pressure to aspirate a volume into a + pipette + meaning: EFO:0010182 + title: mouth pipetting + is_a: OperationsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: operations + SampleProcessingOperationEnum: + title: Sample Processing Operation + description: General sample processing operations in automated laboratories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CENTRIFUGATION: + description: Operation to separate components of a sample using centrifugal force + title: centrifugation + INCUBATION: + description: Operation to maintain samples at controlled environmental conditions over time + title: incubation + THERMAL_CYCLING: + description: Operation to cycle samples through different temperatures for PCR or similar processes + title: thermal cycling + WASHING: + description: Operation to wash samples or plates to remove unwanted material + title: washing + DETECTION: + description: Operation to detect signals from samples (absorbance, fluorescence, luminescence) + title: detection + MEASUREMENT: + description: Operation to measure a property or characteristic of a sample + title: measurement + SEPARATION: + description: Operation to separate components of a sample mixture + title: separation + EXTRACTION: + description: Operation to extract specific components from a sample + title: extraction + HEATING: + description: Operation to heat samples to a specified temperature + title: heating + COOLING: + description: Operation to cool samples to a specified temperature + title: cooling + SHAKING: + description: Operation to shake samples for mixing or agitation + title: shaking + PLATE_MOVEMENT: + description: Operation to move plates between different locations or devices + title: plate movement + BARCODE_READING: + description: Operation to read barcode labels on samples or containers + title: barcode reading + is_a: OperationsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: operations + ProtocolsSchemaEnum: + description: Schema-level enum for protocols in lab_automation + is_a: LabAutomationDomainEnum + abstract: true + annotations: + source_file: lab_automation/protocols.yaml + WorkflowOrchestrationTypeEnum: + title: Workflow Orchestration Type + description: Types of workflow orchestration in laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + STATIC_ORCHESTRATION: + description: Pre-planned orchestration based on known constraints and fixed workflow + title: static orchestration + DYNAMIC_ORCHESTRATION: + description: Real-time orchestration that adapts to changing conditions and events + title: dynamic orchestration + HYBRID_ORCHESTRATION: + description: Combination of static planning with dynamic replanning capabilities + title: hybrid orchestration + EVENT_DRIVEN: + description: Orchestration triggered by specific events in the system + title: event-driven orchestration + PARALLEL_PROCESSING: + description: Orchestration that enables concurrent execution of independent tasks + title: parallel processing + is_a: ProtocolsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: protocols + SchedulerTypeEnum: + title: Scheduler Type + description: Types of scheduling algorithms for laboratory automation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + STATIC_SCHEDULER: + description: Makes decisions based on known constraints requiring upfront planning + title: static scheduler + DYNAMIC_SCHEDULER: + description: Adapts scheduling decisions in real-time based on system state + title: dynamic scheduler + PRIORITY_BASED: + description: Schedules tasks based on assigned priority levels + title: priority-based scheduler + FIFO: + description: First-in-first-out scheduling + title: FIFO scheduler + RESOURCE_AWARE: + description: Schedules tasks considering available resources and constraints + title: resource-aware scheduler + DEADLINE_DRIVEN: + description: Schedules tasks to meet specified deadlines + title: deadline-driven scheduler + is_a: ProtocolsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: protocols + ProtocolStateEnum: + title: Protocol State + description: Execution states of laboratory protocols + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PENDING: + description: Protocol is queued but not yet started + title: pending + RUNNING: + description: Protocol is currently executing + title: running + PAUSED: + description: Protocol execution has been temporarily suspended + title: paused + COMPLETED: + description: Protocol has finished successfully + title: completed + FAILED: + description: Protocol execution has failed + title: failed + ABORTED: + description: Protocol execution was manually aborted + title: aborted + VALIDATING: + description: Protocol is being validated before execution + title: validating + WAITING_FOR_RESOURCE: + description: Protocol is waiting for required resources to become available + title: waiting for resource + is_a: ProtocolsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: protocols + ExecutionModeEnum: + title: Execution Mode + description: Modes of protocol execution + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AUTOMATED: + description: Fully automated execution without human intervention + title: automated + MANUAL: + description: Manual execution by human operator + title: manual + SEMI_AUTOMATED: + description: Combination of automated and manual steps + title: semi-automated + SUPERVISED: + description: Automated execution with human supervision + title: supervised + SIMULATION: + description: Simulated execution for testing and validation + title: simulation + DRY_RUN: + description: Test execution without actual operations + title: dry run + is_a: ProtocolsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: protocols + WorkflowErrorHandlingEnum: + title: Workflow Error Handling + description: Error handling strategies in laboratory automation workflows + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ABORT_ON_ERROR: + description: Terminate workflow immediately upon encountering an error + title: abort on error + RETRY: + description: Attempt to retry the failed operation + title: retry + SKIP_AND_CONTINUE: + description: Skip the failed operation and continue with the workflow + title: skip and continue + NOTIFY_AND_PAUSE: + description: Notify operator and pause workflow for intervention + title: notify and pause + ROLLBACK: + description: Revert to previous stable state + title: rollback + FAILOVER: + description: Switch to backup resource or alternative execution path + title: failover + is_a: ProtocolsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: protocols + IntegrationSystemEnum: + title: Integration System + description: Types of systems integrated with laboratory automation platforms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LIMS: + description: Laboratory Information Management System + title: LIMS + annotations: + full_name: Laboratory Information Management System + ELN: + description: Electronic Laboratory Notebook + title: ELN + annotations: + full_name: Electronic Laboratory Notebook + MES: + description: Manufacturing Execution System + title: MES + annotations: + full_name: Manufacturing Execution System + SCADA: + description: Supervisory Control and Data Acquisition + title: SCADA + annotations: + full_name: Supervisory Control and Data Acquisition + CLOUD_STORAGE: + description: Cloud-based data storage systems + title: cloud storage + DATABASE: + description: Laboratory database systems + title: database + is_a: ProtocolsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: protocols + StandardsSchemaEnum: + description: Schema-level enum for standards in lab_automation + is_a: LabAutomationDomainEnum + abstract: true + annotations: + source_file: lab_automation/standards.yaml + AutomationStandardEnum: + title: Automation Standard + description: Industry standards for laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SILA_2: + description: Standardization in Lab Automation version 2 - international standard for open connectivity in lab automation + title: SiLA 2 + annotations: + organization: Society for Laboratory Automation and Screening + architecture: microservice-based + protocol: gRPC + LABOP: + description: Laboratory Open Protocol Language - open specification for laboratory protocols + title: LabOP + annotations: + format: RDF/OWL + organization: Bioprotocols Working Group + AUTOPROTOCOL: + description: JSON-based language for specifying experimental protocols + title: Autoprotocol + annotations: + format: JSON + CLSI_AUTO01: + description: CLSI standard for Specimen Container/Specimen Carrier + title: CLSI AUTO01 + annotations: + organization: Clinical and Laboratory Standards Institute + CLSI_AUTO02: + description: CLSI standard for Bar Codes for Specimen Container Identification + title: CLSI AUTO02 + annotations: + organization: Clinical and Laboratory Standards Institute + CLSI_AUTO03: + description: CLSI standard for Communications with Automated Clinical Laboratory Systems + title: CLSI AUTO03 + annotations: + organization: Clinical and Laboratory Standards Institute + CLSI_AUTO04: + description: CLSI standard for Systems Operational Requirements, Characteristics, and Information Elements + title: CLSI AUTO04 + annotations: + organization: Clinical and Laboratory Standards Institute + CLSI_AUTO05: + description: CLSI standard for Electromechanical Interfaces + title: CLSI AUTO05 + annotations: + organization: Clinical and Laboratory Standards Institute + is_a: StandardsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: standards + CommunicationProtocolEnum: + title: Communication Protocol + description: Communication protocols for laboratory automation integration + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GRPC: + description: gRPC protocol used in SiLA 2 + title: gRPC + annotations: + used_by: SiLA 2 + REST_API: + description: RESTful HTTP-based API + title: REST API + SOAP: + description: Simple Object Access Protocol + title: SOAP + OPC_UA: + description: OPC Unified Architecture for industrial automation + title: OPC UA + annotations: + full_name: OPC Unified Architecture + MODBUS: + description: Serial communication protocol for industrial devices + title: Modbus + CUSTOM_API: + description: Vendor-specific custom API + title: custom API + SERIAL: + description: Serial communication protocol (RS-232, RS-485) + title: serial + TCP_IP: + description: TCP/IP network protocol + title: TCP/IP + USB: + description: Universal Serial Bus communication + title: USB + is_a: StandardsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: standards + LabwareStandardEnum: + title: Labware Standard + description: Standardization specifications for laboratory labware + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ANSI_SLAS_1_2004: + description: Microplates - Footprint Dimensions + title: ANSI/SLAS 1-2004 + annotations: + reaffirmed: 2012 + specification: Footprint Dimensions + ANSI_SLAS_2_2004: + description: Microplates - Height Dimensions + title: ANSI/SLAS 2-2004 + annotations: + reaffirmed: 2012 + specification: Height Dimensions + ANSI_SLAS_3_2004: + description: Microplates - Bottom Outside Flange Dimensions + title: ANSI/SLAS 3-2004 + annotations: + reaffirmed: 2012 + specification: Bottom Outside Flange Dimensions + ANSI_SLAS_4_2004: + description: Microplates - Well Positions + title: ANSI/SLAS 4-2004 + annotations: + reaffirmed: 2012 + specification: Well Positions + ANSI_SLAS_6_2012: + description: Microplates - Well Bottom Elevation + title: ANSI/SLAS 6-2012 + annotations: + specification: Well Bottom Elevation + SBS_FOOTPRINT: + description: Society for Biomolecular Screening standard footprint (127.76mm x 85.5mm) + title: SBS footprint + annotations: + dimensions: 127.76mm x 85.5mm + is_a: StandardsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: standards + IntegrationFeatureEnum: + title: Integration Feature + description: Integration features for laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BARCODE_TRACKING: + description: Integration feature for tracking samples via barcodes + title: barcode tracking + AUTOMATED_DATA_TRANSFER: + description: Automatic transfer of data between systems + title: automated data transfer + CLOUD_STORAGE_INTEGRATION: + description: Integration with cloud-based storage systems + title: cloud storage integration + SAMPLE_TRACKING: + description: Real-time tracking of sample location and status + title: sample tracking + WORKFLOW_VALIDATION: + description: Automated validation of workflow definitions + title: workflow validation + ERROR_RECOVERY: + description: Automated error detection and recovery mechanisms + title: error recovery + AUDIT_TRAIL: + description: Complete logging of all operations for compliance + title: audit trail + ELECTRONIC_SIGNATURES: + description: Support for electronic signatures for regulatory compliance + title: electronic signatures + is_a: StandardsSchemaEnum + annotations: + source_domain: lab_automation + source_schema: standards + ThermalCyclingSchemaEnum: + description: Schema-level enum for thermal_cycling in lab_automation + is_a: LabAutomationDomainEnum + abstract: true + annotations: + source_file: lab_automation/thermal_cycling.yaml + ThermalCyclerTypeEnum: + title: Thermal Cycler Type + description: Types of thermal cycling instruments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + STANDARD_THERMAL_CYCLER: + description: Standard thermal cycler for endpoint PCR + title: standard thermal cycler + REAL_TIME_PCR: + description: Thermal cycler with real-time fluorescence detection + title: real-time PCR + annotations: + abbreviation: qPCR + DIGITAL_PCR: + description: Thermal cycler for digital PCR applications + title: digital PCR + annotations: + abbreviation: dPCR + GRADIENT_THERMAL_CYCLER: + description: Thermal cycler capable of running temperature gradients across the block + title: gradient thermal cycler + FAST_THERMAL_CYCLER: + description: Thermal cycler optimized for rapid cycling + title: fast thermal cycler + AUTOMATED_THERMAL_CYCLER: + description: Thermal cycler with integrated automation for high-throughput applications + title: automated thermal cycler + annotations: + example: Biometra TRobot II + IN_SITU_THERMAL_CYCLER: + description: Thermal cycler designed for in situ PCR applications + title: in situ thermal cycler + is_a: ThermalCyclingSchemaEnum + annotations: + source_domain: lab_automation + source_schema: thermal_cycling + PCROperationTypeEnum: + title: PCR Operation Type + description: Types of PCR operations and techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + STANDARD_PCR: + description: Standard endpoint PCR amplification + title: standard PCR + QUANTITATIVE_PCR: + description: Real-time quantitative PCR + title: quantitative PCR + annotations: + abbreviation: qPCR + REVERSE_TRANSCRIPTION_PCR: + description: PCR with reverse transcription step for RNA amplification + title: reverse transcription PCR + annotations: + abbreviation: RT-PCR + RT_QPCR: + description: Real-time quantitative RT-PCR + title: RT-qPCR + MULTIPLEX_PCR: + description: PCR amplifying multiple targets simultaneously + title: multiplex PCR + NESTED_PCR: + description: Two-stage PCR for increased specificity + title: nested PCR + TOUCHDOWN_PCR: + description: PCR with decreasing annealing temperature + title: touchdown PCR + HOT_START_PCR: + description: PCR with heat-activated polymerase + title: hot start PCR + LONG_RANGE_PCR: + description: PCR optimized for amplifying long DNA fragments + title: long range PCR + COLONY_PCR: + description: PCR directly from bacterial colonies + title: colony PCR + HIGH_FIDELITY_PCR: + description: PCR using proofreading polymerases + title: high fidelity PCR + DIGITAL_PCR: + description: Absolute quantification PCR using partitioning + title: digital PCR + is_a: ThermalCyclingSchemaEnum + annotations: + source_domain: lab_automation + source_schema: thermal_cycling + DetectionModeEnum: + title: Detection Mode + description: Detection modes for real-time PCR instruments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SYBR_GREEN: + description: DNA-binding dye detection + title: SYBR Green + TAQMAN: + description: Hydrolysis probe-based detection + title: TaqMan + MOLECULAR_BEACON: + description: Hairpin probe-based detection + title: molecular beacon + FRET: + description: Fluorescence resonance energy transfer detection + title: FRET + annotations: + full_name: Fluorescence Resonance Energy Transfer + SCORPION: + description: Unimolecular probe-based detection + title: Scorpion + HYBRIDIZATION_PROBE: + description: Two-probe FRET-based detection + title: hybridization probe + MULTI_CHANNEL: + description: Multi-channel fluorescence detection + title: multi-channel + is_a: ThermalCyclingSchemaEnum + annotations: + source_domain: lab_automation + source_schema: thermal_cycling + PCRPlateTypeEnum: + title: PCR Plate Type + description: Types of plates used for PCR applications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + PCR_96_WELL: + description: 96-well plate for PCR + title: 96-well PCR plate + PCR_384_WELL: + description: 384-well plate for PCR + title: 384-well PCR plate + PCR_TUBE_STRIP: + description: Strip of 8 or 12 PCR tubes + title: PCR tube strip + INDIVIDUAL_PCR_TUBE: + description: Individual PCR tube + title: individual PCR tube + LOW_PROFILE_PLATE: + description: Low-profile PCR plate for automated systems + title: low profile plate + SKIRTED_PLATE: + description: PCR plate with skirted base for stability + title: skirted plate + SEMI_SKIRTED_PLATE: + description: PCR plate with partial skirt + title: semi-skirted plate + is_a: ThermalCyclingSchemaEnum + annotations: + source_domain: lab_automation + source_schema: thermal_cycling + ThermalCyclingStepEnum: + title: Thermal Cycling Step + description: Steps in thermal cycling protocols + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + INITIAL_DENATURATION: + description: Initial high-temperature step to denature template DNA + title: initial denaturation + DENATURATION: + description: High-temperature step to separate DNA strands + title: denaturation + ANNEALING: + description: Cooling step to allow primer binding + title: annealing + EXTENSION: + description: Temperature-optimized step for polymerase activity + title: extension + FINAL_EXTENSION: + description: Extended final extension step + title: final extension + HOLD: + description: Temperature hold step + title: hold + MELT_CURVE: + description: Gradual temperature increase for melt curve analysis + title: melt curve + GRADIENT: + description: Temperature gradient across block + title: gradient + is_a: ThermalCyclingSchemaEnum + annotations: + source_domain: lab_automation + source_schema: thermal_cycling MaterialsScienceDomainEnum: description: Domain-level enum for materials_science value sets is_a: ValueSetEnum @@ -21015,7 +40174,14 @@ enums: annotations: source_file: materials_science/characterization_methods.yaml MicroscopyMethodEnum: + title: Microscopy Method description: Microscopy techniques for material characterization + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SEM: description: Scanning Electron Microscopy @@ -21071,7 +40237,14 @@ enums: source_domain: materials_science source_schema: characterization_methods SpectroscopyMethodEnum: + title: Spectroscopy Method description: Spectroscopy techniques for material analysis + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: XRD: description: X-ray Diffraction @@ -21134,7 +40307,14 @@ enums: source_domain: materials_science source_schema: characterization_methods ThermalAnalysisMethodEnum: + title: Thermal Analysis Method description: Thermal analysis techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DSC: description: Differential Scanning Calorimetry @@ -21171,7 +40351,14 @@ enums: source_domain: materials_science source_schema: characterization_methods MechanicalTestingMethodEnum: + title: Mechanical Testing Method description: Mechanical testing methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TENSILE: description: Tensile strength testing @@ -21200,2031 +40387,6845 @@ enums: is_a: CharacterizationMethodsSchemaEnum annotations: source_domain: materials_science - source_schema: characterization_methods - CrystalStructuresSchemaEnum: - description: Schema-level enum for crystal_structures in materials_science - is_a: MaterialsScienceDomainEnum - abstract: true - annotations: - source_file: materials_science/crystal_structures.yaml - CrystalSystemEnum: - description: The seven crystal systems in crystallography - conforms_to: https://en.wikipedia.org/wiki/Crystal_system + source_schema: characterization_methods + ComputationalMaterialsSchemaEnum: + description: Schema-level enum for computational_materials in materials_science + is_a: MaterialsScienceDomainEnum + abstract: true + annotations: + source_file: materials_science/computational_materials.yaml + MaterialsSimulationType: + title: Materials Simulation Type + description: Computational simulation methods used in materials science for predicting structure, properties, and behavior + of materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + DENSITY_FUNCTIONAL_THEORY: + description: Quantum mechanical method for computing electronic structure based on electron density functionals + MOLECULAR_DYNAMICS: + title: Molecular Dynamics + description: Simulation of atomic and molecular motion by numerically integrating equations of motion + meaning: NCIT:C18097 + MONTE_CARLO: + description: Stochastic simulation method using random sampling to explore configuration space + meaning: SWO:4000008 + PHASE_FIELD_MODELING: + description: Continuum method for simulating microstructure evolution using order parameter fields + FINITE_ELEMENT_ANALYSIS: + description: Numerical method for solving partial differential equations by dividing a domain into discrete elements + CONTINUUM_MECHANICS: + description: Modeling material behavior at the macroscopic scale using continuous field equations + TIGHT_BINDING: + description: Semi-empirical quantum mechanical method using parameterized Hamiltonian matrices + AB_INITIO_MOLECULAR_DYNAMICS: + description: Molecular dynamics with forces computed from first-principles electronic structure calculations + MACHINE_LEARNING_POTENTIAL: + description: Interatomic potentials trained on quantum mechanical data using machine learning methods + COARSE_GRAINED_SIMULATION: + description: Simulation using simplified representations that group atoms into larger effective interaction sites + is_a: ComputationalMaterialsSchemaEnum + annotations: + source_domain: materials_science + source_schema: computational_materials + MaterialPropertyPredictionType: + title: Material Property Prediction Type + description: Material properties that are commonly targeted for computational prediction in materials discovery and design + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BAND_GAP: + description: Energy difference between the valence band and conduction band in a semiconductor or insulator + ELASTIC_MODULUS: + description: Measure of material stiffness defined as the ratio of stress to strain in the elastic regime + broad_mappings: + - PATO:0001031 + THERMAL_CONDUCTIVITY: + title: heat conductivity + description: Ability of a material to conduct heat, measured in watts per meter-kelvin + meaning: PATO:0001756 + DIELECTRIC_CONSTANT: + description: Ratio of the permittivity of a material to the permittivity of free space + MAGNETIC_MOMENT: + description: Magnetic dipole moment of a material arising from electron spin and orbital contributions + FORMATION_ENERGY: + description: Energy required to form a compound from its constituent elements in their standard states + SURFACE_ENERGY: + description: Excess energy at the surface of a material relative to its bulk + DEFECT_ENERGY: + description: Energy associated with the formation or migration of point defects and dislocations + PHASE_STABILITY: + description: Thermodynamic stability of a material phase relative to competing phases + MECHANICAL_STRENGTH: + description: Maximum stress a material can withstand before failure under applied load + broad_mappings: + - PATO:0001230 + is_a: ComputationalMaterialsSchemaEnum + annotations: + source_domain: materials_science + source_schema: computational_materials + CrystalStructuresSchemaEnum: + description: Schema-level enum for crystal_structures in materials_science + is_a: MaterialsScienceDomainEnum + abstract: true + annotations: + source_file: materials_science/crystal_structures.yaml + CrystalSystemEnum: + title: Crystal System + description: The seven crystal systems in crystallography + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + conforms_to: https://en.wikipedia.org/wiki/Crystal_system + permissible_values: + TRICLINIC: + description: Crystal system with no symmetry constraints (a≠b≠c, α≠β≠γ≠90°) + title: Triclinic + meaning: ENM:9000022 + aliases: + - anorthic + MONOCLINIC: + description: Crystal system with one twofold axis of symmetry (a≠b≠c, α=γ=90°≠β) + title: Monoclinic + meaning: ENM:9000029 + ORTHORHOMBIC: + description: Crystal system with three mutually perpendicular axes (a≠b≠c, α=β=γ=90°) + title: Orthorhombic + meaning: ENM:9000031 + aliases: + - rhombic + TETRAGONAL: + description: Crystal system with one fourfold axis (a=b≠c, α=β=γ=90°) + title: Tetragonal + meaning: ENM:9000032 + TRIGONAL: + description: Crystal system with one threefold axis (a=b=c, α=β=γ≠90°) + title: Trigonal + meaning: ENM:9000054 + aliases: + - rhombohedral + HEXAGONAL: + description: Crystal system with one sixfold axis (a=b≠c, α=β=90°, γ=120°) + title: Hexagonal + meaning: PATO:0002509 + CUBIC: + description: Crystal system with four threefold axes (a=b=c, α=β=γ=90°) + title: Cubic + meaning: ENM:9000035 + aliases: + - isometric + is_a: CrystalStructuresSchemaEnum + annotations: + source_domain: materials_science + source_schema: crystal_structures + BravaisLatticeEnum: + title: Bravais Lattice + description: The 14 Bravais lattices describing all possible crystal lattices + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + conforms_to: https://en.wikipedia.org/wiki/Bravais_lattice + permissible_values: + PRIMITIVE_TRICLINIC: + description: Primitive triclinic lattice (aP) + title: Primitive Triclinic + aliases: + - aP + PRIMITIVE_MONOCLINIC: + description: Primitive monoclinic lattice (mP) + title: Primitive Monoclinic + aliases: + - mP + BASE_CENTERED_MONOCLINIC: + description: Base-centered monoclinic lattice (mC) + title: Base-Centered Monoclinic + aliases: + - mC + - mS + PRIMITIVE_ORTHORHOMBIC: + description: Primitive orthorhombic lattice (oP) + title: Primitive Orthorhombic + aliases: + - oP + BASE_CENTERED_ORTHORHOMBIC: + description: Base-centered orthorhombic lattice (oC) + title: Base-Centered Orthorhombic + aliases: + - oC + - oS + BODY_CENTERED_ORTHORHOMBIC: + description: Body-centered orthorhombic lattice (oI) + title: Body-Centered Orthorhombic + aliases: + - oI + FACE_CENTERED_ORTHORHOMBIC: + description: Face-centered orthorhombic lattice (oF) + title: Face-Centered Orthorhombic + aliases: + - oF + PRIMITIVE_TETRAGONAL: + description: Primitive tetragonal lattice (tP) + title: Primitive Tetragonal + aliases: + - tP + BODY_CENTERED_TETRAGONAL: + description: Body-centered tetragonal lattice (tI) + title: Body-Centered Tetragonal + aliases: + - tI + PRIMITIVE_TRIGONAL: + description: Primitive trigonal/rhombohedral lattice (hR) + title: Primitive Trigonal + aliases: + - hR + PRIMITIVE_HEXAGONAL: + description: Primitive hexagonal lattice (hP) + title: Primitive Hexagonal + aliases: + - hP + PRIMITIVE_CUBIC: + description: Simple cubic lattice (cP) + title: Primitive Cubic + aliases: + - cP + - SC + BODY_CENTERED_CUBIC: + description: Body-centered cubic lattice (cI) + title: Body-Centered Cubic + aliases: + - cI + - BCC + FACE_CENTERED_CUBIC: + description: Face-centered cubic lattice (cF) + title: Face-Centered Cubic + aliases: + - cF + - FCC + is_a: CrystalStructuresSchemaEnum + annotations: + source_domain: materials_science + source_schema: crystal_structures + MaterialPropertiesSchemaEnum: + description: Schema-level enum for material_properties in materials_science + is_a: MaterialsScienceDomainEnum + abstract: true + annotations: + source_file: materials_science/material_properties.yaml + ElectricalConductivityEnum: + title: Electrical Conductivity + description: Classification of materials by electrical conductivity + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CONDUCTOR: + description: Material with high electrical conductivity (resistivity < 10^-5 Ω·m) + title: Conductor + aliases: + - metal + SEMICONDUCTOR: + description: Material with intermediate electrical conductivity (10^-5 to 10^8 Ω·m) + title: Semiconductor + meaning: NCIT:C172788 + aliases: + - semi + INSULATOR: + description: Material with very low electrical conductivity (resistivity > 10^8 Ω·m) + title: Insulator + aliases: + - dielectric + SUPERCONDUCTOR: + description: Material with zero electrical resistance below critical temperature + title: Superconductor + is_a: MaterialPropertiesSchemaEnum + annotations: + source_domain: materials_science + source_schema: material_properties + MagneticPropertyEnum: + title: Magnetic Property + description: Classification of materials by magnetic properties + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + DIAMAGNETIC: + description: Weakly repelled by magnetic fields + title: Diamagnetic + PARAMAGNETIC: + description: Weakly attracted to magnetic fields + title: Paramagnetic + FERROMAGNETIC: + description: Strongly attracted to magnetic fields, can be permanently magnetized + title: Ferromagnetic + FERRIMAGNETIC: + description: Similar to ferromagnetic but with opposing magnetic moments + title: Ferrimagnetic + ANTIFERROMAGNETIC: + description: Adjacent magnetic moments cancel each other + title: Antiferromagnetic + is_a: MaterialPropertiesSchemaEnum + annotations: + source_domain: materials_science + source_schema: material_properties + OpticalPropertyEnum: + title: Optical Property + description: Optical properties of materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TRANSPARENT: + description: Allows light to pass through with minimal scattering + title: Transparent + meaning: PATO:0000964 + TRANSLUCENT: + description: Allows light to pass through but with significant scattering + title: Translucent + OPAQUE: + description: Does not allow light to pass through + title: Opaque + meaning: PATO:0000963 + REFLECTIVE: + description: Reflects most incident light + title: Reflective + ABSORBING: + description: Absorbs most incident light + title: Absorbing + FLUORESCENT: + description: Emits light when excited by radiation + title: Fluorescent + PHOSPHORESCENT: + description: Continues to emit light after excitation stops + title: Phosphorescent + is_a: MaterialPropertiesSchemaEnum + annotations: + source_domain: materials_science + source_schema: material_properties + ThermalConductivityEnum: + title: Thermal Conductivity + description: Classification by thermal conductivity + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - TRICLINIC: - description: Crystal system with no symmetry constraints (a≠b≠c, α≠β≠γ≠90°) - title: Triclinic - meaning: ENM:9000022 - aliases: - - anorthic - MONOCLINIC: - description: Crystal system with one twofold axis of symmetry (a≠b≠c, α=γ=90°≠β) - title: Monoclinic - meaning: ENM:9000029 - ORTHORHOMBIC: - description: Crystal system with three mutually perpendicular axes (a≠b≠c, α=β=γ=90°) - title: Orthorhombic - meaning: ENM:9000031 - aliases: - - rhombic - TETRAGONAL: - description: Crystal system with one fourfold axis (a=b≠c, α=β=γ=90°) - title: Tetragonal - meaning: ENM:9000032 - TRIGONAL: - description: Crystal system with one threefold axis (a=b=c, α=β=γ≠90°) - title: Trigonal - meaning: ENM:9000054 + HIGH_THERMAL_CONDUCTOR: + description: High thermal conductivity (>100 W/m·K) + title: High Thermal Conductor aliases: - - rhombohedral - HEXAGONAL: - description: Crystal system with one sixfold axis (a=b≠c, α=β=90°, γ=120°) - title: Hexagonal - meaning: PATO:0002509 - CUBIC: - description: Crystal system with four threefold axes (a=b=c, α=β=γ=90°) - title: Cubic - meaning: ENM:9000035 + - thermal conductor + MODERATE_THERMAL_CONDUCTOR: + description: Moderate thermal conductivity (1-100 W/m·K) + title: Moderate Thermal Conductor + THERMAL_INSULATOR: + description: Low thermal conductivity (<1 W/m·K) + title: Thermal Insulator aliases: - - isometric - is_a: CrystalStructuresSchemaEnum + - thermal barrier + is_a: MaterialPropertiesSchemaEnum annotations: source_domain: materials_science - source_schema: crystal_structures - BravaisLatticeEnum: - description: The 14 Bravais lattices describing all possible crystal lattices - conforms_to: https://en.wikipedia.org/wiki/Bravais_lattice + source_schema: material_properties + MechanicalBehaviorEnum: + title: Mechanical Behavior + description: Mechanical behavior of materials under stress + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - PRIMITIVE_TRICLINIC: - description: Primitive triclinic lattice (aP) - title: Primitive Triclinic - aliases: - - aP - PRIMITIVE_MONOCLINIC: - description: Primitive monoclinic lattice (mP) - title: Primitive Monoclinic - aliases: - - mP - BASE_CENTERED_MONOCLINIC: - description: Base-centered monoclinic lattice (mC) - title: Base-Centered Monoclinic - aliases: - - mC - - mS - PRIMITIVE_ORTHORHOMBIC: - description: Primitive orthorhombic lattice (oP) - title: Primitive Orthorhombic + ELASTIC: + description: Returns to original shape after stress removal + title: Elastic + meaning: PATO:0001171 + PLASTIC: + description: Undergoes permanent deformation under stress + title: inelastic + meaning: PATO:0001172 + BRITTLE: + description: Breaks without significant plastic deformation + title: Brittle + meaning: PATO:0002477 + DUCTILE: + description: Can be drawn into wires, undergoes large plastic deformation + title: Ductile + MALLEABLE: + description: Can be hammered into sheets + title: Malleable + TOUGH: + description: High resistance to fracture + title: Tough + VISCOELASTIC: + description: Exhibits both viscous and elastic characteristics + title: Viscoelastic + is_a: MaterialPropertiesSchemaEnum + annotations: + source_domain: materials_science + source_schema: material_properties + MaterialClassEnum: + title: Material Class + description: Major classes of materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + METAL: + description: Metallic materials with metallic bonding + title: metallic material + meaning: ENVO:01001069 aliases: - - oP - BASE_CENTERED_ORTHORHOMBIC: - description: Base-centered orthorhombic lattice (oC) - title: Base-Centered Orthorhombic + - Metal + - METAL + CERAMIC: + description: Inorganic non-metallic materials + title: Ceramic + meaning: ENVO:03501307 + POLYMER: + description: Large molecules composed of repeating units + title: Polymer + meaning: CHEBI:60027 + COMPOSITE: + description: Materials made from two or more constituent materials + title: Composite + meaning: NCIT:C61520 + SEMICONDUCTOR: + description: Materials with electrical conductivity between conductors and insulators + title: Semiconductor + meaning: NCIT:C172788 + BIOMATERIAL: + description: Materials designed to interact with biological systems + title: Biomedical Material + meaning: NCIT:C16338 aliases: - - oC - - oS - BODY_CENTERED_ORTHORHOMBIC: - description: Body-centered orthorhombic lattice (oI) - title: Body-Centered Orthorhombic + - Biomaterial + - BIOMATERIAL + NANOMATERIAL: + description: Materials with at least one dimension in nanoscale (1-100 nm) + title: Nanomaterial + meaning: NCIT:C62371 + is_a: MaterialTypesSchemaEnum + annotations: + source_domain: materials_science + source_schema: material_types + PolymerTypeEnum: + title: Polymer Type + description: Types of polymer materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + THERMOPLASTIC: + description: Polymer that becomes moldable above specific temperature + title: Thermoplastic + meaning: PATO:0040070 + THERMOSET: + description: Polymer that irreversibly hardens when cured + title: thermoset polymer + meaning: ENVO:06105005 aliases: - - oI - FACE_CENTERED_ORTHORHOMBIC: - description: Face-centered orthorhombic lattice (oF) - title: Face-Centered Orthorhombic + - thermosetting polymer + - Thermoset + - THERMOSET + ELASTOMER: + description: Polymer with elastic properties + title: Elastomer + meaning: SNOMED:261777007 aliases: - - oF - PRIMITIVE_TETRAGONAL: - description: Primitive tetragonal lattice (tP) - title: Primitive Tetragonal + - rubber + BIOPOLYMER: + description: Polymer produced by living organisms + title: Biopolymer + meaning: NCIT:C73478 + CONDUCTING_POLYMER: + description: Polymer that conducts electricity + title: Conducting Polymer aliases: - - tP - BODY_CENTERED_TETRAGONAL: - description: Body-centered tetragonal lattice (tI) - title: Body-Centered Tetragonal + - conducting polymer + is_a: MaterialTypesSchemaEnum + annotations: + source_domain: materials_science + source_schema: material_types + MetalTypeEnum: + title: Metal Type + description: Types of metallic materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FERROUS: + description: Iron-based metals and alloys + title: Ferrous Metal + meaning: SNOMED:264354006 aliases: - - tI - PRIMITIVE_TRIGONAL: - description: Primitive trigonal/rhombohedral lattice (hR) - title: Primitive Trigonal + - iron-based + NON_FERROUS: + description: Metals and alloys not containing iron + title: Non-Ferrous Metal + meaning: SNOMED:264879001 + NOBLE_METAL: + description: Metals resistant to corrosion and oxidation + title: Noble Metal + REFRACTORY_METAL: + description: Metals with very high melting points (>2000°C) + title: Refractory Metal + LIGHT_METAL: + description: Low density metals (density < 5 g/cm³) + title: Light Metal + meaning: SNOMED:65436002 + HEAVY_METAL: + description: High density metals (density > 5 g/cm³) + title: Heavy Metal + meaning: CHEBI:5631 + is_a: MaterialTypesSchemaEnum + annotations: + source_domain: materials_science + source_schema: material_types + CompositeTypeEnum: + title: Composite Type + description: Types of composite materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FIBER_REINFORCED: + description: Composite with fiber reinforcement + title: Fiber-Reinforced Composite aliases: - - hR - PRIMITIVE_HEXAGONAL: - description: Primitive hexagonal lattice (hP) - title: Primitive Hexagonal + - FRC + PARTICLE_REINFORCED: + description: Composite with particle reinforcement + title: Particle-Reinforced Composite + LAMINAR_COMPOSITE: + description: Composite with layered structure + title: Laminar Composite aliases: - - hP - PRIMITIVE_CUBIC: - description: Simple cubic lattice (cP) - title: Primitive Cubic + - laminate + METAL_MATRIX_COMPOSITE: + description: Composite with metal matrix + title: Metal Matrix Composite aliases: - - cP - - SC - BODY_CENTERED_CUBIC: - description: Body-centered cubic lattice (cI) - title: Body-Centered Cubic + - MMC + CERAMIC_MATRIX_COMPOSITE: + description: Composite with ceramic matrix + title: Ceramic Matrix Composite aliases: - - cI - - BCC - FACE_CENTERED_CUBIC: - description: Face-centered cubic lattice (cF) - title: Face-Centered Cubic + - CMC + POLYMER_MATRIX_COMPOSITE: + description: Composite with polymer matrix + title: Polymer Matrix Composite aliases: - - cF - - FCC - is_a: CrystalStructuresSchemaEnum + - PMC + is_a: MaterialTypesSchemaEnum annotations: source_domain: materials_science - source_schema: crystal_structures - MaterialPropertiesSchemaEnum: - description: Schema-level enum for material_properties in materials_science + source_schema: material_types + PigmentsDyesSchemaEnum: + description: Schema-level enum for pigments_dyes in materials_science is_a: MaterialsScienceDomainEnum abstract: true annotations: - source_file: materials_science/material_properties.yaml - ElectricalConductivityEnum: - description: Classification of materials by electrical conductivity - permissible_values: - CONDUCTOR: - description: Material with high electrical conductivity (resistivity < 10^-5 Ω·m) - title: Conductor - aliases: - - metal - SEMICONDUCTOR: - description: Material with intermediate electrical conductivity (10^-5 to 10^8 Ω·m) - title: Semiconductor - meaning: NCIT:C172788 - aliases: - - semi - INSULATOR: - description: Material with very low electrical conductivity (resistivity > 10^8 Ω·m) - title: Insulator - aliases: - - dielectric - SUPERCONDUCTOR: - description: Material with zero electrical resistance below critical temperature - title: Superconductor - is_a: MaterialPropertiesSchemaEnum - annotations: - source_domain: materials_science - source_schema: material_properties - MagneticPropertyEnum: - description: Classification of materials by magnetic properties + source_file: materials_science/pigments_dyes.yaml + TraditionalPigmentEnum: + title: Traditional Pigment + description: Traditional artist pigments and their colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - DIAMAGNETIC: - description: Weakly repelled by magnetic fields - title: Diamagnetic - PARAMAGNETIC: - description: Weakly attracted to magnetic fields - title: Paramagnetic - FERROMAGNETIC: - description: Strongly attracted to magnetic fields, can be permanently magnetized - title: Ferromagnetic - FERRIMAGNETIC: - description: Similar to ferromagnetic but with opposing magnetic moments - title: Ferrimagnetic - ANTIFERROMAGNETIC: - description: Adjacent magnetic moments cancel each other - title: Antiferromagnetic - is_a: MaterialPropertiesSchemaEnum + TITANIUM_WHITE: + title: titanium dioxide nanoparticle + description: Titanium white (Titanium dioxide) + meaning: CHEBI:51050 + annotations: + hex: FFFFFF + chemical: TiO2 + discovered: '1916' + ZINC_WHITE: + title: zinc oxide + description: Zinc white (Zinc oxide) + meaning: CHEBI:36560 + annotations: + hex: FEFEFE + chemical: ZnO + LEAD_WHITE: + description: Lead white (Basic lead carbonate) - toxic + annotations: + hex: F8F8F8 + chemical: 2PbCO3·Pb(OH)2 + warning: highly toxic, historical use + CADMIUM_YELLOW: + title: cadmium selenide + description: Cadmium yellow (Cadmium sulfide) + meaning: CHEBI:50834 + annotations: + hex: FFF600 + chemical: CdS + warning: toxic + CHROME_YELLOW: + description: Chrome yellow (Lead chromate) - toxic + annotations: + hex: FFC200 + chemical: PbCrO4 + warning: highly toxic + NAPLES_YELLOW: + description: Naples yellow (Lead antimonate) + annotations: + hex: FDD5B1 + chemical: Pb(SbO3)2 + historical: ancient pigment + YELLOW_OCHRE: + description: Yellow ochre (Iron oxide hydroxide) + annotations: + hex: CC7722 + chemical: FeO(OH)·nH2O + natural: earth pigment + CADMIUM_ORANGE: + description: Cadmium orange (Cadmium selenide) + annotations: + hex: FF6600 + chemical: CdS·CdSe + warning: toxic + CADMIUM_RED: + title: cadmium selenide nanoparticle + description: Cadmium red (Cadmium selenide) + meaning: CHEBI:50835 + annotations: + hex: E30022 + chemical: CdSe + warning: toxic + VERMILION: + description: Vermilion/Cinnabar (Mercury sulfide) + annotations: + hex: E34234 + chemical: HgS + warning: highly toxic + ALIZARIN_CRIMSON: + title: alizarin + description: Alizarin crimson (synthetic) + meaning: CHEBI:16866 + annotations: + hex: E32636 + chemical: C14H8O4 + organic: synthetic organic + CARMINE: + description: Carmine (from cochineal insects) + annotations: + hex: '960018' + source: cochineal insects + natural: organic pigment + BURNT_SIENNA: + description: Burnt sienna (heated iron oxide) + annotations: + hex: E97451 + chemical: Fe2O3 + process: calcined raw sienna + RAW_SIENNA: + description: Raw sienna (Iron oxide with clay) + annotations: + hex: C69D52 + chemical: Fe2O3 with clay + natural: earth pigment + BURNT_UMBER: + description: Burnt umber (heated iron/manganese oxide) + annotations: + hex: 8B4513 + chemical: Fe2O3 + MnO2 + process: calcined raw umber + RAW_UMBER: + description: Raw umber (Iron/manganese oxide) + annotations: + hex: 734A12 + chemical: Fe2O3 + MnO2 + natural: earth pigment + VAN_DYKE_BROWN: + description: Van Dyke brown (organic earth) + annotations: + hex: '664228' + source: peat, lignite + warning: fugitive color + PRUSSIAN_BLUE: + title: ferric ferrocyanide + description: Prussian blue (Ferric ferrocyanide) + meaning: CHEBI:30069 + annotations: + hex: '003153' + chemical: Fe4[Fe(CN)6]3 + discovered: '1706' + ULTRAMARINE: + description: Ultramarine blue (originally lapis lazuli) + annotations: + hex: 120A8F + chemical: Na8[Al6Si6O24]Sn + historical: most expensive pigment + COBALT_BLUE: + description: Cobalt blue (Cobalt aluminate) + annotations: + hex: 0047AB + chemical: CoAl2O4 + CERULEAN_BLUE: + description: Cerulean blue (Cobalt stannate) + annotations: + hex: 2A52BE + chemical: Co2SnO4 + PHTHALO_BLUE: + description: Phthalocyanine blue + annotations: + hex: 000F89 + chemical: C32H16CuN8 + modern: synthetic organic + VIRIDIAN: + description: Viridian (Chromium oxide green) + annotations: + hex: 40826D + chemical: Cr2O3·2H2O + CHROME_GREEN: + description: Chrome oxide green + annotations: + hex: 2E5E26 + chemical: Cr2O3 + PHTHALO_GREEN: + description: Phthalocyanine green + annotations: + hex: '123524' + chemical: C32H16ClCuN8 + modern: synthetic organic + TERRE_VERTE: + description: Terre verte/Green earth + annotations: + hex: 6B7F59 + chemical: complex silicate + natural: earth pigment + TYRIAN_PURPLE: + description: Tyrian purple (from murex snails) + annotations: + hex: 66023C + source: murex snails + historical: ancient royal purple + MANGANESE_VIOLET: + description: Manganese violet + annotations: + hex: 8B3E5F + chemical: NH4MnP2O7 + MARS_BLACK: + description: Mars black (Synthetic iron oxide) + annotations: + hex: '010101' + chemical: Fe3O4 + synthetic: iron oxide + IVORY_BLACK: + description: Ivory black (Bone char) + annotations: + hex: 1B1B1B + source: charred bones + LAMP_BLACK: + description: Lamp black (Carbon black) + annotations: + hex: 2B2B2B + chemical: C + source: soot + is_a: PigmentsDyesSchemaEnum annotations: source_domain: materials_science - source_schema: material_properties - OpticalPropertyEnum: - description: Optical properties of materials + source_schema: pigments_dyes + IndustrialDyeEnum: + title: Industrial Dye + description: Industrial and textile dyes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - TRANSPARENT: - description: Allows light to pass through with minimal scattering - title: Transparent - meaning: PATO:0000964 - TRANSLUCENT: - description: Allows light to pass through but with significant scattering - title: Translucent - OPAQUE: - description: Does not allow light to pass through - title: Opaque - meaning: PATO:0000963 - REFLECTIVE: - description: Reflects most incident light - title: Reflective - ABSORBING: - description: Absorbs most incident light - title: Absorbing - FLUORESCENT: - description: Emits light when excited by radiation - title: Fluorescent - PHOSPHORESCENT: - description: Continues to emit light after excitation stops - title: Phosphorescent - is_a: MaterialPropertiesSchemaEnum + INDIGO: + description: Indigo dye + annotations: + hex: 4B0082 + source: originally plant-based, now synthetic + use: denim, textiles + ANILINE_BLACK: + description: Aniline black + annotations: + hex: '000000' + chemical: polyaniline + use: cotton dyeing + METHYLENE_BLUE: + description: Methylene blue + annotations: + hex: 1E90FF + chemical: C16H18ClN3S + use: biological stain, medical + CONGO_RED: + description: Congo red + meaning: CHEBI:34653 + annotations: + hex: CC0000 + chemical: C32H22N6Na2O6S2 + use: pH indicator, textile + MALACHITE_GREEN: + description: Malachite green + meaning: CHEBI:72449 + annotations: + hex: 0BDA51 + chemical: C23H25ClN2 + use: biological stain + CRYSTAL_VIOLET: + description: Crystal violet/Gentian violet + meaning: CHEBI:41688 + annotations: + hex: 9400D3 + chemical: C25H30ClN3 + use: gram staining + EOSIN: + description: Eosin Y + meaning: CHEBI:52053 + aliases: + - eosin YS dye + annotations: + hex: FF6B6B + chemical: C20H6Br4Na2O5 + use: histology stain + SAFRANIN: + description: Safranin O + annotations: + hex: FF0066 + chemical: C20H19ClN4 + use: biological stain + ACID_ORANGE_7: + description: Acid Orange 7 (Orange II) + annotations: + hex: FF7F00 + chemical: C16H11N2NaO4S + use: wool, silk dyeing + REACTIVE_BLACK_5: + description: Reactive Black 5 + annotations: + hex: '000000' + use: cotton reactive dye + DISPERSE_BLUE_1: + description: Disperse Blue 1 + annotations: + hex: 1560BD + use: polyester dyeing + VAT_BLUE_1: + description: Vat Blue 1 (Indanthrene blue) + annotations: + hex: 002F5C + use: cotton vat dyeing + is_a: PigmentsDyesSchemaEnum annotations: source_domain: materials_science - source_schema: material_properties - ThermalConductivityEnum: - description: Classification by thermal conductivity + source_schema: pigments_dyes + FoodColoringEnum: + title: Food Coloring + description: Food coloring and natural food dyes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - HIGH_THERMAL_CONDUCTOR: - description: High thermal conductivity (>100 W/m·K) - title: High Thermal Conductor + FD_C_RED_40: + description: FD&C Red No. 40 (Allura Red) + annotations: + hex: E40000 + E_number: E129 + use: beverages, candies + FD_C_YELLOW_5: + description: FD&C Yellow No. 5 (Tartrazine) + annotations: + hex: FFFF00 + E_number: E102 + use: beverages, desserts + FD_C_YELLOW_6: + description: FD&C Yellow No. 6 (Sunset Yellow) + annotations: + hex: FFA500 + E_number: E110 + use: snacks, beverages + FD_C_BLUE_1: + title: Brilliant Blue + description: FD&C Blue No. 1 (Brilliant Blue) + meaning: CHEBI:82411 + annotations: + hex: 0033FF + E_number: E133 + use: beverages, candies + FD_C_BLUE_2: + description: FD&C Blue No. 2 (Indigo Carmine) + annotations: + hex: 4B0082 + E_number: E132 + use: beverages, confections + FD_C_GREEN_3: + description: FD&C Green No. 3 (Fast Green) + annotations: + hex: 00FF00 + E_number: E143 + use: beverages, desserts + CARAMEL_COLOR: + description: Caramel coloring + annotations: + hex: 8B4513 + E_number: E150 + use: cola, sauces + ANNATTO: + description: Annatto (natural orange) + meaning: CHEBI:3136 aliases: - - thermal conductor - MODERATE_THERMAL_CONDUCTOR: - description: Moderate thermal conductivity (1-100 W/m·K) - title: Moderate Thermal Conductor - THERMAL_INSULATOR: - description: Low thermal conductivity (<1 W/m·K) - title: Thermal Insulator + - bixin + annotations: + hex: FF6600 + E_number: E160b + source: achiote seeds + TURMERIC: + title: curcumin + description: Turmeric/Curcumin (natural yellow) + meaning: CHEBI:3962 + annotations: + hex: F0E442 + E_number: E100 + source: turmeric root + BEETROOT_RED: + description: Beetroot red/Betanin + meaning: CHEBI:3080 aliases: - - thermal barrier - is_a: MaterialPropertiesSchemaEnum - annotations: - source_domain: materials_science - source_schema: material_properties - MechanicalBehaviorEnum: - description: Mechanical behavior of materials under stress - permissible_values: - ELASTIC: - description: Returns to original shape after stress removal - title: Elastic - meaning: PATO:0001171 - PLASTIC: - description: Undergoes permanent deformation under stress - title: inelastic - meaning: PATO:0001172 - BRITTLE: - description: Breaks without significant plastic deformation - title: Brittle - meaning: PATO:0002477 - DUCTILE: - description: Can be drawn into wires, undergoes large plastic deformation - title: Ductile - MALLEABLE: - description: Can be hammered into sheets - title: Malleable - TOUGH: - description: High resistance to fracture - title: Tough - VISCOELASTIC: - description: Exhibits both viscous and elastic characteristics - title: Viscoelastic - is_a: MaterialPropertiesSchemaEnum + - Betanin + annotations: + hex: BC2A4D + E_number: E162 + source: beets + CHLOROPHYLL: + description: Chlorophyll (natural green) + meaning: CHEBI:28966 + annotations: + hex: 4D7C0F + E_number: E140 + source: plants + ANTHOCYANINS: + description: Anthocyanins (natural purple/red) + annotations: + hex: 6B3AA0 + E_number: E163 + source: berries, grapes + PAPRIKA_EXTRACT: + description: Paprika extract + annotations: + hex: E85D00 + E_number: E160c + source: paprika peppers + SPIRULINA_BLUE: + description: Spirulina extract (phycocyanin) + annotations: + hex: 1E88E5 + source: spirulina algae + natural: 'true' + is_a: PigmentsDyesSchemaEnum annotations: source_domain: materials_science - source_schema: material_properties - MaterialTypesSchemaEnum: - description: Schema-level enum for material_types in materials_science + source_schema: pigments_dyes + AutomobilePaintColorEnum: + title: Automobile Paint Color + description: Common automobile paint colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ARCTIC_WHITE: + description: Arctic White + meaning: HEX:FFFFFF + annotations: + type: solid + MIDNIGHT_BLACK: + description: Midnight Black + meaning: HEX:000000 + annotations: + type: metallic + SILVER_METALLIC: + description: Silver Metallic + meaning: HEX:C0C0C0 + annotations: + type: metallic + GUNMETAL_GRAY: + description: Gunmetal Gray + meaning: HEX:2A3439 + annotations: + type: metallic + RACING_RED: + description: Racing Red + meaning: HEX:CE1620 + annotations: + type: solid + CANDY_APPLE_RED: + description: Candy Apple Red + meaning: HEX:FF0800 + annotations: + type: metallic + ELECTRIC_BLUE: + description: Electric Blue + meaning: HEX:7DF9FF + annotations: + type: metallic + BRITISH_RACING_GREEN: + description: British Racing Green + meaning: HEX:004225 + annotations: + type: solid + historical: British racing color + PEARL_WHITE: + description: Pearl White + meaning: HEX:F8F8FF + annotations: + type: pearl + finish: pearlescent + CHAMPAGNE_GOLD: + description: Champagne Gold + meaning: HEX:D4AF37 + annotations: + type: metallic + COPPER_BRONZE: + description: Copper Bronze + meaning: HEX:B87333 + annotations: + type: metallic + MIAMI_BLUE: + description: Miami Blue + meaning: HEX:00BFFF + annotations: + type: metallic + brand: Porsche + is_a: PigmentsDyesSchemaEnum + annotations: + source_domain: materials_science + source_schema: pigments_dyes + SynthesisMethodsSchemaEnum: + description: Schema-level enum for synthesis_methods in materials_science is_a: MaterialsScienceDomainEnum abstract: true annotations: - source_file: materials_science/material_types.yaml - MaterialClassEnum: - description: Major classes of materials + source_file: materials_science/synthesis_methods.yaml + SynthesisMethodEnum: + title: Synthesis Method + description: Common material synthesis and processing methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - METAL: - description: Metallic materials with metallic bonding - title: metallic material - meaning: ENVO:01001069 + SOL_GEL: + description: Synthesis from solution through gel formation + title: Sol-Gel aliases: - - Metal - - METAL - CERAMIC: - description: Inorganic non-metallic materials - title: Ceramic - meaning: ENVO:03501307 - POLYMER: - description: Large molecules composed of repeating units - title: Polymer - meaning: CHEBI:60027 - COMPOSITE: - description: Materials made from two or more constituent materials - title: Composite - meaning: NCIT:C61520 - SEMICONDUCTOR: - description: Materials with electrical conductivity between conductors and insulators - title: Semiconductor - meaning: NCIT:C172788 - BIOMATERIAL: - description: Materials designed to interact with biological systems - title: Biomedical Material - meaning: NCIT:C16338 + - sol-gel process + HYDROTHERMAL: + description: Synthesis using high temperature aqueous solutions + title: Hydrothermal aliases: - - Biomaterial - - BIOMATERIAL - NANOMATERIAL: - description: Materials with at least one dimension in nanoscale (1-100 nm) - title: Nanomaterial - meaning: NCIT:C62371 - is_a: MaterialTypesSchemaEnum + - hydrothermal synthesis + SOLVOTHERMAL: + description: Synthesis using non-aqueous solvents at high temperature/pressure + title: Solvothermal + CVD: + description: Chemical Vapor Deposition + title: chemical vapour deposition + meaning: CHMO:0001314 + aliases: + - Chemical Vapor Deposition + - CVD + PVD: + description: Physical Vapor Deposition + title: physical vapour deposition + meaning: CHMO:0001356 + aliases: + - Physical Vapor Deposition + - PVD + ALD: + description: Atomic Layer Deposition + title: ALD + aliases: + - Atomic Layer Deposition + ELECTRODEPOSITION: + description: Deposition using electric current + title: electrochemical deposition + meaning: CHMO:0001331 + aliases: + - electroplating + - Electrodeposition + - ELECTRODEPOSITION + BALL_MILLING: + description: Mechanical alloying using ball mill + title: Ball Milling + aliases: + - mechanical alloying + PRECIPITATION: + description: Formation of solid from solution + title: precipitation + meaning: CHMO:0001688 + aliases: + - Precipitation + - PRECIPITATION + SINTERING: + description: Compacting and forming solid mass by heat/pressure + title: Sintering + MELT_PROCESSING: + description: Processing from molten state + title: Melt Processing + aliases: + - melt casting + SOLUTION_CASTING: + description: Casting from solution + title: Solution Casting + SPIN_COATING: + description: Coating by spinning substrate + title: Spin Coating + meaning: CHMO:0001472 + DIP_COATING: + description: Coating by dipping in solution + title: Dip Coating + meaning: CHMO:0001471 + SPRAY_COATING: + description: Coating by spraying + title: Spray Coating + is_a: SynthesisMethodsSchemaEnum annotations: source_domain: materials_science - source_schema: material_types - PolymerTypeEnum: - description: Types of polymer materials + source_schema: synthesis_methods + CrystalGrowthMethodEnum: + title: Crystal Growth Method + description: Methods for growing single crystals + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - THERMOPLASTIC: - description: Polymer that becomes moldable above specific temperature - title: Thermoplastic - meaning: PATO:0040070 - THERMOSET: - description: Polymer that irreversibly hardens when cured - title: thermoset polymer - meaning: ENVO:06105005 + CZOCHRALSKI: + description: Crystal pulling from melt + title: Czochralski Method aliases: - - thermosetting polymer - - Thermoset - - THERMOSET - ELASTOMER: - description: Polymer with elastic properties - title: Elastomer - meaning: SNOMED:261777007 + - CZ + - crystal pulling + BRIDGMAN: + description: Directional solidification method + title: Bridgman Method + aliases: + - Bridgman-Stockbarger + FLOAT_ZONE: + description: Zone melting without crucible + title: Float Zone + aliases: + - FZ + - zone refining + FLUX_GROWTH: + description: Crystal growth from high temperature solution + title: Flux Growth + VAPOR_TRANSPORT: + description: Crystal growth via vapor phase transport + title: Vapor Transport + aliases: + - CVT + HYDROTHERMAL_GROWTH: + description: Crystal growth in aqueous solution under pressure + title: Hydrothermal Growth + LPE: + description: Liquid Phase Epitaxy + title: LPE + aliases: + - Liquid Phase Epitaxy + MBE: + description: Molecular Beam Epitaxy + title: molecular beam epitaxy + meaning: CHMO:0001341 aliases: - - rubber - BIOPOLYMER: - description: Polymer produced by living organisms - title: Biopolymer - meaning: NCIT:C73478 - CONDUCTING_POLYMER: - description: Polymer that conducts electricity - title: Conducting Polymer + - Molecular Beam Epitaxy + - MBE + MOCVD: + description: Metal-Organic Chemical Vapor Deposition + title: MOCVD aliases: - - conducting polymer - is_a: MaterialTypesSchemaEnum + - MOVPE + is_a: SynthesisMethodsSchemaEnum annotations: source_domain: materials_science - source_schema: material_types - MetalTypeEnum: - description: Types of metallic materials + source_schema: synthesis_methods + AdditiveManufacturingEnum: + title: Additive Manufacturing + description: 3D printing and additive manufacturing methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - FERROUS: - description: Iron-based metals and alloys - title: Ferrous Metal - meaning: SNOMED:264354006 + FDM: + description: Fused Deposition Modeling + title: FDM aliases: - - iron-based - NON_FERROUS: - description: Metals and alloys not containing iron - title: Non-Ferrous Metal - meaning: SNOMED:264879001 - NOBLE_METAL: - description: Metals resistant to corrosion and oxidation - title: Noble Metal - REFRACTORY_METAL: - description: Metals with very high melting points (>2000°C) - title: Refractory Metal - LIGHT_METAL: - description: Low density metals (density < 5 g/cm³) - title: Light Metal - meaning: SNOMED:65436002 - HEAVY_METAL: - description: High density metals (density > 5 g/cm³) - title: Heavy Metal - meaning: CHEBI:5631 - is_a: MaterialTypesSchemaEnum - annotations: - source_domain: materials_science - source_schema: material_types - CompositeTypeEnum: - description: Types of composite materials - permissible_values: - FIBER_REINFORCED: - description: Composite with fiber reinforcement - title: Fiber-Reinforced Composite + - FFF + - Fused Filament Fabrication + SLA: + description: Stereolithography + title: SLA aliases: - - FRC - PARTICLE_REINFORCED: - description: Composite with particle reinforcement - title: Particle-Reinforced Composite - LAMINAR_COMPOSITE: - description: Composite with layered structure - title: Laminar Composite + - Stereolithography + SLS: + description: Selective Laser Sintering + title: SLS aliases: - - laminate - METAL_MATRIX_COMPOSITE: - description: Composite with metal matrix - title: Metal Matrix Composite + - Selective Laser Sintering + SLM: + description: Selective Laser Melting + title: SLM aliases: - - MMC - CERAMIC_MATRIX_COMPOSITE: - description: Composite with ceramic matrix - title: Ceramic Matrix Composite + - Selective Laser Melting + EBM: + description: Electron Beam Melting + title: EBM aliases: - - CMC - POLYMER_MATRIX_COMPOSITE: - description: Composite with polymer matrix - title: Polymer Matrix Composite + - Electron Beam Melting + BINDER_JETTING: + description: Powder bed with liquid binder + title: Binder Jetting + MATERIAL_JETTING: + description: Droplet deposition of materials + title: Material Jetting aliases: - - PMC - is_a: MaterialTypesSchemaEnum + - PolyJet + DED: + description: Directed Energy Deposition + title: DED + aliases: + - Directed Energy Deposition + is_a: SynthesisMethodsSchemaEnum annotations: source_domain: materials_science - source_schema: material_types - PigmentsDyesSchemaEnum: - description: Schema-level enum for pigments_dyes in materials_science - is_a: MaterialsScienceDomainEnum + source_schema: synthesis_methods + MedicalDomainEnum: + description: Domain-level enum for medical value sets + is_a: ValueSetEnum + abstract: true + ClinicalSchemaEnum: + description: Schema-level enum for clinical in medical + is_a: MedicalDomainEnum abstract: true annotations: - source_file: materials_science/pigments_dyes.yaml - TraditionalPigmentEnum: - description: Traditional artist pigments and their colors + source_file: medical/clinical.yaml + BloodTypeEnum: + title: Blood Type + description: ABO and Rh blood group classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - TITANIUM_WHITE: - title: titanium dioxide nanoparticle - description: Titanium white (Titanium dioxide) - meaning: CHEBI:51050 + A_POSITIVE: + description: Blood type A, Rh positive + meaning: SNOMED:278149003 annotations: - hex: FFFFFF - chemical: TiO2 - discovered: '1916' - ZINC_WHITE: - title: zinc oxide - description: Zinc white (Zinc oxide) - meaning: CHEBI:36560 + abo: A + rh: positive + can_receive: A+, A-, O+, O- + can_donate: A+, AB+ + A_NEGATIVE: + description: Blood type A, Rh negative + meaning: SNOMED:278152006 annotations: - hex: FEFEFE - chemical: ZnO - LEAD_WHITE: - description: Lead white (Basic lead carbonate) - toxic + abo: A + rh: negative + can_receive: A-, O- + can_donate: A+, A-, AB+, AB- + B_POSITIVE: + description: Blood type B, Rh positive + meaning: SNOMED:278150003 annotations: - hex: F8F8F8 - chemical: 2PbCO3·Pb(OH)2 - warning: highly toxic, historical use - CADMIUM_YELLOW: - title: cadmium selenide - description: Cadmium yellow (Cadmium sulfide) - meaning: CHEBI:50834 + abo: B + rh: positive + can_receive: B+, B-, O+, O- + can_donate: B+, AB+ + B_NEGATIVE: + description: Blood type B, Rh negative + meaning: SNOMED:278153001 annotations: - hex: FFF600 - chemical: CdS - warning: toxic - CHROME_YELLOW: - description: Chrome yellow (Lead chromate) - toxic + abo: B + rh: negative + can_receive: B-, O- + can_donate: B+, B-, AB+, AB- + AB_POSITIVE: + description: Blood type AB, Rh positive (universal recipient) + meaning: SNOMED:278151004 annotations: - hex: FFC200 - chemical: PbCrO4 - warning: highly toxic - NAPLES_YELLOW: - description: Naples yellow (Lead antimonate) + abo: AB + rh: positive + can_receive: all types + can_donate: AB+ + special: universal recipient + AB_NEGATIVE: + description: Blood type AB, Rh negative + meaning: SNOMED:278154007 annotations: - hex: FDD5B1 - chemical: Pb(SbO3)2 - historical: ancient pigment - YELLOW_OCHRE: - description: Yellow ochre (Iron oxide hydroxide) + abo: AB + rh: negative + can_receive: A-, B-, AB-, O- + can_donate: AB+, AB- + O_POSITIVE: + description: Blood type O, Rh positive + meaning: SNOMED:278147001 annotations: - hex: CC7722 - chemical: FeO(OH)·nH2O - natural: earth pigment - CADMIUM_ORANGE: - description: Cadmium orange (Cadmium selenide) + abo: O + rh: positive + can_receive: O+, O- + can_donate: A+, B+, AB+, O+ + O_NEGATIVE: + description: Blood type O, Rh negative (universal donor) + meaning: SNOMED:278148006 annotations: - hex: FF6600 - chemical: CdS·CdSe - warning: toxic - CADMIUM_RED: - title: cadmium selenide nanoparticle - description: Cadmium red (Cadmium selenide) - meaning: CHEBI:50835 + abo: O + rh: negative + can_receive: O- + can_donate: all types + special: universal donor + is_a: ClinicalSchemaEnum + annotations: + source_domain: medical + source_schema: clinical + AnatomicalSystemEnum: + title: Anatomical System + description: Major anatomical systems of the body + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CARDIOVASCULAR: + title: Heart and blood vessels + aliases: + - cardiovascular system + meaning: UBERON:0004535 + annotations: + components: heart, arteries, veins, capillaries + RESPIRATORY: + title: Lungs and airways + aliases: + - respiratory system + meaning: UBERON:0001004 annotations: - hex: E30022 - chemical: CdSe - warning: toxic - VERMILION: - description: Vermilion/Cinnabar (Mercury sulfide) + components: lungs, trachea, bronchi, diaphragm + NERVOUS: + title: Brain, spinal cord, and nerves + aliases: + - nervous system + meaning: UBERON:0001016 annotations: - hex: E34234 - chemical: HgS - warning: highly toxic - ALIZARIN_CRIMSON: - title: alizarin - description: Alizarin crimson (synthetic) - meaning: CHEBI:16866 + components: brain, spinal cord, nerves + DIGESTIVE: + title: GI tract and accessory organs + aliases: + - digestive system + meaning: UBERON:0001007 annotations: - hex: E32636 - chemical: C14H8O4 - organic: synthetic organic - CARMINE: - description: Carmine (from cochineal insects) + components: mouth, esophagus, stomach, intestines, liver, pancreas + MUSCULOSKELETAL: + title: Bones, muscles, and connective tissue + aliases: + - musculoskeletal system + meaning: UBERON:0002204 annotations: - hex: '960018' - source: cochineal insects - natural: organic pigment - BURNT_SIENNA: - description: Burnt sienna (heated iron oxide) + components: bones, muscles, tendons, ligaments, cartilage + INTEGUMENTARY: + title: Skin and related structures + aliases: + - integumental system + meaning: UBERON:0002416 annotations: - hex: E97451 - chemical: Fe2O3 - process: calcined raw sienna - RAW_SIENNA: - description: Raw sienna (Iron oxide with clay) + components: skin, hair, nails, glands + ENDOCRINE: + title: Hormone-producing glands + aliases: + - endocrine system + meaning: UBERON:0000949 annotations: - hex: C69D52 - chemical: Fe2O3 with clay - natural: earth pigment - BURNT_UMBER: - description: Burnt umber (heated iron/manganese oxide) + components: pituitary, thyroid, adrenals, pancreas + URINARY: + title: Kidneys and urinary tract + aliases: + - renal system + meaning: UBERON:0001008 annotations: - hex: 8B4513 - chemical: Fe2O3 + MnO2 - process: calcined raw umber - RAW_UMBER: - description: Raw umber (Iron/manganese oxide) + components: kidneys, ureters, bladder, urethra + REPRODUCTIVE: + title: Reproductive organs + aliases: + - reproductive system + meaning: UBERON:0000990 annotations: - hex: 734A12 - chemical: Fe2O3 + MnO2 - natural: earth pigment - VAN_DYKE_BROWN: - description: Van Dyke brown (organic earth) + components: gonads, ducts, external genitalia + IMMUNE: + title: Immune and lymphatic system + aliases: + - immune system + meaning: UBERON:0002405 annotations: - hex: '664228' - source: peat, lignite - warning: fugitive color - PRUSSIAN_BLUE: - title: ferric ferrocyanide - description: Prussian blue (Ferric ferrocyanide) - meaning: CHEBI:30069 + components: lymph nodes, spleen, thymus, bone marrow + HEMATOLOGIC: + title: Blood and blood-forming organs + aliases: + - hematopoietic system + meaning: UBERON:0002390 annotations: - hex: '003153' - chemical: Fe4[Fe(CN)6]3 - discovered: '1706' - ULTRAMARINE: - description: Ultramarine blue (originally lapis lazuli) + components: blood, bone marrow, spleen + is_a: ClinicalSchemaEnum + annotations: + source_domain: medical + source_schema: clinical + MedicalSpecialtyEnum: + title: Medical specialties and subspecialties + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ANESTHESIOLOGY: + title: Anesthesia and perioperative medicine + CARDIOLOGY: + title: Heart and cardiovascular diseases + DERMATOLOGY: + title: Skin diseases + EMERGENCY_MEDICINE: + title: Emergency and acute care + ENDOCRINOLOGY: + title: Hormonal and metabolic disorders + FAMILY_MEDICINE: + title: Primary care for all ages + GASTROENTEROLOGY: + title: Digestive system disorders + HEMATOLOGY: + title: Blood disorders + INFECTIOUS_DISEASE: + title: Infectious diseases + INTERNAL_MEDICINE: + title: Adult internal medicine + NEPHROLOGY: + title: Kidney diseases + NEUROLOGY: + title: Nervous system disorders + OBSTETRICS_GYNECOLOGY: + title: Women's health and childbirth + ONCOLOGY: + title: Cancer treatment + OPHTHALMOLOGY: + title: Eye diseases + ORTHOPEDICS: + title: Musculoskeletal disorders + OTOLARYNGOLOGY: + title: Ear, nose, and throat + PATHOLOGY: + title: Disease diagnosis through lab analysis + PEDIATRICS: + title: Children's health + PSYCHIATRY: + title: Mental health disorders + PULMONOLOGY: + title: Lung and respiratory diseases + RADIOLOGY: + title: Medical imaging + RHEUMATOLOGY: + title: Joint and autoimmune diseases + SURGERY: + title: Surgical procedures + UROLOGY: + title: Urinary and male reproductive system + is_a: ClinicalSchemaEnum + description: 'Enum: MedicalSpecialtyEnum' + annotations: + source_domain: medical + source_schema: clinical + DrugRouteEnum: + title: Routes of drug administration + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ORAL: + title: By mouth + aliases: + - Oral Route of Administration + meaning: NCIT:C38288 annotations: - hex: 120A8F - chemical: Na8[Al6Si6O24]Sn - historical: most expensive pigment - COBALT_BLUE: - description: Cobalt blue (Cobalt aluminate) + abbreviation: PO + absorption: GI tract + INTRAVENOUS: + title: Into a vein + aliases: + - Intravenous Route of Administration + meaning: NCIT:C38276 annotations: - hex: 0047AB - chemical: CoAl2O4 - CERULEAN_BLUE: - description: Cerulean blue (Cobalt stannate) + abbreviation: IV + onset: immediate + INTRAMUSCULAR: + title: Into muscle + aliases: + - Intramuscular Route of Administration + meaning: NCIT:C28161 annotations: - hex: 2A52BE - chemical: Co2SnO4 - PHTHALO_BLUE: - description: Phthalocyanine blue + abbreviation: IM + sites: deltoid, gluteus, vastus lateralis + SUBCUTANEOUS: + title: Under the skin + aliases: + - Subcutaneous Route of Administration + meaning: NCIT:C38299 annotations: - hex: 000F89 - chemical: C32H16CuN8 - modern: synthetic organic - VIRIDIAN: - description: Viridian (Chromium oxide green) + abbreviation: SC, SubQ + absorption: slow + TOPICAL: + title: On the skin surface + aliases: + - Topical Route of Administration + meaning: NCIT:C38304 annotations: - hex: 40826D - chemical: Cr2O3·2H2O - CHROME_GREEN: - description: Chrome oxide green + forms: cream, ointment, gel + INHALATION: + title: By breathing in + aliases: + - Inhalation Route of Administration + meaning: NCIT:C38216 annotations: - hex: 2E5E26 - chemical: Cr2O3 - PHTHALO_GREEN: - description: Phthalocyanine green + devices: inhaler, nebulizer + RECTAL: + title: Into the rectum + aliases: + - Rectal Route of Administration + meaning: NCIT:C38295 annotations: - hex: '123524' - chemical: C32H16ClCuN8 - modern: synthetic organic - TERRE_VERTE: - description: Terre verte/Green earth + forms: suppository, enema + INTRANASAL: + title: Into the nose + aliases: + - Nasal Route of Administration + meaning: NCIT:C38284 annotations: - hex: 6B7F59 - chemical: complex silicate - natural: earth pigment - TYRIAN_PURPLE: - description: Tyrian purple (from murex snails) + forms: spray, drops + TRANSDERMAL: + title: Through the skin + aliases: + - Transdermal Route of Administration + meaning: NCIT:C38305 annotations: - hex: 66023C - source: murex snails - historical: ancient royal purple - MANGANESE_VIOLET: - description: Manganese violet + forms: patch + SUBLINGUAL: + title: Under the tongue + aliases: + - Sublingual Route of Administration + meaning: NCIT:C38300 annotations: - hex: 8B3E5F - chemical: NH4MnP2O7 - MARS_BLACK: - description: Mars black (Synthetic iron oxide) + absorption: rapid + EPIDURAL: + title: Into epidural space + aliases: + - Intraepidermal Route of Administration + meaning: NCIT:C38243 annotations: - hex: '010101' - chemical: Fe3O4 - synthetic: iron oxide - IVORY_BLACK: - description: Ivory black (Bone char) + use: anesthesia, analgesia + INTRATHECAL: + title: Into spinal fluid + aliases: + - Intraventricular Route of Administration + meaning: NCIT:C38277 annotations: - hex: 1B1B1B - source: charred bones - LAMP_BLACK: - description: Lamp black (Carbon black) + use: CNS drugs + OPHTHALMIC: + title: Into the eye + aliases: + - Ophthalmic Route of Administration + meaning: NCIT:C38287 annotations: - hex: 2B2B2B - chemical: C - source: soot - is_a: PigmentsDyesSchemaEnum + forms: drops, ointment + OTIC: + title: Into the ear + aliases: + - Auricular Route of Administration + meaning: NCIT:C38192 + annotations: + forms: drops + is_a: ClinicalSchemaEnum + description: 'Enum: DrugRouteEnum' annotations: - source_domain: materials_science - source_schema: pigments_dyes - IndustrialDyeEnum: - description: Industrial and textile dyes + source_domain: medical + source_schema: clinical + VitalSignEnum: + title: Standard vital signs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - INDIGO: - description: Indigo dye + HEART_RATE: + title: Heart beats per minute + meaning: LOINC:8867-4 annotations: - hex: 4B0082 - source: originally plant-based, now synthetic - use: denim, textiles - ANILINE_BLACK: - description: Aniline black + normal_range: 60-100 bpm + units: beats/min + BLOOD_PRESSURE_SYSTOLIC: + title: Systolic blood pressure + meaning: LOINC:8480-6 annotations: - hex: '000000' - chemical: polyaniline - use: cotton dyeing - METHYLENE_BLUE: - description: Methylene blue + normal_range: <120 mmHg + units: mmHg + BLOOD_PRESSURE_DIASTOLIC: + title: Diastolic blood pressure + meaning: LOINC:8462-4 annotations: - hex: 1E90FF - chemical: C16H18ClN3S - use: biological stain, medical - CONGO_RED: - description: Congo red - meaning: CHEBI:34653 + normal_range: <80 mmHg + units: mmHg + RESPIRATORY_RATE: + title: Breaths per minute + meaning: LOINC:9279-1 annotations: - hex: CC0000 - chemical: C32H22N6Na2O6S2 - use: pH indicator, textile - MALACHITE_GREEN: - description: Malachite green - meaning: CHEBI:72449 + normal_range: 12-20 breaths/min + units: breaths/min + TEMPERATURE: + title: Body temperature + meaning: LOINC:8310-5 annotations: - hex: 0BDA51 - chemical: C23H25ClN2 - use: biological stain - CRYSTAL_VIOLET: - description: Crystal violet/Gentian violet - meaning: CHEBI:41688 + normal_range: 36.5-37.5°C + units: °C or °F + OXYGEN_SATURATION: + title: Blood oxygen saturation + meaning: LOINC:2708-6 annotations: - hex: 9400D3 - chemical: C25H30ClN3 - use: gram staining - EOSIN: - description: Eosin Y - meaning: CHEBI:52053 + normal_range: 95-100% + units: '%' + PAIN_SCALE: + title: Pain level (0-10) + meaning: LOINC:38208-5 + annotations: + scale: 0-10 + type: subjective + is_a: ClinicalSchemaEnum + description: 'Enum: VitalSignEnum' + annotations: + source_domain: medical + source_schema: clinical + DiagnosticTestTypeEnum: + title: Types of diagnostic tests + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BLOOD_TEST: + title: Blood sample analysis aliases: - - eosin YS dye + - Biopsy Procedure + meaning: NCIT:C15189 annotations: - hex: FF6B6B - chemical: C20H6Br4Na2O5 - use: histology stain - SAFRANIN: - description: Safranin O + samples: serum, plasma, whole blood + URINE_TEST: + title: Urine sample analysis + aliases: + - Tissue Factor annotations: - hex: FF0066 - chemical: C20H19ClN4 - use: biological stain - ACID_ORANGE_7: - description: Acid Orange 7 (Orange II) + types: urinalysis, culture, drug screen + IMAGING_XRAY: + title: X-ray imaging + aliases: + - X-Ray + meaning: NCIT:C17262 annotations: - hex: FF7F00 - chemical: C16H11N2NaO4S - use: wool, silk dyeing - REACTIVE_BLACK_5: - description: Reactive Black 5 + radiation: 'yes' + IMAGING_CT: + title: Computed tomography scan + aliases: + - Computed Tomography + meaning: NCIT:C17204 annotations: - hex: '000000' - use: cotton reactive dye - DISPERSE_BLUE_1: - description: Disperse Blue 1 + radiation: 'yes' + IMAGING_MRI: + title: Magnetic resonance imaging + aliases: + - Magnetic Resonance Imaging + meaning: NCIT:C16809 annotations: - hex: 1560BD - use: polyester dyeing - VAT_BLUE_1: - description: Vat Blue 1 (Indanthrene blue) + radiation: 'no' + IMAGING_ULTRASOUND: + title: Ultrasound imaging + aliases: + - Ultrasound Imaging + meaning: NCIT:C17230 annotations: - hex: 002F5C - use: cotton vat dyeing - is_a: PigmentsDyesSchemaEnum - annotations: - source_domain: materials_science - source_schema: pigments_dyes - FoodColoringEnum: - description: Food coloring and natural food dyes - permissible_values: - FD_C_RED_40: - description: FD&C Red No. 40 (Allura Red) + radiation: 'no' + IMAGING_PET: + title: Positron emission tomography + aliases: + - Positron Emission Tomography + meaning: NCIT:C17007 annotations: - hex: E40000 - E_number: E129 - use: beverages, candies - FD_C_YELLOW_5: - description: FD&C Yellow No. 5 (Tartrazine) + uses: radiotracer + ECG: + title: Electrocardiogram + aliases: + - Electroencephalography + meaning: NCIT:C38054 + annotations: + measures: heart electrical activity + EEG: + title: Electroencephalogram + aliases: + - Djibouti + annotations: + measures: brain electrical activity + BIOPSY: + title: Tissue sample analysis + aliases: + - Biopsy Procedure + meaning: NCIT:C15189 annotations: - hex: FFFF00 - E_number: E102 - use: beverages, desserts - FD_C_YELLOW_6: - description: FD&C Yellow No. 6 (Sunset Yellow) + invasive: 'yes' + ENDOSCOPY: + title: Internal visualization + aliases: + - Endoscopic Procedure + meaning: NCIT:C16546 annotations: - hex: FFA500 - E_number: E110 - use: snacks, beverages - FD_C_BLUE_1: - title: Brilliant Blue - description: FD&C Blue No. 1 (Brilliant Blue) - meaning: CHEBI:82411 + types: colonoscopy, gastroscopy, bronchoscopy + GENETIC_TEST: + title: DNA/RNA analysis + aliases: + - Genetic Testing + meaning: NCIT:C15709 annotations: - hex: 0033FF - E_number: E133 - use: beverages, candies - FD_C_BLUE_2: - description: FD&C Blue No. 2 (Indigo Carmine) + types: karyotype, sequencing, PCR + is_a: ClinicalSchemaEnum + description: 'Enum: DiagnosticTestTypeEnum' + annotations: + source_domain: medical + source_schema: clinical + SymptomSeverityEnum: + title: Severity levels for symptoms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ABSENT: + title: No symptoms + aliases: + - Blood group B annotations: - hex: 4B0082 - E_number: E132 - use: beverages, confections - FD_C_GREEN_3: - description: FD&C Green No. 3 (Fast Green) + grade: '0' + MILD: + title: Mild symptoms, minimal impact + meaning: HP:0012825 annotations: - hex: 00FF00 - E_number: E143 - use: beverages, desserts - CARAMEL_COLOR: - description: Caramel coloring + grade: '1' + impact: minimal daily activity limitation + MODERATE: + title: Moderate symptoms, some limitation + meaning: HP:0012826 annotations: - hex: 8B4513 - E_number: E150 - use: cola, sauces - ANNATTO: - description: Annatto (natural orange) - meaning: CHEBI:3136 - aliases: - - bixin + grade: '2' + impact: some daily activity limitation + SEVERE: + title: Severe symptoms, significant limitation + meaning: HP:0012828 annotations: - hex: FF6600 - E_number: E160b - source: achiote seeds - TURMERIC: - title: curcumin - description: Turmeric/Curcumin (natural yellow) - meaning: CHEBI:3962 + grade: '3' + impact: significant daily activity limitation + LIFE_THREATENING: + title: Life-threatening symptoms + aliases: + - Profound annotations: - hex: F0E442 - E_number: E100 - source: turmeric root - BEETROOT_RED: - description: Beetroot red/Betanin - meaning: CHEBI:3080 + grade: '4' + impact: urgent intervention required + is_a: ClinicalSchemaEnum + description: 'Enum: SymptomSeverityEnum' + annotations: + source_domain: medical + source_schema: clinical + AllergyTypeEnum: + title: Types of allergic reactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + DRUG: + title: Drug allergy aliases: - - Betanin + - Hypersensitivity + meaning: NCIT:C3114 annotations: - hex: BC2A4D - E_number: E162 - source: beets - CHLOROPHYLL: - description: Chlorophyll (natural green) - meaning: CHEBI:28966 + examples: penicillin, sulfa drugs + FOOD: + title: Food allergy annotations: - hex: 4D7C0F - E_number: E140 - source: plants - ANTHOCYANINS: - description: Anthocyanins (natural purple/red) + common: nuts, shellfish, eggs, milk + ENVIRONMENTAL: + title: Environmental allergy annotations: - hex: 6B3AA0 - E_number: E163 - source: berries, grapes - PAPRIKA_EXTRACT: - description: Paprika extract + examples: pollen, dust, mold + CONTACT: + title: Contact dermatitis annotations: - hex: E85D00 - E_number: E160c - source: paprika peppers - SPIRULINA_BLUE: - description: Spirulina extract (phycocyanin) + examples: latex, nickel, poison ivy + INSECT: + title: Insect sting allergy annotations: - hex: 1E88E5 - source: spirulina algae - natural: 'true' - is_a: PigmentsDyesSchemaEnum + examples: bee, wasp, hornet + ANAPHYLAXIS: + title: Severe systemic reaction + annotations: + severity: life-threatening + is_a: ClinicalSchemaEnum + description: 'Enum: AllergyTypeEnum' annotations: - source_domain: materials_science - source_schema: pigments_dyes - AutomobilePaintColorEnum: - description: Common automobile paint colors + source_domain: medical + source_schema: clinical + VaccineTypeEnum: + title: Types of vaccines + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ARCTIC_WHITE: - description: Arctic White - meaning: HEX:FFFFFF - annotations: - type: solid - MIDNIGHT_BLACK: - description: Midnight Black - meaning: HEX:000000 + LIVE_ATTENUATED: + title: Weakened live pathogen annotations: - type: metallic - SILVER_METALLIC: - description: Silver Metallic - meaning: HEX:C0C0C0 + examples: MMR, varicella, yellow fever + INACTIVATED: + title: Killed pathogen annotations: - type: metallic - GUNMETAL_GRAY: - description: Gunmetal Gray - meaning: HEX:2A3439 + examples: flu shot, hepatitis A, rabies + SUBUNIT: + title: Pathogen pieces annotations: - type: metallic - RACING_RED: - description: Racing Red - meaning: HEX:CE1620 + examples: hepatitis B, HPV, pertussis + TOXOID: + title: Inactivated toxin annotations: - type: solid - CANDY_APPLE_RED: - description: Candy Apple Red - meaning: HEX:FF0800 + examples: diphtheria, tetanus + MRNA: + title: mRNA vaccine annotations: - type: metallic - ELECTRIC_BLUE: - description: Electric Blue - meaning: HEX:7DF9FF + examples: COVID-19 (Pfizer, Moderna) + VIRAL_VECTOR: + title: Modified virus carrier annotations: - type: metallic - BRITISH_RACING_GREEN: - description: British Racing Green - meaning: HEX:004225 + examples: COVID-19 (J&J, AstraZeneca) + is_a: ClinicalSchemaEnum + description: 'Enum: VaccineTypeEnum' + annotations: + source_domain: medical + source_schema: clinical + BMIClassificationEnum: + title: Body Mass Index classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + UNDERWEIGHT: + title: BMI less than 18.5 annotations: - type: solid - historical: British racing color - PEARL_WHITE: - description: Pearl White - meaning: HEX:F8F8FF + bmi_range: <18.5 + NORMAL_WEIGHT: + title: BMI 18.5-24.9 annotations: - type: pearl - finish: pearlescent - CHAMPAGNE_GOLD: - description: Champagne Gold - meaning: HEX:D4AF37 + bmi_range: 18.5-24.9 + OVERWEIGHT: + title: BMI 25.0-29.9 annotations: - type: metallic - COPPER_BRONZE: - description: Copper Bronze - meaning: HEX:B87333 + bmi_range: 25.0-29.9 + OBESE_CLASS_I: + title: BMI 30.0-34.9 annotations: - type: metallic - MIAMI_BLUE: - description: Miami Blue - meaning: HEX:00BFFF + bmi_range: 30.0-34.9 + OBESE_CLASS_II: + title: BMI 35.0-39.9 annotations: - type: metallic - brand: Porsche - is_a: PigmentsDyesSchemaEnum + bmi_range: 35.0-39.9 + OBESE_CLASS_III: + title: BMI 40.0 or greater + annotations: + bmi_range: ≥40.0 + aliases: morbid obesity + is_a: ClinicalSchemaEnum + description: 'Enum: BMIClassificationEnum' annotations: - source_domain: materials_science - source_schema: pigments_dyes - SynthesisMethodsSchemaEnum: - description: Schema-level enum for synthesis_methods in materials_science - is_a: MaterialsScienceDomainEnum + source_domain: medical + source_schema: clinical + FamilyHistorySchemaEnum: + description: Schema-level enum for family_history in medical + is_a: MedicalDomainEnum abstract: true annotations: - source_file: materials_science/synthesis_methods.yaml - SynthesisMethodEnum: - description: Common material synthesis and processing methods - permissible_values: - SOL_GEL: - description: Synthesis from solution through gel formation - title: Sol-Gel - aliases: - - sol-gel process - HYDROTHERMAL: - description: Synthesis using high temperature aqueous solutions - title: Hydrothermal - aliases: - - hydrothermal synthesis - SOLVOTHERMAL: - description: Synthesis using non-aqueous solvents at high temperature/pressure - title: Solvothermal - CVD: - description: Chemical Vapor Deposition - title: chemical vapour deposition - meaning: CHMO:0001314 - aliases: - - Chemical Vapor Deposition - - CVD - PVD: - description: Physical Vapor Deposition - title: physical vapour deposition - meaning: CHMO:0001356 - aliases: - - Physical Vapor Deposition - - PVD - ALD: - description: Atomic Layer Deposition - title: ALD - aliases: - - Atomic Layer Deposition - ELECTRODEPOSITION: - description: Deposition using electric current - title: electrochemical deposition - meaning: CHMO:0001331 - aliases: - - electroplating - - Electrodeposition - - ELECTRODEPOSITION - BALL_MILLING: - description: Mechanical alloying using ball mill - title: Ball Milling - aliases: - - mechanical alloying - PRECIPITATION: - description: Formation of solid from solution - title: precipitation - meaning: CHMO:0001688 - aliases: - - Precipitation - - PRECIPITATION - SINTERING: - description: Compacting and forming solid mass by heat/pressure - title: Sintering - MELT_PROCESSING: - description: Processing from molten state - title: Melt Processing - aliases: - - melt casting - SOLUTION_CASTING: - description: Casting from solution - title: Solution Casting - SPIN_COATING: - description: Coating by spinning substrate - title: Spin Coating - meaning: CHMO:0001472 - DIP_COATING: - description: Coating by dipping in solution - title: Dip Coating - meaning: CHMO:0001471 - SPRAY_COATING: - description: Coating by spraying - title: Spray Coating - is_a: SynthesisMethodsSchemaEnum + source_file: medical/family_history.yaml + FamilyRelationship: + title: Family Relationship + description: Family relationships used in pedigree and family history documentation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource + source: https://terminology.hl7.org/2.1.0/ValueSet-v3-FamilyMember.html + permissible_values: + PARENT: + description: The player of the role is one who begets, gives birth to, or nurtures and raises the scoping entity (child) + meaning: HL7:v3-RoleCode#PRN + MOTHER: + description: The player of the role is a female who conceives, gives birth to, or raises and nurtures the scoping + entity (child) + meaning: HL7:v3-RoleCode#MTH + FATHER: + description: The player of the role is a male who begets or raises or nurtures the scoping entity (child) + meaning: HL7:v3-RoleCode#FTH + NATURAL_MOTHER: + description: The player of the role is a female who conceives or gives birth to the scoping entity (child) + meaning: HL7:v3-RoleCode#NMTH + NATURAL_FATHER: + description: The player of the role is a male who begets the scoping entity (child) + meaning: HL7:v3-RoleCode#NFTH + ADOPTIVE_PARENT: + description: The player of the role (parent) has taken the scoper (child) into their family through legal means and + raises them as his or her own child + meaning: HL7:v3-RoleCode#ADOPTP + ADOPTIVE_MOTHER: + description: The player of the role (mother) is a female who has taken the scoper (child) into their family through + legal means and raises them as her own child + meaning: HL7:v3-RoleCode#ADOPTM + ADOPTIVE_FATHER: + description: The player of the role (father) is a male who has taken the scoper (child) into their family through + legal means and raises them as his own child + meaning: HL7:v3-RoleCode#ADOPTF + STEP_PARENT: + description: The player of the role is the spouse of the scoping person's parent and not the scoping person's natural + parent + meaning: HL7:v3-RoleCode#STPPRN + STEP_MOTHER: + description: The player of the role is the female spouse of the scoping person's parent and not the scoping person's + natural mother + meaning: HL7:v3-RoleCode#STPMTH + STEP_FATHER: + description: The player of the role is the male spouse of the scoping person's parent and not the scoping person's + natural father + meaning: HL7:v3-RoleCode#STPFTH + FOSTER_PARENT: + description: The player of the role (parent) who is a state-certified caregiver responsible for the scoper (child) + meaning: HL7:v3-RoleCode#PRNFOST + GESTATIONAL_MOTHER: + description: The player is a female whose womb carries the fetus of the scoper + meaning: HL7:v3-RoleCode#GESTM + SIBLING: + description: The player of the role shares one or both parents in common with the scoping entity + meaning: HL7:v3-RoleCode#SIB + BROTHER: + description: The player of the role is a male sharing one or both parents with the scoping entity + meaning: HL7:v3-RoleCode#BRO + SISTER: + description: The player of the role is a female sharing one or both parents with the scoping entity + meaning: HL7:v3-RoleCode#SIS + NATURAL_BROTHER: + description: The player of the role is a male related to the scoping entity by sharing only the same natural parents + meaning: HL7:v3-RoleCode#NBRO + NATURAL_SISTER: + description: The player of the role is a female related to the scoping entity by sharing only the same natural parents + meaning: HL7:v3-RoleCode#NSIS + HALF_BROTHER: + description: The player of the role is a male related to the scoping entity by sharing only one biological parent + meaning: HL7:v3-RoleCode#HBRO + HALF_SISTER: + description: The player of the role is a female related to the scoping entity by sharing only one biological parent + meaning: HL7:v3-RoleCode#HSIS + STEP_BROTHER: + description: The player of the role is a male child of the scoping person's stepparent + meaning: HL7:v3-RoleCode#STPBRO + STEP_SISTER: + description: The player of the role is a female child of the scoping person's stepparent + meaning: HL7:v3-RoleCode#STPSIS + TWIN: + description: The scoper and player were carried in the same womb and delivered in the same birth + meaning: HL7:v3-RoleCode#TWIN + TWIN_BROTHER: + description: The player of the role is a male born from the same pregnancy as the scoping entity + meaning: HL7:v3-RoleCode#TWINBRO + TWIN_SISTER: + description: The player of the role is a female born from the same pregnancy as the scoping entity + meaning: HL7:v3-RoleCode#TWINSIS + FRATERNAL_TWIN: + description: The player of the role is born from the same pregnancy as the scoping entity but does not share the same + genotype + meaning: HL7:v3-RoleCode#FTWIN + IDENTICAL_TWIN: + description: The player of the role is born from the same pregnancy as the scoping entity and shares the same genotype + meaning: HL7:v3-RoleCode#ITWIN + CHILD: + description: The player of the role is a child of the scoping entity + meaning: HL7:v3-RoleCode#CHILD + SON: + description: The player of the role is a male offspring of the scoping entity (parent) + meaning: HL7:v3-RoleCode#SON + DAUGHTER: + description: The player of the role is a female offspring of the scoping entity (parent) + meaning: HL7:v3-RoleCode#DAU + NATURAL_CHILD: + description: The player of the role is an offspring of the scoping entity as determined by birth + meaning: HL7:v3-RoleCode#NCHILD + ADOPTIVE_CHILD: + description: The player of the role is a child taken into a family through legal means and raised by the scoping person + (parent) as his or her own child + meaning: HL7:v3-RoleCode#CHLDADOPT + FOSTER_CHILD: + description: The player of the role is a child receiving parental care and nurture from the scoping person (parent) + but not related to him or her through legal or blood relationship + meaning: HL7:v3-RoleCode#CHLDFOST + STEP_CHILD: + description: The player of the role is a child of the scoping person's spouse by a previous union + meaning: HL7:v3-RoleCode#STPCHLD + GRANDPARENT: + description: The player of the role is a parent of the scoping person's mother or father + meaning: HL7:v3-RoleCode#GRPRN + GRANDMOTHER: + description: The player of the role is the mother of the scoping person's mother or father + meaning: HL7:v3-RoleCode#GRMTH + GRANDFATHER: + description: The player of the role is the father of the scoping person's mother or father + meaning: HL7:v3-RoleCode#GRFTH + MATERNAL_GRANDMOTHER: + description: The player of the role is the mother of the scoping person's mother + meaning: HL7:v3-RoleCode#MGRMTH + MATERNAL_GRANDFATHER: + description: The player of the role is the father of the scoping person's mother + meaning: HL7:v3-RoleCode#MGRFTH + PATERNAL_GRANDMOTHER: + description: The player of the role is the mother of the scoping person's father + meaning: HL7:v3-RoleCode#PGRMTH + PATERNAL_GRANDFATHER: + description: The player of the role is the father of the scoping person's father + meaning: HL7:v3-RoleCode#PGRFTH + GRANDCHILD: + description: The player of the role is a child of the scoping person's son or daughter + meaning: HL7:v3-RoleCode#GRNDCHILD + GRANDSON: + description: The player of the role is a son of the scoping person's son or daughter + meaning: HL7:v3-RoleCode#GRNDSN + GRANDDAUGHTER: + description: The player of the role is a daughter of the scoping person's son or daughter + meaning: HL7:v3-RoleCode#GRNDDAU + AUNT: + description: The player of the role is a sister of the scoping person's mother or father + meaning: HL7:v3-RoleCode#AUNT + UNCLE: + description: The player of the role is a brother of the scoping person's mother or father + meaning: HL7:v3-RoleCode#UNCLE + MATERNAL_AUNT: + description: The player of the role is a sister of the scoping person's mother + meaning: HL7:v3-RoleCode#MAUNT + MATERNAL_UNCLE: + description: The player of the role is a brother of the scoping person's mother + meaning: HL7:v3-RoleCode#MUNCLE + PATERNAL_AUNT: + description: The player of the role is a sister of the scoping person's father + meaning: HL7:v3-RoleCode#PAUNT + PATERNAL_UNCLE: + description: The player of the role is a brother of the scoping person's father + meaning: HL7:v3-RoleCode#PUNCLE + COUSIN: + description: The player of the role is a relative descended from a common ancestor, such as a grandparent, by two + or more steps in a diverging line + meaning: HL7:v3-RoleCode#COUSN + MATERNAL_COUSIN: + description: The player of the role is a child of a maternal aunt or uncle of the scoping person + meaning: HL7:v3-RoleCode#MCOUSN + PATERNAL_COUSIN: + description: The player of the role is a child of a paternal aunt or uncle of the scoping person + meaning: HL7:v3-RoleCode#PCOUSN + NIECE: + description: The player of the role is a daughter of the scoping person's brother or sister or of the brother or sister + of the scoping person's spouse + meaning: HL7:v3-RoleCode#NIECE + NEPHEW: + description: The player of the role is a son of the scoping person's brother or sister or of the brother or sister + of the scoping person's spouse + meaning: HL7:v3-RoleCode#NEPHEW + SPOUSE: + description: The player of the role is a marriage partner of the scoping person + meaning: HL7:v3-RoleCode#SPS + HUSBAND: + description: The player of the role is a man joined to a woman (scoping person) in marriage + meaning: HL7:v3-RoleCode#HUSB + WIFE: + description: The player of the role is a woman joined to a man (scoping person) in marriage + meaning: HL7:v3-RoleCode#WIFE + DOMESTIC_PARTNER: + description: The player of the role cohabits with the scoping person but is not the scoping person's spouse + meaning: HL7:v3-RoleCode#DOMPART + GREAT_GRANDPARENT: + description: The player of the role is a grandparent of the scoping person's mother or father + meaning: HL7:v3-RoleCode#GGRPRN + GREAT_GRANDMOTHER: + description: The player of the role is a grandmother of the scoping person's mother or father + meaning: HL7:v3-RoleCode#GGRMTH + GREAT_GRANDFATHER: + description: The player of the role is a grandfather of the scoping person's mother or father + meaning: HL7:v3-RoleCode#GGRFTH + MOTHER_IN_LAW: + description: The player of the role is the mother of the scoping person's spouse + meaning: HL7:v3-RoleCode#MTHINLAW + FATHER_IN_LAW: + description: The player of the role is the father of the scoping person's spouse + meaning: HL7:v3-RoleCode#FTHINLAW + DAUGHTER_IN_LAW: + description: The player of the role is the wife of scoping person's son + meaning: HL7:v3-RoleCode#DAUINLAW + SON_IN_LAW: + description: The player of the role is the husband of scoping person's daughter + meaning: HL7:v3-RoleCode#SONINLAW + BROTHER_IN_LAW: + description: The player of the role is a brother of the scoping person's spouse, or the husband of the scoping person's + sister, or the husband of a sister of the scoping person's spouse + meaning: HL7:v3-RoleCode#BROINLAW + SISTER_IN_LAW: + description: The player of the role is a sister of the scoping person's spouse, or the wife of the scoping person's + brother, or the wife of a brother of the scoping person's spouse + meaning: HL7:v3-RoleCode#SISINLAW + FAMILY_MEMBER: + description: A relationship between two people characterizing their "familial" relationship + meaning: HL7:v3-RoleCode#FAMMEMB + EXTENDED_FAMILY_MEMBER: + description: Description of an extended family member + meaning: HL7:v3-RoleCode#EXT + SIGNIFICANT_OTHER: + description: A person who is important to one's well being; especially a spouse or one in a similar relationship + meaning: HL7:v3-RoleCode#SIGOTHR + is_a: FamilyHistorySchemaEnum annotations: - source_domain: materials_science - source_schema: synthesis_methods - CrystalGrowthMethodEnum: - description: Methods for growing single crystals + source_domain: medical + source_schema: family_history + FamilyHistoryStatus: + title: Family History Status + description: Status of family history information availability + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - CZOCHRALSKI: - description: Crystal pulling from melt - title: Czochralski Method - aliases: - - CZ - - crystal pulling - BRIDGMAN: - description: Directional solidification method - title: Bridgman Method - aliases: - - Bridgman-Stockbarger - FLOAT_ZONE: - description: Zone melting without crucible - title: Float Zone - aliases: - - FZ - - zone refining - FLUX_GROWTH: - description: Crystal growth from high temperature solution - title: Flux Growth - VAPOR_TRANSPORT: - description: Crystal growth via vapor phase transport - title: Vapor Transport - aliases: - - CVT - HYDROTHERMAL_GROWTH: - description: Crystal growth in aqueous solution under pressure - title: Hydrothermal Growth - LPE: - description: Liquid Phase Epitaxy - title: LPE - aliases: - - Liquid Phase Epitaxy - MBE: - description: Molecular Beam Epitaxy - title: molecular beam epitaxy - meaning: CHMO:0001341 - aliases: - - Molecular Beam Epitaxy - - MBE - MOCVD: - description: Metal-Organic Chemical Vapor Deposition - title: MOCVD - aliases: - - MOVPE - is_a: SynthesisMethodsSchemaEnum + COMPLETED: + description: All relevant family history information has been obtained + meaning: HL7:observation-status#final + PARTIAL: + description: Some family history information is available but not complete + meaning: HL7:observation-status#preliminary + UNKNOWN: + description: Family history status is unknown + meaning: HL7:data-absent-reason#unknown + UNABLE_TO_OBTAIN: + description: Information could not be obtained due to patient/family constraints + meaning: HL7:data-absent-reason#patient-refused + NOT_ASKED: + description: Family history information was not requested + meaning: HL7:data-absent-reason#not-asked + is_a: FamilyHistorySchemaEnum annotations: - source_domain: materials_science - source_schema: synthesis_methods - AdditiveManufacturingEnum: - description: 3D printing and additive manufacturing methods + source_domain: medical + source_schema: family_history + GeneticRelationship: + title: Genetic Relationship + description: Genetic relationship types for pedigree analysis + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BIOLOGICAL: + description: Genetic relationship through biological inheritance + meaning: SNOMED:444018008 + FULL_SIBLING: + description: Siblings sharing both biological parents + meaning: SNOMED:444301002 + HALF_SIBLING: + description: Siblings sharing one biological parent + meaning: SNOMED:445295006 + ADOPTIVE: + description: Relationship established through adoption + meaning: SNOMED:160499008 + NO_GENETIC_RELATIONSHIP: + description: No genetic relationship exists + meaning: SNOMED:373068000 + UNKNOWN_GENETIC_RELATIONSHIP: + description: Genetic relationship status is unknown + meaning: SNOMED:261665006 + is_a: FamilyHistorySchemaEnum + annotations: + source_domain: medical + source_schema: family_history + ImagingPlatformsSchemaEnum: + description: Schema-level enum for imaging_platforms in medical + is_a: MedicalDomainEnum + abstract: true + annotations: + source_file: medical/imaging_platforms.yaml + MRIPlatformEnum: + title: MRI Scanner Platforms + description: Specific MRI scanner models from major manufacturers. Includes field strength information (1.5T, 3T, 7T) + for proper data interpretation. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - FDM: - description: Fused Deposition Modeling - title: FDM + SIEMENS_AVANTO_1_5T: + description: Siemens Magnetom Avanto 1.5T MRI scanner aliases: - - FFF - - Fused Filament Fabrication - SLA: - description: Stereolithography - title: SLA + - Siemens Avanto 1.5T + annotations: + manufacturer: Siemens + field_strength: 1.5T + SIEMENS_AVANTO_FIT_1_5T: + description: Siemens Magnetom Avanto Fit 1.5T MRI scanner aliases: - - Stereolithography - SLS: - description: Selective Laser Sintering - title: SLS + - Siemens Avanto Fit 1.5T + annotations: + manufacturer: Siemens + field_strength: 1.5T + SIEMENS_AERA_1_5T: + description: Siemens Magnetom Aera 1.5T MRI scanner aliases: - - Selective Laser Sintering - SLM: - description: Selective Laser Melting - title: SLM + - Siemens Magnetom Aera 1.5T + annotations: + manufacturer: Siemens + field_strength: 1.5T + SIEMENS_ESPREE_1_5T: + description: Siemens Magnetom Espree 1.5T MRI scanner aliases: - - Selective Laser Melting - EBM: - description: Electron Beam Melting - title: EBM + - Siemens Magnetom Espree 1.5T + annotations: + manufacturer: Siemens + field_strength: 1.5T + SIEMENS_TRIO_3T: + description: Siemens Magnetom Trio 3T MRI scanner aliases: - - Electron Beam Melting - BINDER_JETTING: - description: Powder bed with liquid binder - title: Binder Jetting - MATERIAL_JETTING: - description: Droplet deposition of materials - title: Material Jetting + - Siemens Magnetom Trio 3T + annotations: + manufacturer: Siemens + field_strength: 3T + SIEMENS_VERIO_3T: + description: Siemens Magnetom Verio 3T MRI scanner aliases: - - PolyJet - DED: - description: Directed Energy Deposition - title: DED + - Siemens Magnetom Verio 3T + annotations: + manufacturer: Siemens + field_strength: 3T + SIEMENS_SKYRA_3T: + description: Siemens Magnetom Skyra 3T MRI scanner aliases: - - Directed Energy Deposition - is_a: SynthesisMethodsSchemaEnum - annotations: - source_domain: materials_science - source_schema: synthesis_methods - MedicalDomainEnum: - description: Domain-level enum for medical value sets - is_a: ValueSetEnum - abstract: true - ClinicalSchemaEnum: - description: Schema-level enum for clinical in medical - is_a: MedicalDomainEnum - abstract: true - annotations: - source_file: medical/clinical.yaml - BloodTypeEnum: - description: ABO and Rh blood group classifications - permissible_values: - A_POSITIVE: - description: Blood type A, Rh positive - meaning: SNOMED:278149003 + - Siemens Magnetom Skyra 3T annotations: - abo: A - rh: positive - can_receive: A+, A-, O+, O- - can_donate: A+, AB+ - A_NEGATIVE: - description: Blood type A, Rh negative - meaning: SNOMED:278152006 + manufacturer: Siemens + field_strength: 3T + SIEMENS_PRISMA_3T: + description: Siemens Magnetom Prisma 3T MRI scanner + aliases: + - Siemens Magnetom Prisma 3T annotations: - abo: A - rh: negative - can_receive: A-, O- - can_donate: A+, A-, AB+, AB- - B_POSITIVE: - description: Blood type B, Rh positive - meaning: SNOMED:278150003 + manufacturer: Siemens + field_strength: 3T + SIEMENS_PRISMA_FIT_3T: + description: Siemens Magnetom Prisma Fit 3T MRI scanner + aliases: + - Siemens Magnetom Prisma Fit 3T annotations: - abo: B - rh: positive - can_receive: B+, B-, O+, O- - can_donate: B+, AB+ - B_NEGATIVE: - description: Blood type B, Rh negative - meaning: SNOMED:278153001 + manufacturer: Siemens + field_strength: 3T + GE_SIGNA_EXCITE_1_5T: + description: GE Signa Excite 1.5T MRI scanner + aliases: + - GE Signa Excite 1.5T annotations: - abo: B - rh: negative - can_receive: B-, O- - can_donate: B+, B-, AB+, AB- - AB_POSITIVE: - description: Blood type AB, Rh positive (universal recipient) - meaning: SNOMED:278151004 + manufacturer: GE Healthcare + field_strength: 1.5T + GE_SIGNA_GENESIS_1_5T: + description: GE Signa Genesis 1.5T MRI scanner + aliases: + - GE Signa Genesis 1.5T annotations: - abo: AB - rh: positive - can_receive: all types - can_donate: AB+ - special: universal recipient - AB_NEGATIVE: - description: Blood type AB, Rh negative - meaning: SNOMED:278154007 + manufacturer: GE Healthcare + field_strength: 1.5T + GE_SIGNA_HDXT_1_5T: + description: GE Signa HDxt 1.5T MRI scanner + aliases: + - GE Signa HDxt 1.5T + annotations: + manufacturer: GE Healthcare + field_strength: 1.5T + GE_OPTIMA_MR450W_1_5T: + description: GE Optima MR450W 1.5T MRI scanner + aliases: + - GE Optima MR450W 1.5T annotations: - abo: AB - rh: negative - can_receive: A-, B-, AB-, O- - can_donate: AB+, AB- - O_POSITIVE: - description: Blood type O, Rh positive - meaning: SNOMED:278147001 + manufacturer: GE Healthcare + field_strength: 1.5T + GE_SIGNA_HDXT_3T: + description: GE Signa HDxt 3T MRI scanner + aliases: + - GE Signa HDxt 3T annotations: - abo: O - rh: positive - can_receive: O+, O- - can_donate: A+, B+, AB+, O+ - O_NEGATIVE: - description: Blood type O, Rh negative (universal donor) - meaning: SNOMED:278148006 + manufacturer: GE Healthcare + field_strength: 3T + GE_DISCOVERY_MR750_3T: + description: GE Discovery MR750 3T MRI scanner + aliases: + - GE Discovery MR750 3T annotations: - abo: O - rh: negative - can_receive: O- - can_donate: all types - special: universal donor - is_a: ClinicalSchemaEnum - annotations: - source_domain: medical - source_schema: clinical - AnatomicalSystemEnum: - description: Major anatomical systems of the body - permissible_values: - CARDIOVASCULAR: - title: Heart and blood vessels + manufacturer: GE Healthcare + field_strength: 3T + GE_SIGNA_PREMIER_3T: + description: GE Signa Premier 3T MRI scanner aliases: - - cardiovascular system - meaning: UBERON:0004535 + - GE Signa Premier 3T annotations: - components: heart, arteries, veins, capillaries - RESPIRATORY: - title: Lungs and airways + manufacturer: GE Healthcare + field_strength: 3T + PHILIPS_PANORAMA_1_0T: + description: Philips Panorama 1.0T MRI scanner aliases: - - respiratory system - meaning: UBERON:0001004 + - Philips Panorama 1.0T annotations: - components: lungs, trachea, bronchi, diaphragm - NERVOUS: - title: Brain, spinal cord, and nerves + manufacturer: Philips Healthcare + field_strength: 1.0T + PHILIPS_ACHIEVA_1_5T: + description: Philips Achieva 1.5T MRI scanner aliases: - - nervous system - meaning: UBERON:0001016 + - Philips Achieva 1.5T annotations: - components: brain, spinal cord, nerves - DIGESTIVE: - title: GI tract and accessory organs + manufacturer: Philips Healthcare + field_strength: 1.5T + PHILIPS_INGENIA_1_5T: + description: Philips Ingenia 1.5T MRI scanner aliases: - - digestive system - meaning: UBERON:0001007 + - Philips Ingenia 1.5T annotations: - components: mouth, esophagus, stomach, intestines, liver, pancreas - MUSCULOSKELETAL: - title: Bones, muscles, and connective tissue + manufacturer: Philips Healthcare + field_strength: 1.5T + PHILIPS_ACHIEVA_3T: + description: Philips Achieva 3T MRI scanner aliases: - - musculoskeletal system - meaning: UBERON:0002204 + - Philips Achieva 3T annotations: - components: bones, muscles, tendons, ligaments, cartilage - INTEGUMENTARY: - title: Skin and related structures + manufacturer: Philips Healthcare + field_strength: 3T + PHILIPS_INTERA_ACHIEVA_3T: + description: Philips Intera Achieva 3T MRI scanner aliases: - - integumental system - meaning: UBERON:0002416 + - Philips Intera Achieva 3T annotations: - components: skin, hair, nails, glands - ENDOCRINE: - title: Hormone-producing glands + manufacturer: Philips Healthcare + field_strength: 3T + PHILIPS_INGENIA_3T: + description: Philips Ingenia 3T MRI scanner aliases: - - endocrine system - meaning: UBERON:0000949 + - Philips Ingenia 3T annotations: - components: pituitary, thyroid, adrenals, pancreas - URINARY: - title: Kidneys and urinary tract + manufacturer: Philips Healthcare + field_strength: 3T + HITACHI_ECHELON_1_5T: + description: Hitachi Echelon 1.5T MRI scanner aliases: - - renal system - meaning: UBERON:0001008 + - Hitachi Echelon 1.5T annotations: - components: kidneys, ureters, bladder, urethra - REPRODUCTIVE: - title: Reproductive organs + manufacturer: Hitachi + field_strength: 1.5T + HITACHI_OASIS_1_2T: + description: Hitachi Oasis 1.2T MRI scanner aliases: - - reproductive system - meaning: UBERON:0000990 + - Hitachi Oasis 1.2T annotations: - components: gonads, ducts, external genitalia - IMMUNE: - title: Immune and lymphatic system + manufacturer: Hitachi + field_strength: 1.2T + TOSHIBA_VANTAGE_TITAN_1_5T: + description: Toshiba Vantage Titan 1.5T MRI scanner aliases: - - immune system - meaning: UBERON:0002405 + - Toshiba Vantage Titan 1.5T annotations: - components: lymph nodes, spleen, thymus, bone marrow - HEMATOLOGIC: - title: Blood and blood-forming organs + manufacturer: Toshiba/Canon + field_strength: 1.5T + BRUKER_BIOSPEC_7T: + description: Bruker Biospec 7T research MRI scanner aliases: - - hematopoietic system - meaning: UBERON:0002390 + - 7T Bruker Biospec annotations: - components: blood, bone marrow, spleen - is_a: ClinicalSchemaEnum - annotations: - source_domain: medical - source_schema: clinical - MedicalSpecialtyEnum: - title: Medical specialties and subspecialties - permissible_values: - ANESTHESIOLOGY: - title: Anesthesia and perioperative medicine - CARDIOLOGY: - title: Heart and cardiovascular diseases - DERMATOLOGY: - title: Skin diseases - EMERGENCY_MEDICINE: - title: Emergency and acute care - ENDOCRINOLOGY: - title: Hormonal and metabolic disorders - FAMILY_MEDICINE: - title: Primary care for all ages - GASTROENTEROLOGY: - title: Digestive system disorders - HEMATOLOGY: - title: Blood disorders - INFECTIOUS_DISEASE: - title: Infectious diseases - INTERNAL_MEDICINE: - title: Adult internal medicine - NEPHROLOGY: - title: Kidney diseases - NEUROLOGY: - title: Nervous system disorders - OBSTETRICS_GYNECOLOGY: - title: Women's health and childbirth - ONCOLOGY: - title: Cancer treatment - OPHTHALMOLOGY: - title: Eye diseases - ORTHOPEDICS: - title: Musculoskeletal disorders - OTOLARYNGOLOGY: - title: Ear, nose, and throat - PATHOLOGY: - title: Disease diagnosis through lab analysis - PEDIATRICS: - title: Children's health - PSYCHIATRY: - title: Mental health disorders - PULMONOLOGY: - title: Lung and respiratory diseases - RADIOLOGY: - title: Medical imaging - RHEUMATOLOGY: - title: Joint and autoimmune diseases - SURGERY: - title: Surgical procedures - UROLOGY: - title: Urinary and male reproductive system - is_a: ClinicalSchemaEnum - description: 'Enum: MedicalSpecialtyEnum' + manufacturer: Bruker + field_strength: 7T + type: research + is_a: ImagingPlatformsSchemaEnum annotations: source_domain: medical - source_schema: clinical - DrugRouteEnum: - title: Routes of drug administration + source_schema: imaging_platforms + MicroscopyPlatformEnum: + title: Microscopy Platforms + description: Microscopy imaging systems and platforms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ORAL: - title: By mouth + ZEISS_LSM_700: + description: Zeiss LSM 700 confocal microscope aliases: - - Oral Route of Administration - meaning: NCIT:C38288 + - Zeiss LSM 700 annotations: - abbreviation: PO - absorption: GI tract - INTRAVENOUS: - title: Into a vein + manufacturer: Zeiss + type: confocal + ZEISS_LSM_980: + description: Zeiss LSM 980 confocal microscope aliases: - - Intravenous Route of Administration - meaning: NCIT:C38276 + - Zeiss LSM 980 annotations: - abbreviation: IV - onset: immediate - INTRAMUSCULAR: - title: Into muscle + manufacturer: Zeiss + type: confocal + ZEISS_LSM: + description: Zeiss LSM confocal microscope (general) aliases: - - Intramuscular Route of Administration - meaning: NCIT:C28161 + - Zeiss LSM annotations: - abbreviation: IM - sites: deltoid, gluteus, vastus lateralis - SUBCUTANEOUS: - title: Under the skin + manufacturer: Zeiss + type: confocal + LEICA_APERIO_AT2: + description: Leica Aperio AT2 whole slide scanner aliases: - - Subcutaneous Route of Administration - meaning: NCIT:C38299 + - Leica Aperio AT2 annotations: - abbreviation: SC, SubQ - absorption: slow - TOPICAL: - title: On the skin surface + manufacturer: Leica + type: slide scanner + APERIO_CS2: + description: Aperio CS2 slide scanner aliases: - - Topical Route of Administration - meaning: NCIT:C38304 + - Aperio CS2 annotations: - forms: cream, ointment, gel - INHALATION: - title: By breathing in + manufacturer: Leica + type: slide scanner + LEICA_MZ16: + description: Leica MZ16 stereomicroscope aliases: - - Inhalation Route of Administration - meaning: NCIT:C38216 + - Leica MZ16 annotations: - devices: inhaler, nebulizer - RECTAL: - title: Into the rectum + manufacturer: Leica + type: stereomicroscope + LEICA_S9: + description: Leica S9 stereomicroscope aliases: - - Rectal Route of Administration - meaning: NCIT:C38295 + - Leica S9 Stereomicroscope annotations: - forms: suppository, enema - INTRANASAL: - title: Into the nose + manufacturer: Leica + type: stereomicroscope + OLYMPUS_IX73: + description: Olympus IX73 inverted microscope aliases: - - Nasal Route of Administration - meaning: NCIT:C38284 + - Olympus IX73 annotations: - forms: spray, drops - TRANSDERMAL: - title: Through the skin + manufacturer: Olympus + type: inverted fluorescence + OLYMPUS_DP80: + description: Olympus DP80 camera system aliases: - - Transdermal Route of Administration - meaning: NCIT:C38305 + - Olympus DP80 annotations: - forms: patch - SUBLINGUAL: - title: Under the tongue + manufacturer: Olympus + type: camera + PANNORAMIC_250_FLASH: + description: 3DHISTECH Pannoramic 250 Flash slide scanner aliases: - - Sublingual Route of Administration - meaning: NCIT:C38300 + - Pannoramic 250 Flash annotations: - absorption: rapid - EPIDURAL: - title: Into epidural space + manufacturer: 3DHISTECH + type: slide scanner + PHILIPS_FEI_TECNAI_12: + description: Philips FEI Tecnai 12 electron microscope aliases: - - Intraepidermal Route of Administration - meaning: NCIT:C38243 + - Philips FEI Tecnai 12 annotations: - use: anesthesia, analgesia - INTRATHECAL: - title: Into spinal fluid + manufacturer: FEI/Thermo Fisher + type: TEM + ECHO_CONFOCAL: + description: ECHO confocal imaging system aliases: - - Intraventricular Route of Administration - meaning: NCIT:C38277 + - ECHO Confocal annotations: - use: CNS drugs - OPHTHALMIC: - title: Into the eye + type: confocal + is_a: ImagingPlatformsSchemaEnum + annotations: + source_domain: medical + source_schema: imaging_platforms + ImagingSystemPlatformEnum: + title: Other Imaging System Platforms + description: Other imaging systems including plate readers, flow cytometers, and specialized systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://nf-osi.github.io/nf-metadata-dictionary/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ENVISION_MULTIPLATE_READER: + description: PerkinElmer EnVision 2103 Multiplate Reader aliases: - - Ophthalmic Route of Administration - meaning: NCIT:C38287 + - EnVision 2103 Multiplate Reader annotations: - forms: drops, ointment - OTIC: - title: Into the ear + manufacturer: PerkinElmer + type: plate reader + SPECTRAMAX_M_SERIES: + description: Molecular Devices SpectraMax M Series aliases: - - Auricular Route of Administration - meaning: NCIT:C38192 + - Spectramax M Series annotations: - forms: drops - is_a: ClinicalSchemaEnum - description: 'Enum: DrugRouteEnum' - annotations: - source_domain: medical - source_schema: clinical - VitalSignEnum: - title: Standard vital signs - permissible_values: - HEART_RATE: - title: Heart beats per minute - meaning: LOINC:8867-4 + manufacturer: Molecular Devices + type: plate reader + VARIOSKAN_LUX: + description: Thermo Scientific Varioskan LUX + aliases: + - Varioskan LUX annotations: - normal_range: 60-100 bpm - units: beats/min - BLOOD_PRESSURE_SYSTOLIC: - title: Systolic blood pressure - meaning: LOINC:8480-6 + manufacturer: Thermo Fisher + type: plate reader + PROMEGA_GLOMAX_DISCOVER: + description: Promega GloMax Discover + aliases: + - Promega GloMax Discover annotations: - normal_range: <120 mmHg - units: mmHg - BLOOD_PRESSURE_DIASTOLIC: - title: Diastolic blood pressure - meaning: LOINC:8462-4 + manufacturer: Promega + type: plate reader + BD_FACS_CALIBUR: + description: BD FACS Calibur flow cytometer + aliases: + - BD FACS Calibur + annotations: + manufacturer: BD Biosciences + type: flow cytometer + BD_FACSSYMPHONY: + description: BD FACSymphony flow cytometer + aliases: + - BD FACSymphony + annotations: + manufacturer: BD Biosciences + type: flow cytometer + IVIS_SPECTRUM: + description: PerkinElmer IVIS Spectrum In Vivo Imaging System + aliases: + - IVIS Spectrum In Vivo Imaging System + annotations: + manufacturer: PerkinElmer + type: in vivo bioluminescence + NANOSTRING_COSMX: + description: NanoString CosMx Spatial Molecular Imager + aliases: + - Nanostring CosMx + annotations: + manufacturer: NanoString + type: spatial transcriptomics + NANOSTRING_GEOMX: + description: NanoString GeoMx Digital Spatial Profiler + aliases: + - Nanostring GeoMx + annotations: + manufacturer: NanoString + type: spatial profiling + VISIUM_10X: + description: 10x Genomics Visium Spatial Gene Expression + aliases: + - 10x Visium Spatial Gene Expression annotations: - normal_range: <80 mmHg - units: mmHg - RESPIRATORY_RATE: - title: Breaths per minute - meaning: LOINC:9279-1 + manufacturer: 10x Genomics + type: spatial transcriptomics + VEVO_3100: + description: Vevo 3100 Imaging System (ultrasound) + aliases: + - Vevo 3100 Imaging System annotations: - normal_range: 12-20 breaths/min - units: breaths/min - TEMPERATURE: - title: Body temperature - meaning: LOINC:8310-5 + manufacturer: FUJIFILM VisualSonics + type: ultrasound + VENTANA_BENCHMARK_XT: + description: Ventana Benchmark XT automated staining + aliases: + - Ventana Benchmark XT annotations: - normal_range: 36.5-37.5°C - units: °C or °F - OXYGEN_SATURATION: - title: Blood oxygen saturation - meaning: LOINC:2708-6 + manufacturer: Roche + type: automated IHC stainer + VECTRA_H1: + description: Vectra H1 3D Imaging System (Perkin Elmer) + aliases: + - Vectra H1 3D Imaging System annotations: - normal_range: 95-100% - units: '%' - PAIN_SCALE: - title: Pain level (0-10) - meaning: LOINC:38208-5 + manufacturer: PerkinElmer + type: multispectral imaging + XF24_EXTRACELLULAR_FLUX: + description: Agilent XF24 Extracellular Flux Analyzer + aliases: + - XF24 Extracellular Flux Analyzer annotations: - scale: 0-10 - type: subjective - is_a: ClinicalSchemaEnum - description: 'Enum: VitalSignEnum' + manufacturer: Agilent/Seahorse + type: metabolic analyzer + LICOR_ODYSSEY_CLX: + description: LI-COR Odyssey CLx Imaging System + aliases: + - LI-COR Odyssey CLx + annotations: + manufacturer: LI-COR + type: western blot imager + BIORAD_CHEMIDOC_MP: + description: BioRad ChemiDoc MP Imaging System + aliases: + - BioRad ChemiDoc MP Imaging System + annotations: + manufacturer: BioRad + type: gel/western imager + is_a: ImagingPlatformsSchemaEnum annotations: source_domain: medical - source_schema: clinical - DiagnosticTestTypeEnum: - title: Types of diagnostic tests + source_schema: imaging_platforms + NeuroimagingSchemaEnum: + description: Schema-level enum for neuroimaging in medical + is_a: MedicalDomainEnum + abstract: true + annotations: + source_file: medical/neuroimaging.yaml + MRIModalityEnum: + title: MRI Modality + description: MRI imaging modalities and techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BLOOD_TEST: - title: Blood sample analysis + STRUCTURAL_T1: + title: T1-weighted structural MRI + description: High-resolution anatomical imaging with T1 contrast + meaning: NCIT:C116455 aliases: - - Biopsy Procedure - meaning: NCIT:C15189 + - High Field Strength Magnetic Resonance Imaging annotations: - samples: serum, plasma, whole blood - URINE_TEST: - title: Urine sample analysis + contrast_mechanism: T1 relaxation + typical_use: anatomical reference, volumetric analysis + tissue_contrast: good gray/white matter contrast + STRUCTURAL_T2: + title: T2-weighted structural MRI + description: Structural imaging with T2 contrast + meaning: NCIT:C116456 aliases: - - Tissue Factor + - Low Field Strength Magnetic Resonance Imaging annotations: - types: urinalysis, culture, drug screen - IMAGING_XRAY: - title: X-ray imaging + contrast_mechanism: T2 relaxation + typical_use: pathology detection, CSF visualization + tissue_contrast: good fluid contrast + FLAIR: + title: Fluid-attenuated inversion recovery + description: T2-weighted sequence with CSF signal suppressed + meaning: NCIT:C82392 + annotations: + contrast_mechanism: T2 with fluid suppression + typical_use: lesion detection, periventricular pathology + advantage: suppresses CSF signal + BOLD_FMRI: + title: Blood oxygen level dependent fMRI + description: Functional MRI based on blood oxygenation changes + meaning: NCIT:C17958 aliases: - - X-Ray - meaning: NCIT:C17262 + - Functional Magnetic Resonance Imaging annotations: - radiation: 'yes' - IMAGING_CT: - title: Computed tomography scan + contrast_mechanism: BOLD signal + typical_use: brain activation mapping + temporal_resolution: seconds + ASL: + title: Arterial spin labeling + description: Perfusion imaging using magnetically labeled blood + meaning: NCIT:C116450 aliases: - - Computed Tomography - meaning: NCIT:C17204 + - Arterial Spin Labeling Magnetic Resonance Imaging annotations: - radiation: 'yes' - IMAGING_MRI: - title: Magnetic resonance imaging + contrast_mechanism: arterial blood labeling + typical_use: cerebral blood flow measurement + advantage: no contrast agent required + DWI: + title: Diffusion-weighted imaging + description: Imaging sensitive to water molecule diffusion + meaning: mesh:D038524 + annotations: + contrast_mechanism: water diffusion + typical_use: stroke detection, fiber tracking + parameter: apparent diffusion coefficient + DTI: + title: Diffusion tensor imaging + description: Advanced diffusion imaging with directional information + meaning: NCIT:C64862 + annotations: + contrast_mechanism: directional diffusion + typical_use: white matter tractography + parameters: fractional anisotropy, mean diffusivity + PERFUSION_DSC: + title: Dynamic susceptibility contrast perfusion + description: Perfusion imaging using contrast agent bolus + meaning: NCIT:C116459 aliases: - - Magnetic Resonance Imaging - meaning: NCIT:C16809 + - Secretin-Enhanced Magnetic Resonance Imaging annotations: - radiation: 'no' - IMAGING_ULTRASOUND: - title: Ultrasound imaging + contrast_mechanism: contrast agent dynamics + typical_use: cerebral blood flow, blood volume + requires: gadolinium contrast + PERFUSION_DCE: + title: Dynamic contrast-enhanced perfusion + description: Perfusion imaging with pharmacokinetic modeling + meaning: NCIT:C116458 aliases: - - Ultrasound Imaging - meaning: NCIT:C17230 + - Multiparametric Magnetic Resonance Imaging annotations: - radiation: 'no' - IMAGING_PET: - title: Positron emission tomography + contrast_mechanism: contrast enhancement kinetics + typical_use: blood-brain barrier permeability + analysis: pharmacokinetic modeling + SWI: + title: Susceptibility-weighted imaging + description: High-resolution venography and iron detection + meaning: NCIT:C121377 + annotations: + contrast_mechanism: magnetic susceptibility + typical_use: venography, microbleeds, iron deposits + strength: high field preferred + TASK_FMRI: + title: Task-based functional MRI + description: fMRI during specific cognitive or motor tasks + meaning: NCIT:C178023 aliases: - - Positron Emission Tomography - meaning: NCIT:C17007 + - Task Functional Magnetic Resonance Imaging annotations: - uses: radiotracer - ECG: - title: Electrocardiogram + paradigm: stimulus-response + typical_use: localization of brain functions + analysis: statistical parametric mapping + RESTING_STATE_FMRI: + title: Resting-state functional MRI + description: fMRI acquired at rest without explicit tasks + meaning: NCIT:C178024 aliases: - - Electroencephalography - meaning: NCIT:C38054 + - Resting Functional Magnetic Resonance Imaging annotations: - measures: heart electrical activity - EEG: - title: Electroencephalogram + paradigm: no task + typical_use: functional connectivity analysis + networks: default mode, attention, executive + FUNCTIONAL_CONNECTIVITY: + title: Functional connectivity MRI + description: Analysis of temporal correlations between brain regions + meaning: NCIT:C116454 aliases: - - Djibouti + - Functional Connectivity Magnetic Resonance Imaging annotations: - measures: brain electrical activity - BIOPSY: - title: Tissue sample analysis + analysis_type: connectivity mapping + typical_use: network analysis + metric: correlation coefficients + is_a: NeuroimagingSchemaEnum + annotations: + source_domain: medical + source_schema: neuroimaging + MRISequenceTypeEnum: + title: MRI Sequence Type + description: MRI pulse sequence types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GRADIENT_ECHO: + title: Gradient echo sequence + description: Fast imaging sequence using gradient reversal + meaning: NCIT:C154542 aliases: - - Biopsy Procedure - meaning: NCIT:C15189 + - Gradient Echo MRI annotations: - invasive: 'yes' - ENDOSCOPY: - title: Internal visualization + speed: fast + typical_use: T2*, functional imaging + artifact_sensitivity: susceptible to magnetic field inhomogeneity + SPIN_ECHO: + title: Spin echo sequence + description: Sequence using 180-degree refocusing pulse + meaning: CHMO:0001868 aliases: - - Endoscopic Procedure - meaning: NCIT:C16546 + - spin echo pulse sequence annotations: - types: colonoscopy, gastroscopy, bronchoscopy - GENETIC_TEST: - title: DNA/RNA analysis + speed: slower + typical_use: T2 imaging, reduced artifacts + artifact_resistance: good + EPI: + title: Echo planar imaging + description: Ultrafast imaging sequence + meaning: NCIT:C17558 + annotations: + speed: very fast + typical_use: functional MRI, diffusion imaging + temporal_resolution: subsecond + MPRAGE: + title: Magnetization prepared rapid gradient echo + description: T1-weighted 3D sequence with preparation pulse + meaning: NCIT:C118462 aliases: - - Genetic Testing - meaning: NCIT:C15709 + - Magnetization-Prepared Rapid Gradient Echo MRI + annotations: + image_type: T1-weighted + typical_use: high-resolution anatomical imaging + dimension: 3D + SPACE: + title: Sampling perfection with application optimized contrasts + description: 3D turbo spin echo sequence + annotations: + image_type: T2-weighted + typical_use: high-resolution T2 imaging + dimension: 3D + TRUFI: + title: True fast imaging with steady-state precession + description: Balanced steady-state free precession sequence + meaning: NCIT:C200534 + aliases: + - Constructive Interference In Steady State annotations: - types: karyotype, sequencing, PCR - is_a: ClinicalSchemaEnum - description: 'Enum: DiagnosticTestTypeEnum' + contrast: mixed T1/T2 + typical_use: cardiac imaging, fast scanning + signal: high + is_a: NeuroimagingSchemaEnum annotations: source_domain: medical - source_schema: clinical - SymptomSeverityEnum: - title: Severity levels for symptoms + source_schema: neuroimaging + MRIContrastTypeEnum: + title: MRI Contrast Type + description: MRI image contrast mechanisms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - ABSENT: - title: No symptoms + T1_WEIGHTED: + title: T1-weighted contrast + description: Image contrast based on T1 relaxation times + meaning: NCIT:C180727 aliases: - - Blood group B + - T1-Weighted Magnetic Resonance Imaging annotations: - grade: '0' - MILD: - title: Mild symptoms, minimal impact - meaning: HP:0012825 + tissue_contrast: gray matter darker than white matter + typical_use: anatomical structure + T2_WEIGHTED: + title: T2-weighted contrast + description: Image contrast based on T2 relaxation times + meaning: NCIT:C180729 + aliases: + - T2-Weighted Magnetic Resonance Imaging annotations: - grade: '1' - impact: minimal daily activity limitation - MODERATE: - title: Moderate symptoms, some limitation - meaning: HP:0012826 + tissue_contrast: CSF bright, gray matter brighter than white + typical_use: pathology detection + T2_STAR: + title: T2*-weighted contrast + description: Image contrast sensitive to magnetic susceptibility + meaning: NCIT:C156447 + aliases: + - T2 (Observed)-Weighted Imaging annotations: - grade: '2' - impact: some daily activity limitation - SEVERE: - title: Severe symptoms, significant limitation - meaning: HP:0012828 + sensitivity: blood, iron, air-tissue interfaces + typical_use: functional imaging, venography + PROTON_DENSITY: + title: Proton density weighted + description: Image contrast based on hydrogen density + meaning: NCIT:C170797 + aliases: + - Proton Density MRI annotations: - grade: '3' - impact: significant daily activity limitation - LIFE_THREATENING: - title: Life-threatening symptoms + tissue_contrast: proportional to water content + typical_use: joint imaging, some brain pathology + DIFFUSION_WEIGHTED: + title: Diffusion-weighted contrast + description: Image contrast based on water diffusion + meaning: NCIT:C111116 aliases: - - Profound + - Diffusion Weighted Imaging annotations: - grade: '4' - impact: urgent intervention required - is_a: ClinicalSchemaEnum - description: 'Enum: SymptomSeverityEnum' + sensitivity: molecular motion + typical_use: stroke, tumor cellularity + PERFUSION_WEIGHTED: + title: Perfusion-weighted contrast + description: Image contrast based on blood flow dynamics + meaning: mesh:D000098642 + annotations: + measurement: cerebral blood flow/volume + typical_use: stroke, tumor vascularity + is_a: NeuroimagingSchemaEnum annotations: source_domain: medical - source_schema: clinical - AllergyTypeEnum: - title: Types of allergic reactions + source_schema: neuroimaging + FMRIParadigmTypeEnum: + title: FMRI Paradigm Type + description: fMRI experimental paradigm types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - DRUG: - title: Drug allergy - aliases: - - Hypersensitivity - meaning: NCIT:C3114 - annotations: - examples: penicillin, sulfa drugs - FOOD: - title: Food allergy + BLOCK_DESIGN: + title: Block design paradigm + description: Alternating blocks of task and rest conditions + meaning: STATO:0000046 annotations: - common: nuts, shellfish, eggs, milk - ENVIRONMENTAL: - title: Environmental allergy + duration: typically 15-30 seconds per block + advantage: high statistical power + typical_use: robust activation detection + EVENT_RELATED: + title: Event-related design + description: Brief stimuli presented at varying intervals + meaning: EDAM:topic_3678 + aliases: + - Experimental design and studies annotations: - examples: pollen, dust, mold - CONTACT: - title: Contact dermatitis + duration: single events (seconds) + advantage: flexible timing, event separation + typical_use: studying cognitive processes + MIXED_DESIGN: + title: Mixed block and event-related design + description: Combination of block and event-related elements + meaning: EDAM:topic_3678 + aliases: + - Experimental design and studies annotations: - examples: latex, nickel, poison ivy - INSECT: - title: Insect sting allergy + flexibility: high + advantage: sustained and transient responses + complexity: high + RESTING_STATE: + title: Resting state paradigm + description: No explicit task, spontaneous brain activity + meaning: NCIT:C178024 + aliases: + - Resting Functional Magnetic Resonance Imaging annotations: - examples: bee, wasp, hornet - ANAPHYLAXIS: - title: Severe systemic reaction + instruction: rest, eyes open/closed + duration: typically 5-10 minutes + analysis: functional connectivity + NATURALISTIC: + title: Naturalistic paradigm + description: Ecologically valid stimuli (movies, stories) + meaning: EDAM:topic_3678 + aliases: + - Experimental design and studies annotations: - severity: life-threatening - is_a: ClinicalSchemaEnum - description: 'Enum: AllergyTypeEnum' + stimulus_type: complex, realistic + advantage: ecological validity + analysis: inter-subject correlation + is_a: NeuroimagingSchemaEnum annotations: source_domain: medical - source_schema: clinical - VaccineTypeEnum: - title: Types of vaccines + source_schema: neuroimaging + IcdoSchemaEnum: + description: Schema-level enum for icdo in medical + is_a: MedicalDomainEnum + abstract: true + annotations: + source_file: medical/oncology/icdo.yaml + TumorTopography: + title: Tumor Topography + description: Major anatomic sites for tumor classification based on ICD-O topography codes (C00-C80). These represent + primary sites where neoplasms occur. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + axis: topography + source_domain: medical + source_schema: icdo + permissible_values: + LIP_ORAL_CAVITY_PHARYNX: + title: Lip, oral cavity, and pharynx + description: Malignant neoplasms of lip, oral cavity and pharynx (C00-C14) + annotations: + icdo_range: C00-C14 + DIGESTIVE_ORGANS: + title: Digestive organs + description: Malignant neoplasms of digestive organs (C15-C26) + annotations: + icdo_range: C15-C26 + ESOPHAGUS: + title: Esophagus + description: Malignant neoplasm of esophagus (C15) + annotations: + icdo_code: C15 + uberon: UBERON:0001043 + is_a: DIGESTIVE_ORGANS + STOMACH: + title: Stomach + description: Malignant neoplasm of stomach (C16) + annotations: + icdo_code: C16 + uberon: UBERON:0000945 + is_a: DIGESTIVE_ORGANS + COLON: + title: Colon + description: Malignant neoplasm of colon (C18) + annotations: + icdo_code: C18 + uberon: UBERON:0001155 + is_a: DIGESTIVE_ORGANS + RECTUM: + title: Rectum + description: Malignant neoplasm of rectum (C20) + annotations: + icdo_code: C20 + uberon: UBERON:0001052 + is_a: DIGESTIVE_ORGANS + LIVER: + title: Liver + description: Malignant neoplasm of liver and intrahepatic bile ducts (C22) + annotations: + icdo_code: C22 + uberon: UBERON:0002107 + is_a: DIGESTIVE_ORGANS + PANCREAS: + title: Pancreas + description: Malignant neoplasm of pancreas (C25) + annotations: + icdo_code: C25 + uberon: UBERON:0001264 + is_a: DIGESTIVE_ORGANS + RESPIRATORY_INTRATHORACIC: + title: Respiratory and intrathoracic organs + description: Malignant neoplasms of respiratory and intrathoracic organs (C30-C39) + annotations: + icdo_range: C30-C39 + LUNG: + title: Lung + description: Malignant neoplasm of bronchus and lung (C34) + annotations: + icdo_code: C34 + uberon: UBERON:0002048 + is_a: RESPIRATORY_INTRATHORACIC + BONE_ARTICULAR_CARTILAGE: + title: Bone and articular cartilage + description: Malignant neoplasms of bone and articular cartilage (C40-C41) + annotations: + icdo_range: C40-C41 + SKIN: + title: Skin + description: Melanoma and other malignant neoplasms of skin (C43-C44) + annotations: + icdo_range: C43-C44 + uberon: UBERON:0002097 + SOFT_TISSUE: + title: Mesothelial and soft tissue + description: Malignant neoplasms of mesothelial and soft tissues (C45-C49) + annotations: + icdo_range: C45-C49 + BREAST: + title: Breast + description: Malignant neoplasm of breast (C50) + annotations: + icdo_code: C50 + uberon: UBERON:0000310 + FEMALE_GENITAL: + title: Female genital organs + description: Malignant neoplasms of female genital organs (C51-C58) + annotations: + icdo_range: C51-C58 + CERVIX_UTERI: + title: Cervix uteri + description: Malignant neoplasm of cervix uteri (C53) + annotations: + icdo_code: C53 + is_a: FEMALE_GENITAL + OVARY: + title: Ovary + description: Malignant neoplasm of ovary (C56) + annotations: + icdo_code: C56 + uberon: UBERON:0000992 + is_a: FEMALE_GENITAL + MALE_GENITAL: + title: Male genital organs + description: Malignant neoplasms of male genital organs (C60-C63) + annotations: + icdo_range: C60-C63 + PROSTATE: + title: Prostate + description: Malignant neoplasm of prostate (C61) + annotations: + icdo_code: C61 + uberon: UBERON:0002367 + is_a: MALE_GENITAL + TESTIS: + title: Testis + description: Malignant neoplasm of testis (C62) + annotations: + icdo_code: C62 + uberon: UBERON:0000473 + is_a: MALE_GENITAL + URINARY_TRACT: + title: Urinary tract + description: Malignant neoplasms of urinary tract (C64-C68) + annotations: + icdo_range: C64-C68 + KIDNEY: + title: Kidney + description: Malignant neoplasm of kidney (C64) + annotations: + icdo_code: C64 + uberon: UBERON:0002113 + is_a: URINARY_TRACT + BLADDER: + title: Bladder + description: Malignant neoplasm of bladder (C67) + annotations: + icdo_code: C67 + uberon: UBERON:0001255 + is_a: URINARY_TRACT + EYE_BRAIN_CNS: + title: Eye, brain, and CNS + description: Malignant neoplasms of eye, brain and other parts of CNS (C69-C72) + annotations: + icdo_range: C69-C72 + BRAIN: + title: Brain + description: Malignant neoplasm of brain (C71) + annotations: + icdo_code: C71 + uberon: UBERON:0000955 + is_a: EYE_BRAIN_CNS + THYROID_ENDOCRINE: + title: Thyroid and other endocrine glands + description: Malignant neoplasms of thyroid and other endocrine glands (C73-C75) + annotations: + icdo_range: C73-C75 + THYROID: + title: Thyroid gland + description: Malignant neoplasm of thyroid gland (C73) + annotations: + icdo_code: C73 + uberon: UBERON:0002046 + is_a: THYROID_ENDOCRINE + LYMPH_NODES: + title: Lymph nodes + description: Malignant neoplasms of lymph nodes (C77) + annotations: + icdo_code: C77 + UNKNOWN_PRIMARY: + title: Unknown primary site + description: Malignant neoplasm of unknown primary site (C80) + annotations: + icdo_code: C80 + is_a: IcdoSchemaEnum + TumorMorphology: + title: Tumor Morphology + description: Major histological types for tumor classification based on ICD-O morphology codes. These represent the cell + type and histological pattern of neoplasms. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + axis: morphology + source_domain: medical + source_schema: icdo + permissible_values: + CARCINOMA_NOS: + title: Carcinoma + description: Malignant epithelial neoplasm, not otherwise specified. General term for cancers arising from epithelial + cells. + meaning: NCIT:C2916 + annotations: + icdo_code: 8010 + ADENOCARCINOMA_NOS: + title: Adenocarcinoma + description: Malignant glandular epithelial neoplasm. Cancer arising from glandular epithelium. + meaning: NCIT:C2852 + annotations: + icdo_code: 8140 + is_a: CARCINOMA_NOS + SQUAMOUS_CELL_CARCINOMA: + title: Squamous Cell Carcinoma + description: Malignant neoplasm arising from squamous epithelium. Common in skin, lung, esophagus, and cervix. + meaning: NCIT:C2929 + annotations: + icdo_code: 8070 + is_a: CARCINOMA_NOS + TRANSITIONAL_CELL_CARCINOMA: + title: Transitional Cell Carcinoma + description: Malignant neoplasm arising from transitional epithelium (urothelium). Most common in bladder and urinary + tract. + meaning: NCIT:C2930 + annotations: + icdo_code: 8120 + is_a: CARCINOMA_NOS + SMALL_CELL_CARCINOMA: + title: Small Cell Neuroendocrine Carcinoma + description: Highly malignant neuroendocrine carcinoma with small cells. Most common in lung. + meaning: NCIT:C3915 + annotations: + icdo_code: 8041 + is_a: CARCINOMA_NOS + LARGE_CELL_CARCINOMA: + title: Large cell carcinoma + description: Undifferentiated carcinoma with large cells. + annotations: + icdo_code: 8012 + is_a: CARCINOMA_NOS + SARCOMA_NOS: + title: Sarcoma + description: Malignant mesenchymal neoplasm, not otherwise specified. Cancers arising from connective tissue, bone, + cartilage, fat, muscle, or blood vessels. + meaning: NCIT:C9118 + annotations: + icdo_code: 8800 + OSTEOSARCOMA: + title: Osteosarcoma + description: Malignant bone-forming tumor. Most common primary malignant bone tumor. + meaning: NCIT:C9145 + annotations: + icdo_code: 9180 + is_a: SARCOMA_NOS + CHONDROSARCOMA: + title: Chondrosarcoma + description: Malignant cartilage-forming tumor. + meaning: NCIT:C2946 + annotations: + icdo_code: 9220 + is_a: SARCOMA_NOS + LIPOSARCOMA: + title: Liposarcoma + description: Malignant tumor arising from adipose tissue. + meaning: NCIT:C3194 + annotations: + icdo_code: 8850 + is_a: SARCOMA_NOS + LEIOMYOSARCOMA: + title: Leiomyosarcoma + description: Malignant tumor arising from smooth muscle. + meaning: NCIT:C3158 + annotations: + icdo_code: 8890 + is_a: SARCOMA_NOS + RHABDOMYOSARCOMA: + title: Rhabdomyosarcoma + description: Malignant tumor arising from skeletal muscle. + meaning: NCIT:C3359 + annotations: + icdo_code: 8900 + is_a: SARCOMA_NOS + LYMPHOMA_NOS: + title: Lymphoma + description: Malignant neoplasm of lymphoid tissue, not otherwise specified. Includes Hodgkin and non-Hodgkin lymphomas. + meaning: NCIT:C3208 + annotations: + icdo_code: 9590 + HODGKIN_LYMPHOMA: + title: Hodgkin Lymphoma + description: Lymphoma characterized by presence of Reed-Sternberg cells and specific histological patterns. + meaning: NCIT:C9357 + annotations: + icdo_code: 9650 + is_a: LYMPHOMA_NOS + NON_HODGKIN_LYMPHOMA: + title: Non-Hodgkin Lymphoma + description: All lymphomas other than Hodgkin lymphoma. Includes B-cell and T-cell lymphomas. + meaning: NCIT:C3211 + annotations: + icdo_codes: 9591, 9670-9729 + is_a: LYMPHOMA_NOS + DIFFUSE_LARGE_B_CELL_LYMPHOMA: + title: Diffuse large B-cell lymphoma + description: Most common type of non-Hodgkin lymphoma. + meaning: NCIT:C8851 + annotations: + icdo_code: 9680 + is_a: NON_HODGKIN_LYMPHOMA + LEUKEMIA_NOS: + title: Leukemia + description: Malignant neoplasm of blood-forming tissues, not otherwise specified. + meaning: NCIT:C3161 + annotations: + icdo_code: 9800 + ACUTE_LYMPHOBLASTIC_LEUKEMIA: + title: Acute lymphoblastic leukemia + description: Acute leukemia of lymphoid precursor cells. + meaning: NCIT:C3167 + annotations: + icdo_code: 9811 + is_a: LEUKEMIA_NOS + ACUTE_MYELOID_LEUKEMIA: + title: Acute myeloid leukemia + description: Acute leukemia of myeloid precursor cells. + meaning: NCIT:C3171 + annotations: + icdo_code: 9861 + is_a: LEUKEMIA_NOS + CHRONIC_LYMPHOCYTIC_LEUKEMIA: + title: Chronic lymphocytic leukemia + description: Chronic leukemia of mature B lymphocytes. + meaning: NCIT:C3163 + annotations: + icdo_code: 9823 + is_a: LEUKEMIA_NOS + CHRONIC_MYELOID_LEUKEMIA: + title: Chronic myeloid leukemia + description: Chronic leukemia characterized by BCR-ABL1 fusion gene. + meaning: NCIT:C3174 + annotations: + icdo_code: 9875 + is_a: LEUKEMIA_NOS + MELANOMA: + title: Melanoma + description: Malignant neoplasm arising from melanocytes. + meaning: NCIT:C3224 + annotations: + icdo_code: 8720 + MESOTHELIOMA: + title: Mesothelioma + description: Malignant tumor arising from mesothelial cells lining pleura, peritoneum, or pericardium. Strongly associated + with asbestos exposure. + meaning: NCIT:C3234 + annotations: + icdo_code: 9050 + GERM_CELL_TUMOR: + title: Germ cell tumor + description: Tumor arising from germ cells. Includes seminoma, teratoma, etc. + meaning: NCIT:C3708 + annotations: + icdo_codes: 9060-9110 + NEUROENDOCRINE_TUMOR: + title: Neuroendocrine tumor + description: Tumor arising from neuroendocrine cells. + annotations: + icdo_codes: 8240-8249 + is_a: IcdoSchemaEnum + TumorBehavior: + title: Tumor Behavior + description: Biological behavior codes used in ICD-O morphology (5th digit). Indicates whether a neoplasm is benign, uncertain, + in situ, or malignant. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + source_domain: medical + source_schema: icdo permissible_values: - LIVE_ATTENUATED: - title: Weakened live pathogen + BENIGN: + title: Benign Neoplasm + description: Non-cancerous neoplasm that does not invade surrounding tissue or metastasize. + meaning: NCIT:C3677 annotations: - examples: MMR, varicella, yellow fever - INACTIVATED: - title: Killed pathogen + icdo_behavior: /0 + UNCERTAIN_BORDERLINE: + title: Uncertain whether benign or malignant + description: Neoplasm with borderline malignancy or uncertain behavior. May recur but typically does not metastasize. annotations: - examples: flu shot, hepatitis A, rabies - SUBUNIT: - title: Pathogen pieces + icdo_behavior: /1 + IN_SITU: + title: Carcinoma In Situ + description: Malignant cells confined to epithelium without invasion through basement membrane. Pre-invasive cancer. + meaning: NCIT:C2917 + annotations: + icdo_behavior: /2 + MALIGNANT_PRIMARY: + title: Malignant, primary site + description: Invasive malignant neoplasm at primary site. Cancer that has invaded through basement membrane. + annotations: + icdo_behavior: /3 + MALIGNANT_METASTATIC: + title: Malignant, metastatic site + description: Malignant neoplasm that has spread from primary site to secondary (metastatic) site. + annotations: + icdo_behavior: /6 + MALIGNANT_UNCERTAIN_PRIMARY_METASTATIC: + title: Malignant, uncertain whether primary or metastatic + description: Malignant neoplasm where it is uncertain if this is the primary site or a metastatic site. + annotations: + icdo_behavior: /9 + is_a: IcdoSchemaEnum + TumorGrade: + title: Tumor Grade + description: Histological grade/differentiation codes used in ICD-O (6th digit). Indicates how abnormal the tumor cells + appear compared to normal cells. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + source_domain: medical + source_schema: icdo + permissible_values: + GRADE_1: + title: Grade I - Well differentiated + description: Tumor cells closely resemble normal cells. Typically slow-growing with better prognosis. + annotations: + icdo_grade: 1 + differentiation: well differentiated + GRADE_2: + title: Grade II - Moderately differentiated + description: Tumor cells show moderate resemblance to normal cells. Intermediate behavior. + annotations: + icdo_grade: 2 + differentiation: moderately differentiated + GRADE_3: + title: Grade III - Poorly differentiated + description: Tumor cells show little resemblance to normal cells. More aggressive with poorer prognosis. + annotations: + icdo_grade: 3 + differentiation: poorly differentiated + GRADE_4: + title: Grade IV - Undifferentiated/Anaplastic + description: Tumor cells bear no resemblance to normal cells. Most aggressive with poorest prognosis. + annotations: + icdo_grade: 4 + differentiation: undifferentiated, anaplastic + GRADE_NOT_DETERMINED: + title: Grade not determined + description: Histological grade has not been assessed or is not applicable. + annotations: + icdo_grade: 9 + T_CELL: + title: T-cell + description: Lymphoma/leukemia of T-cell origin. + annotations: + icdo_grade: 5 + use: lymphomas/leukemias + B_CELL: + title: B-cell + description: Lymphoma/leukemia of B-cell origin. + annotations: + icdo_grade: 6 + use: lymphomas/leukemias + NULL_CELL: + title: Null cell (non-T, non-B) + description: Lymphoma/leukemia of neither T-cell nor B-cell origin. + annotations: + icdo_grade: 7 + use: lymphomas/leukemias + NK_CELL: + title: NK cell + description: Lymphoma/leukemia of natural killer cell origin. + annotations: + icdo_grade: 8 + use: lymphomas/leukemias + is_a: IcdoSchemaEnum + DiagnosisCategoriesSchemaEnum: + description: Schema-level enum for diagnosis_categories in medical + is_a: MedicalDomainEnum + abstract: true + annotations: + source_file: medical/pediatric_oncology/diagnosis_categories.yaml + PediatricOncologyDiagnosisCategory: + title: Pediatric Oncology Diagnosis Category + description: High-level groupings for pediatric cancer diagnoses per CCDI CDE 16607972. Designed for cohort aggregation + across federated data resources. Each diagnosis maps to a single dominant category. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://github.com/CBIIT/ccdi-federation-api/discussions/160 + - https://docs.stjude.cloud/cc4k + annotations: + caDSR_CDE: '16607972' + source: CCDI Federation API + alignment: WHO CNS5, WHO-HAEM5, WHO Pediatric Blue Book + source_domain: medical + source_schema: diagnosis_categories + permissible_values: + ATYPICAL_TERATOID_RHABDOID_TUMOR: + title: Atypical Teratoid/Rhabdoid Tumor + description: Highly malignant embryonal CNS tumor characterized by loss of SMARCB1 (INI1) or SMARCA4 expression. Predominantly + occurs in young children. + meaning: NCIT:C6906 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + CHOROID_PLEXUS_TUMOR: + title: Choroid Plexus Neoplasm + description: Neoplasms arising from the choroid plexus epithelium, including papilloma, atypical papilloma, and carcinoma. + meaning: NCIT:C3473 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + CNS_GERM_CELL_TUMOR: + title: Central Nervous System Germ Cell Tumor + description: Germ cell tumors arising within the central nervous system, including germinoma and non-germinomatous + germ cell tumors. + meaning: NCIT:C5461 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + CNS_SARCOMA: + title: Central Nervous System Sarcoma + description: Sarcomas arising primarily in the central nervous system, including Ewing sarcoma and rhabdomyosarcoma + of CNS. + meaning: NCIT:C5153 + annotations: + category: brain_tumor + CRANIOPHARYNGIOMA: + title: Craniopharyngioma + description: Benign epithelial tumors arising from remnants of Rathke pouch, including adamantinomatous and papillary + subtypes. + meaning: NCIT:C2964 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + EPENDYMOMA: + title: Ependymoma + description: Glial tumors arising from ependymal cells lining the ventricular system and central canal. Includes molecular + subtypes defined by WHO CNS5. + meaning: NCIT:C3017 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + GLIONEURONAL_AND_NEURONAL_TUMOR: + title: Glioneuronal and Neuronal Tumors + description: Tumors with neuronal differentiation including ganglioglioma, dysembryoplastic neuroepithelial tumor + (DNET), and central neurocytoma. + meaning: NCIT:C4747 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + HIGH_GRADE_GLIOMA: + title: Malignant Glioma + description: Aggressive glial tumors including pediatric-type diffuse high-grade gliomas (H3 K27-altered, H3 G34-mutant, + and H3/IDH-wildtype), as well as glioblastoma. + meaning: NCIT:C4822 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + grade: high + LOW_GRADE_GLIOMA: + title: Low Grade Glioma + description: Indolent glial tumors including pilocytic astrocytoma and pediatric-type diffuse low-grade gliomas (MYB/MYBL1-altered, + MAPK pathway-altered). + meaning: NCIT:C132067 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + grade: low + MEDULLOBLASTOMA: + title: Medulloblastoma + description: Embryonal tumor of the cerebellum, classified by molecular subgroups (WNT-activated, SHH-activated, Group + 3, Group 4) per WHO CNS5. + meaning: NCIT:C3222 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + OTHER_CNS_EMBRYONAL_TUMOR: + title: Central Nervous System Embryonal Tumor + description: Embryonal tumors of the CNS other than medulloblastoma and ATRT, including embryonal tumor with multilayered + rosettes (ETMR), CNS neuroblastoma, and pineoblastoma. + meaning: NCIT:C6990 + aliases: + - CNS Embryonal Tumor, NOS + annotations: + category: brain_tumor + who_classification: WHO CNS5 + OTHER_GLIOMA: + title: Glioma + description: Glial tumors not classified as high-grade or low-grade glioma, including angiocentric glioma and astroblastoma. + meaning: NCIT:C3059 + annotations: + category: brain_tumor + OTHER_BRAIN_TUMOR: + title: Brain Neoplasm + description: CNS tumors not fitting other brain tumor categories, including meningioma, schwannoma, and hemangioblastoma. + meaning: NCIT:C2907 + annotations: + category: brain_tumor + LYMPHOBLASTIC_LEUKEMIA: + title: Lymphoblastic Leukemia + description: Acute lymphoblastic leukemia (ALL) including B-ALL and T-ALL with all molecular subtypes (BCR::ABL1, + ETV6::RUNX1, KMT2A-r, DUX4, MEF2D, etc.). + meaning: NCIT:C3167 + aliases: + - ALL + - Acute Lymphoblastic Leukemia + annotations: + category: hematologic + who_classification: WHO-HAEM5 + MYELOID_LEUKEMIA: + title: Myeloid Leukemia + description: Acute myeloid leukemia (AML) and related myeloid neoplasms including AML with defining genetic abnormalities, + therapy-related AML, and juvenile myelomonocytic leukemia (JMML). + meaning: NCIT:C3171 + aliases: + - AML + - Acute Myeloid Leukemia + annotations: + category: hematologic + who_classification: WHO-HAEM5 + HODGKIN_LYMPHOMA: + title: Hodgkin Lymphoma + description: Lymphoid neoplasm characterized by Reed-Sternberg cells, including classical Hodgkin lymphoma and nodular + lymphocyte predominant Hodgkin lymphoma. + meaning: NCIT:C9357 + annotations: + category: hematologic + who_classification: WHO-HAEM5 + NON_HODGKIN_LYMPHOMA: + title: Non-Hodgkin Lymphoma + description: Lymphoid neoplasms other than Hodgkin lymphoma, including Burkitt lymphoma, diffuse large B-cell lymphoma, + anaplastic large cell lymphoma, and lymphoblastic lymphoma. + meaning: NCIT:C3211 + aliases: + - NHL + annotations: + category: hematologic + who_classification: WHO-HAEM5 + LYMPHOPROLIFERATIVE_DISEASE: + title: Lymphoproliferative Disorder + description: Disorders characterized by abnormal lymphocyte proliferation, including post-transplant lymphoproliferative + disorder (PTLD) and hemophagocytic lymphohistiocytosis (HLH). + meaning: NCIT:C9308 + annotations: + category: hematologic + OTHER_HEME_TUMOR: + title: Hematopoietic and Lymphoid Cell Neoplasm + description: Hematologic malignancies not classified elsewhere, including histiocytic disorders, myelodysplastic syndromes, + and myeloproliferative neoplasms. + meaning: NCIT:C27134 + annotations: + category: hematologic + NEUROBLASTOMA: + title: Neuroblastoma + description: Embryonal tumor of the peripheral sympathetic nervous system, arising from neural crest cells. Includes + ganglioneuroblastoma and ganglioneuroma. + meaning: NCIT:C3270 + annotations: + category: solid_tumor + who_classification: WHO Pediatric Blue Book + OSTEOSARCOMA: + title: Osteosarcoma + description: Primary malignant bone tumor characterized by osteoid production, including conventional, telangiectatic, + and small cell variants. + meaning: NCIT:C9145 + annotations: + category: solid_tumor + who_classification: WHO Bone/Soft Tissue + EWING_SARCOMA: + title: Ewing Sarcoma + description: Small round cell sarcoma typically harboring EWSR1 rearrangements, arising in bone or soft tissue. Includes + Ewing sarcoma family of tumors. + meaning: NCIT:C4817 + annotations: + category: solid_tumor + who_classification: WHO Bone/Soft Tissue + RHABDOMYOSARCOMA: + title: Rhabdomyosarcoma + description: Malignant soft tissue tumor with skeletal muscle differentiation, including embryonal, alveolar, and + spindle cell/sclerosing subtypes. + meaning: NCIT:C3359 + annotations: + category: solid_tumor + who_classification: WHO Bone/Soft Tissue + SOFT_TISSUE_TUMOR: + title: Soft Tissue Sarcoma + description: Soft tissue neoplasms other than rhabdomyosarcoma and Ewing sarcoma, including synovial sarcoma, fibrosarcoma, + and other sarcomas. Also includes non-sarcomatous soft tissue tumors. + meaning: NCIT:C9306 + aliases: + - Soft Tissue Sarcoma + annotations: + category: solid_tumor + RHABDOID_TUMOR: + title: Rhabdoid Tumor + description: Highly aggressive tumors characterized by SMARCB1 loss, occurring outside the CNS (extracranial rhabdoid + tumor). Includes malignant rhabdoid tumor of kidney. + meaning: NCIT:C3808 + annotations: + category: solid_tumor + RENAL_TUMOR: + title: Malignant Kidney Neoplasm + description: Kidney tumors including Wilms tumor (nephroblastoma), clear cell sarcoma of kidney, renal cell carcinoma, + and congenital mesoblastic nephroma. + meaning: NCIT:C7548 + aliases: + - Kidney Tumor + - Wilms Tumor + - Renal Tumors + annotations: + category: solid_tumor + who_classification: WHO Pediatric Blue Book + RETINOBLASTOMA: + title: Retinoblastoma + description: Malignant neoplasm of the retina arising from developing retinal cells, associated with RB1 mutations. + meaning: NCIT:C7541 + annotations: + category: solid_tumor + who_classification: WHO Pediatric Blue Book + GERM_CELL_TUMOR: + title: Germ Cell Tumors + description: Tumors arising from primordial germ cells, occurring in gonadal or extragonadal sites. Includes teratoma, + yolk sac tumor, germinoma, choriocarcinoma, and mixed germ cell tumors. Excludes CNS germ cell tumors. + meaning: NCIT:C3708 + annotations: + category: solid_tumor + ENDOCRINE_AND_NEUROENDOCRINE_TUMOR: + title: Endocrine Neoplasm + description: Tumors of endocrine glands and neuroendocrine cells, including thyroid carcinoma, adrenocortical carcinoma, + pheochromocytoma, and paraganglioma. + meaning: NCIT:C3010 + annotations: + category: solid_tumor + OTHER_SOLID_TUMOR: + title: Childhood Solid Neoplasm + description: Solid tumors not classified elsewhere, including hepatoblastoma, pleuropulmonary blastoma, nasopharyngeal + carcinoma, melanoma, and carcinomas. + meaning: NCIT:C9107 + annotations: + category: solid_tumor + is_a: DiagnosisCategoriesSchemaEnum + Iccc3SchemaEnum: + description: Schema-level enum for iccc3 in medical + is_a: MedicalDomainEnum + abstract: true + annotations: + source_file: medical/pediatric_oncology/iccc3.yaml + ICCC3MainGroup: + title: ICCC-3 Main Diagnostic Group + description: The 12 main diagnostic groups of the International Classification of Childhood Cancer, Third Edition. Based + on tumor morphology and primary site with emphasis on morphology. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://seer.cancer.gov/iccc/ + - https://seer.cancer.gov/iccc/iccc3.html + - https://pubmed.ncbi.nlm.nih.gov/15712273/ + annotations: + source: SEER/IARC + version: ICCC-3 + coding_system: ICD-O-3 + source_domain: medical + source_schema: iccc3 + permissible_values: + I_LEUKEMIAS_MYELOPROLIFERATIVE_MYELODYSPLASTIC: + title: Leukemia + description: Includes lymphoid leukemias, acute myeloid leukemias, chronic myeloproliferative diseases, myelodysplastic + syndrome and other myeloproliferative diseases, and unspecified and other specified leukemias. + meaning: NCIT:C3161 + annotations: + iccc_code: I + subgroup_count: 5 + II_LYMPHOMAS_RETICULOENDOTHELIAL: + title: Lymphoma + description: Includes Hodgkin lymphomas, non-Hodgkin lymphomas (except Burkitt lymphoma), Burkitt lymphoma, and miscellaneous + lymphoreticular neoplasms. + meaning: NCIT:C3208 + annotations: + iccc_code: II + subgroup_count: 4 + III_CNS_INTRACRANIAL_INTRASPINAL: + title: Brain Neoplasm + description: Includes ependymomas and choroid plexus tumor, astrocytomas, intracranial and intraspinal embryonal tumors, + other gliomas, other specified intracranial and intraspinal neoplasms, and unspecified intracranial and intraspinal + neoplasms. Also includes nonmalignant CNS tumors. + meaning: NCIT:C2907 + annotations: + iccc_code: III + subgroup_count: 6 + includes_nonmalignant: true + IV_NEUROBLASTOMA_PERIPHERAL_NERVOUS: + title: Neuroblastoma + description: Includes neuroblastoma and ganglioneuroblastoma, and other peripheral nervous cell tumors. + meaning: NCIT:C3270 + annotations: + iccc_code: IV + subgroup_count: 2 + V_RETINOBLASTOMA: + title: Retinoblastoma + description: Malignant neoplasm of the retina. Single group with no subgroups. + meaning: NCIT:C7541 + annotations: + iccc_code: V + subgroup_count: 1 + VI_RENAL_TUMORS: + title: Malignant Kidney Neoplasm + description: Includes nephroblastoma and other nonepithelial renal tumors, renal carcinomas, and unspecified malignant + renal tumors. + meaning: NCIT:C7548 + annotations: + iccc_code: VI + subgroup_count: 3 + VII_HEPATIC_TUMORS: + title: Liver Carcinoma + description: Includes hepatoblastoma, hepatic carcinomas, and unspecified malignant hepatic tumors. + meaning: NCIT:C7927 + annotations: + iccc_code: VII + subgroup_count: 3 + VIII_MALIGNANT_BONE_TUMORS: + title: Malignant Bone Neoplasm + description: Includes osteosarcomas, chondrosarcomas, Ewing tumor and related sarcomas of bone, other specified malignant + bone tumors, and unspecified malignant bone tumors. + meaning: NCIT:C4016 + annotations: + iccc_code: VIII + subgroup_count: 5 + IX_SOFT_TISSUE_SARCOMAS: + title: Soft Tissue Sarcoma + description: Includes rhabdomyosarcomas, fibrosarcomas/peripheral nerve sheath tumors/other fibrous neoplasms, Kaposi + sarcoma, other specified soft tissue sarcomas, and unspecified soft tissue sarcomas. + meaning: NCIT:C9306 + annotations: + iccc_code: IX + subgroup_count: 5 + X_GERM_CELL_GONADAL: + title: Germ Cell Tumor + description: Includes intracranial and intraspinal germ cell tumors, malignant extracranial and extragonadal germ + cell tumors, malignant gonadal germ cell tumors, gonadal carcinomas, and other and unspecified malignant gonadal + tumors. + meaning: NCIT:C3708 + annotations: + iccc_code: X + subgroup_count: 5 + XI_EPITHELIAL_MELANOMA: + title: Epithelial Neoplasm + description: Includes adrenocortical carcinomas, thyroid carcinomas, nasopharyngeal carcinomas, malignant melanomas, + skin carcinomas, and other and unspecified carcinomas. + meaning: NCIT:C3709 + annotations: + iccc_code: XI + subgroup_count: 6 + XII_OTHER_UNSPECIFIED: + title: Neoplasm + description: Includes other specified malignant tumors and other unspecified malignant tumors not classifiable in + groups I-XI. + meaning: NCIT:C3262 + annotations: + iccc_code: XII + subgroup_count: 2 + is_a: Iccc3SchemaEnum + ICCC3Subgroup: + title: ICCC-3 Diagnostic Subgroup + description: The 47 diagnostic subgroups of the International Classification of Childhood Cancer, Third Edition. These + provide more detailed classification within each of the 12 main groups. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://seer.cancer.gov/iccc/iccc3.html + - https://seer.cancer.gov/iccc/iccc3_ext.html + annotations: + source: SEER/IARC + version: ICCC-3 + source_domain: medical + source_schema: iccc3 + permissible_values: + Ia_LYMPHOID_LEUKEMIAS: + title: Acute Lymphoblastic Leukemia + description: Precursor cell lymphoblastic leukemia, NOS; precursor cell lymphoblastic leukemia, B-cell; precursor + cell lymphoblastic leukemia, T-cell; Burkitt cell leukemia; and other lymphoid leukemias. + meaning: NCIT:C3167 + annotations: + main_group: I + icdo3_codes: 9820-9827, 9835-9837 + Ib_ACUTE_MYELOID_LEUKEMIAS: + title: Acute Myeloid Leukemia + description: Acute myeloid leukemia and variants including AML with maturation, acute promyelocytic leukemia, acute + myelomonocytic leukemia, acute monoblastic leukemia, acute megakaryoblastic leukemia, etc. + meaning: NCIT:C3171 + annotations: + main_group: I + icdo3_codes: 9840, 9861, 9866-9867, 9870-9874, 9891, 9895-9897, 9910, 9920, 9931 + Ic_CHRONIC_MYELOPROLIFERATIVE: + title: Myeloproliferative Neoplasm + description: Chronic myeloid leukemia, NOS; juvenile myelomonocytic leukemia; and other chronic myeloproliferative + diseases. + meaning: NCIT:C4345 + annotations: + main_group: I + icdo3_codes: 9863, 9875-9876, 9945-9946, 9950, 9960-9964 + Id_MYELODYSPLASTIC_OTHER_MYELOPROLIFERATIVE: + title: Myelodysplastic Syndrome + description: Myelodysplastic syndrome, NOS; refractory anemia; refractory anemia with ringed sideroblasts; refractory + anemia with excess blasts. + meaning: NCIT:C3247 + annotations: + main_group: I + icdo3_codes: 9945, 9980, 9982-9983, 9985-9989 + Ie_UNSPECIFIED_OTHER_LEUKEMIAS: + title: Leukemia + description: Leukemia, NOS and other specified leukemias not elsewhere classified. + meaning: NCIT:C3161 + annotations: + main_group: I + icdo3_codes: 9800-9801, 9805-9809, 9860, 9930 + IIa_HODGKIN_LYMPHOMAS: + title: Hodgkin Lymphoma + description: Classical Hodgkin lymphoma and nodular lymphocyte predominant Hodgkin lymphoma. + meaning: NCIT:C9357 + annotations: + main_group: II + icdo3_codes: 9650-9655, 9659, 9661-9665, 9667 + IIb_NON_HODGKIN_LYMPHOMAS: + title: Non-Hodgkin Lymphoma + description: Diffuse large B-cell lymphoma, follicular lymphoma, peripheral T-cell lymphoma, anaplastic large cell + lymphoma, and other non-Hodgkin lymphomas. + meaning: NCIT:C3211 + annotations: + main_group: II + icdo3_codes: 9591, 9670-9686, 9689-9691, 9695, 9698-9702, 9705, 9708-9709, 9714-9719, 9727-9729 + IIc_BURKITT_LYMPHOMA: + title: Burkitt Lymphoma + description: Burkitt lymphoma and Burkitt-like lymphoma. + meaning: NCIT:C2912 + annotations: + main_group: II + icdo3_codes: '9687' + IId_MISC_LYMPHORETICULAR: + title: Hematopoietic and Lymphoid Cell Neoplasm + description: Lymphoreticular neoplasms not elsewhere classified including lymphomatoid granulomatosis and post-transplant + lymphoproliferative disorder. + meaning: NCIT:C27134 + annotations: + main_group: II + icdo3_codes: 9740-9742, 9750, 9754-9758, 9930, 9970 + IIIa_EPENDYMOMAS: + title: Ependymoma + description: Ependymoma, anaplastic ependymoma, myxopapillary ependymoma, and choroid plexus papilloma and carcinoma. + meaning: NCIT:C3017 + annotations: + main_group: III + icdo3_codes: 9383, 9390-9394 + IIIb_ASTROCYTOMAS: + title: Astrocytoma + description: Pilocytic astrocytoma, diffuse astrocytoma, anaplastic astrocytoma, glioblastoma, and other astrocytic + tumors. + meaning: NCIT:C60781 + annotations: + main_group: III + icdo3_codes: 9380, 9384, 9400-9411, 9420, 9424 + IIIc_INTRACRANIAL_EMBRYONAL: + title: Central Nervous System Embryonal Tumor + description: Medulloblastoma, primitive neuroectodermal tumor, medulloepithelioma, atypical teratoid/rhabdoid tumor, + and other embryonal tumors. + meaning: NCIT:C6990 + annotations: + main_group: III + icdo3_codes: 9470-9474, 9480, 9490, 9500-9508 + IIId_OTHER_GLIOMAS: + title: Glioma + description: Oligodendroglioma, anaplastic oligodendroglioma, mixed glioma, and other gliomas not elsewhere classified. + meaning: NCIT:C3059 + annotations: + main_group: III + icdo3_codes: 9380-9382, 9430, 9440-9460 + IIIe_OTHER_INTRACRANIAL_INTRASPINAL: + title: Brain Neoplasm + description: Pituitary adenoma, craniopharyngioma, pineal tumors, and other specified intracranial neoplasms. + meaning: NCIT:C2907 + annotations: + main_group: III + IIIf_UNSPECIFIED_INTRACRANIAL: + title: Brain Neoplasm + description: Intracranial and intraspinal neoplasms, NOS. + meaning: NCIT:C2907 + annotations: + main_group: III + icdo3_codes: 8000-8005 + IVa_NEUROBLASTOMA_GANGLIONEUROBLASTOMA: + title: Neuroblastoma + description: Neuroblastoma, NOS and ganglioneuroblastoma. + meaning: NCIT:C3270 + annotations: + main_group: IV + icdo3_codes: 9490, 9500 + IVb_OTHER_PERIPHERAL_NERVOUS: + title: Peripheral Nervous System Neoplasm + description: Other peripheral nerve tumors including ganglioneuroma and peripheral nerve sheath tumors. + meaning: NCIT:C3321 + annotations: + main_group: IV + icdo3_codes: 9501-9504, 9520-9523 + V_RETINOBLASTOMA: + title: Retinoblastoma + description: Retinoblastoma. + meaning: NCIT:C7541 + annotations: + main_group: V + icdo3_codes: 9510-9514 + VIa_NEPHROBLASTOMA: + title: Wilms Tumor + description: Wilms tumor (nephroblastoma), clear cell sarcoma of kidney, rhabdoid tumor of kidney, and other nonepithelial + renal tumors. + meaning: NCIT:C3267 + annotations: + main_group: VI + icdo3_codes: 8960, 8963-8964 + VIb_RENAL_CARCINOMAS: + title: Renal Cell Carcinoma + description: Renal cell carcinoma and other renal carcinomas. + meaning: NCIT:C9385 + annotations: + main_group: VI + VIc_UNSPECIFIED_RENAL: + title: Malignant Kidney Neoplasm + description: Malignant renal tumors, NOS. + meaning: NCIT:C7548 + annotations: + main_group: VI + VIIa_HEPATOBLASTOMA: + title: Hepatoblastoma + description: Hepatoblastoma. + meaning: NCIT:C3728 + annotations: + main_group: VII + icdo3_codes: '8970' + VIIb_HEPATIC_CARCINOMAS: + title: Hepatocellular Carcinoma + description: Hepatocellular carcinoma, cholangiocarcinoma, and other hepatic carcinomas. + meaning: NCIT:C3099 + annotations: + main_group: VII + VIIc_UNSPECIFIED_HEPATIC: + title: Liver Carcinoma + description: Malignant hepatic tumors, NOS. + meaning: NCIT:C7927 + annotations: + main_group: VII + VIIIa_OSTEOSARCOMAS: + title: Osteosarcoma + description: Osteosarcoma, NOS and variants including chondroblastic, fibroblastic, telangiectatic, and small cell + osteosarcoma. + meaning: NCIT:C9145 + annotations: + main_group: VIII + icdo3_codes: 9180-9187, 9191-9195 + VIIIb_CHONDROSARCOMAS: + title: Chondrosarcoma + description: Chondrosarcoma, NOS and variants. + meaning: NCIT:C2946 + annotations: + main_group: VIII + icdo3_codes: 9220-9231, 9240-9243 + VIIIc_EWING_TUMOR_BONE: + title: Ewing Sarcoma + description: Ewing sarcoma of bone and peripheral primitive neuroectodermal tumor of bone. + meaning: NCIT:C4817 + annotations: + main_group: VIII + icdo3_codes: 9260, 9364 + VIIId_OTHER_BONE: + title: Malignant Bone Neoplasm + description: Other specified malignant bone tumors including giant cell tumor of bone, malignant and adamantinoma. + meaning: NCIT:C4016 + annotations: + main_group: VIII + VIIIe_UNSPECIFIED_BONE: + title: Malignant Bone Neoplasm + description: Malignant bone tumors, NOS. + meaning: NCIT:C4016 + annotations: + main_group: VIII + IXa_RHABDOMYOSARCOMAS: + title: Rhabdomyosarcoma + description: Rhabdomyosarcoma, NOS; embryonal rhabdomyosarcoma; alveolar rhabdomyosarcoma; and other rhabdomyosarcomas. + meaning: NCIT:C3359 + annotations: + main_group: IX + icdo3_codes: 8900-8905, 8910, 8912, 8920 + IXb_FIBROSARCOMAS: + title: Fibrosarcoma + description: Fibrosarcoma, NOS; infantile fibrosarcoma; dermatofibrosarcoma; and malignant peripheral nerve sheath + tumor. + meaning: NCIT:C3043 + annotations: + main_group: IX + icdo3_codes: 8810-8815, 8820-8823, 8830, 8832-8833, 9540, 9560-9561 + IXc_KAPOSI_SARCOMA: + title: Kaposi Sarcoma + description: Kaposi sarcoma. + meaning: NCIT:C9087 + annotations: + main_group: IX + icdo3_codes: '9140' + IXd_OTHER_SOFT_TISSUE: + title: Soft Tissue Sarcoma + description: Includes liposarcoma, leiomyosarcoma, synovial sarcoma, hemangiosarcoma, and other specified soft tissue + sarcomas. + meaning: NCIT:C9306 + annotations: + main_group: IX + IXe_UNSPECIFIED_SOFT_TISSUE: + title: Soft Tissue Sarcoma + description: Soft tissue sarcomas, NOS. + meaning: NCIT:C9306 + annotations: + main_group: IX + Xa_INTRACRANIAL_GERM_CELL: + title: Central Nervous System Germ Cell Tumor + description: CNS germ cell tumors including germinoma, teratoma, and nongerminomatous germ cell tumors. + meaning: NCIT:C5461 + annotations: + main_group: X + icdo3_codes: 9060-9102 + Xb_EXTRACRANIAL_EXTRAGONADAL_GERM_CELL: + title: Malignant Extragonadal Germ Cell Tumor + description: Extracranial germ cell tumors not involving the gonads including sacrococcygeal, retroperitoneal, and + mediastinal germ cell tumors. + meaning: NCIT:C8881 + annotations: + main_group: X + Xc_GONADAL_GERM_CELL: + title: Germ Cell Tumor + description: Germ cell tumors of the ovary and testis including dysgerminoma, yolk sac tumor, embryonal carcinoma, + and mixed germ cell tumors. + meaning: NCIT:C3708 + annotations: + main_group: X + Xd_GONADAL_CARCINOMAS: + title: Epithelial Neoplasm + description: Carcinomas arising in the ovary and testis. + meaning: NCIT:C3709 + annotations: + main_group: X + Xe_OTHER_GONADAL: + title: Germ Cell Tumor + description: Other specified and unspecified gonadal tumors. + meaning: NCIT:C3708 + annotations: + main_group: X + XIa_ADRENOCORTICAL_CARCINOMAS: + title: Adrenal Cortical Carcinoma + description: Adrenocortical carcinoma. + meaning: NCIT:C9325 + annotations: + main_group: XI + icdo3_codes: '8370' + XIb_THYROID_CARCINOMAS: + title: Malignant Thyroid Gland Neoplasm + description: Papillary thyroid carcinoma, follicular thyroid carcinoma, and medullary thyroid carcinoma. + meaning: NCIT:C7510 + annotations: + main_group: XI + XIc_NASOPHARYNGEAL_CARCINOMAS: + title: Nasopharyngeal Carcinoma + description: Nasopharyngeal carcinoma and related carcinomas. + meaning: NCIT:C3871 + annotations: + main_group: XI + XId_MALIGNANT_MELANOMAS: + title: Melanoma + description: Cutaneous and non-cutaneous malignant melanomas. + meaning: NCIT:C3224 + annotations: + main_group: XI + XIe_SKIN_CARCINOMAS: + title: Skin Neoplasm + description: Basal cell carcinoma, squamous cell carcinoma of skin, and other skin carcinomas. + meaning: NCIT:C3372 + annotations: + main_group: XI + XIf_OTHER_CARCINOMAS: + title: Epithelial Neoplasm + description: Carcinomas at other sites and carcinomas, NOS. + meaning: NCIT:C3709 + annotations: + main_group: XI + XIIa_OTHER_SPECIFIED: + title: Neoplasm + description: Malignant tumors not classifiable in groups I-XI but with specified histology. + meaning: NCIT:C3262 + annotations: + main_group: XII + XIIb_OTHER_UNSPECIFIED: + title: Neoplasm + description: Malignant tumors, NOS not classifiable in groups I-XI. + meaning: NCIT:C3262 + annotations: + main_group: XII + is_a: Iccc3SchemaEnum + NeuroblastomaSchemaEnum: + description: Schema-level enum for neuroblastoma in medical + is_a: MedicalDomainEnum + abstract: true + annotations: + source_file: medical/pediatric_oncology/staging/neuroblastoma.yaml + INRGSSStage: + title: INRGSS Stage + description: International Neuroblastoma Risk Group Staging System (INRGSS) stages. A clinical staging system based on + imaging and image-defined risk factors (IDRFs), effective for diagnosis years 2024+. Allows staging before any treatment, + unlike the surgical INSS system. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://staging.seer.cancer.gov/pediatric/input/1.0/neuroblastoma/inrgss/ + - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650389/ + annotations: + source: SEER/INRG Task Force + effective_year: 2024 + staging_basis: imaging + source_domain: medical + source_schema: neuroblastoma + permissible_values: + L1: + title: INRG Stage L1 + description: Localized tumor not involving vital structures as defined by the list of image-defined risk factors and + confined to one body compartment (neck, chest, abdomen, or pelvis). + meaning: NCIT:C133428 + annotations: + localized: true + idrfs_present: false + L2: + title: INRG Stage L2 + description: Locoregional tumor with presence of one or more image-defined risk factors. The tumor has not spread + far from where it started but has at least one IDRF. + meaning: NCIT:C133429 + annotations: + localized: true + idrfs_present: true + M: + title: INRG Stage M + description: Distant metastatic disease (except as defined for MS). The tumor has spread (metastasized) to distant + parts of the body. + meaning: NCIT:C133430 annotations: - examples: hepatitis B, HPV, pertussis - TOXOID: - title: Inactivated toxin + metastatic: true + MS: + title: INRG Stage MS + description: Metastatic disease in children younger than 18 months with metastases confined to skin, liver, and/or + bone marrow (bone marrow involvement limited to <10% tumor cells). This stage has a favorable prognosis despite + metastatic disease. + meaning: NCIT:C133431 + aliases: + - Stage 4S equivalent + annotations: + metastatic: true + special_category: true + age_restriction: <18 months + favorable_prognosis: true + is_a: NeuroblastomaSchemaEnum + INSSStage: + title: INSS Stage + description: International Neuroblastoma Staging System (INSS) stages. A post-surgical staging system based on extent + of tumor resection, lymph node involvement, and metastatic spread. This is the legacy system; INRGSS is now preferred + for diagnosis years 2024+. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.ncbi.nlm.nih.gov/books/NBK65747.5/table/CDR0000062786__725/ + - https://www.cancer.org/cancer/types/neuroblastoma/detection-diagnosis-staging/staging.html + annotations: + source: INSS Consensus Conference + staging_basis: surgical + legacy_system: true + source_domain: medical + source_schema: neuroblastoma + permissible_values: + STAGE_1: + title: INSS Stage 1 + description: Localized tumor with complete gross excision, with or without microscopic residual disease; representative + ipsilateral lymph nodes negative for tumor microscopically. + meaning: NCIT:C85417 + annotations: + localized: true + resection: complete + STAGE_2A: + title: INSS Stage 2A + description: Localized tumor with incomplete gross excision; representative ipsilateral nonadherent lymph nodes negative + for tumor microscopically. + meaning: NCIT:C85418 + annotations: + localized: true + resection: incomplete + lymph_nodes: negative + STAGE_2B: + title: INSS Stage 2B + description: Localized tumor with or without complete gross excision, with ipsilateral nonadherent lymph nodes positive + for tumor. Enlarged contralateral lymph nodes must be negative microscopically. + meaning: NCIT:C85419 + annotations: + localized: true + lymph_nodes: ipsilateral_positive + STAGE_3: + title: INSS Stage 3 + description: Unresectable unilateral tumor infiltrating across the midline, with or without regional lymph node involvement; + or localized unilateral tumor with contralateral regional lymph node involvement; or midline tumor with bilateral + extension by infiltration (unresectable) or by lymph node involvement. + meaning: NCIT:C85420 + annotations: + localized: false + crosses_midline: true + STAGE_4: + title: INSS Stage 4 + description: Any primary tumor with dissemination to distant lymph nodes, bone, bone marrow, liver, skin, and/or other + organs (except as defined for stage 4S). + meaning: NCIT:C85421 + annotations: + metastatic: true + STAGE_4S: + title: INSS Stage 4S + description: Localized primary tumor (as defined for stage 1, 2A, or 2B) with dissemination limited to skin, liver, + and/or bone marrow (limited to infants <1 year of age). Marrow involvement should be minimal (<10% of total nucleated + cells). + meaning: NCIT:C85422 + aliases: + - Special stage 4 + annotations: + metastatic: true + special_category: true + age_restriction: <12 months + favorable_prognosis: true + is_a: NeuroblastomaSchemaEnum + NeuroblastomaRiskGroup: + title: Neuroblastoma Risk Group + description: International Neuroblastoma Risk Group (INRG) pretreatment risk classification groups. Combines INRGSS stage + with tumor histology, MYCN status, ploidy, and other prognostic factors. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650388/ + annotations: + source: INRG Task Force + source_domain: medical + source_schema: neuroblastoma + permissible_values: + VERY_LOW: + title: Very Low Risk + description: Very low risk neuroblastoma with excellent prognosis. Typically includes L1 tumors and MS without MYCN + amplification. annotations: - examples: diphtheria, tetanus - MRNA: - title: mRNA vaccine + expected_efs: '>85%' + LOW: + title: Low Risk + description: Low risk neuroblastoma with favorable prognosis. Treatment may include surgery alone or observation. annotations: - examples: COVID-19 (Pfizer, Moderna) - VIRAL_VECTOR: - title: Modified virus carrier + expected_efs: '>75%' + INTERMEDIATE: + title: Intermediate Risk + description: Intermediate risk neuroblastoma requiring multimodal treatment including chemotherapy. annotations: - examples: COVID-19 (J&J, AstraZeneca) - is_a: ClinicalSchemaEnum - description: 'Enum: VaccineTypeEnum' + expected_efs: 50-75% + HIGH: + title: High Risk Neuroblastoma + description: High risk neuroblastoma with poor prognosis. Requires intensive multimodal therapy including high-dose + chemotherapy with autologous stem cell rescue, surgery, radiation, and immunotherapy. + meaning: NCIT:C150281 + annotations: + expected_efs: <50% + mycn_amplified: often + is_a: NeuroblastomaSchemaEnum + ImageDefinedRiskFactor: + title: Image-Defined Risk Factor + description: Image-defined risk factors (IDRFs) used in INRGSS staging to determine surgical risk. Presence of any IDRF + upgrades a tumor from L1 to L2. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650389/ + annotations: + source: INRG Task Force + source_domain: medical + source_schema: neuroblastoma + permissible_values: + IPSILATERAL_TUMOR_EXTENSION_TO_BODY_CAVITIES: + title: Ipsilateral tumor extension within two body compartments + description: Tumor extension from neck to chest, chest to abdomen, or abdomen to pelvis. + NECK_ENCASING_CAROTID_OR_VERTEBRAL: + title: Neck - Tumor encasing carotid and/or vertebral artery + description: Tumor encasing carotid artery and/or vertebral artery. + NECK_ENCASING_JUGULAR: + title: Neck - Tumor encasing internal jugular vein + description: Tumor encasing internal jugular vein. + NECK_EXTENDING_TO_SKULL_BASE: + title: Neck - Tumor extending to base of skull + description: Tumor extending to base of skull. + NECK_COMPRESSING_TRACHEA: + title: Neck - Tumor compressing trachea + description: Tumor compressing the trachea. + CERVICOTHORACIC_ENCASING_BRACHIAL_PLEXUS: + title: Cervico-thoracic junction - Tumor encasing brachial plexus roots + description: Tumor encasing brachial plexus roots (C5-T1). + CERVICOTHORACIC_ENCASING_SUBCLAVIAN: + title: Cervico-thoracic junction - Tumor encasing subclavian vessels + description: Tumor encasing subclavian vessels and/or vertebral artery and/or carotid artery. + CERVICOTHORACIC_COMPRESSING_TRACHEA: + title: Cervico-thoracic junction - Tumor compressing trachea + description: Tumor compressing the trachea. + THORAX_ENCASING_AORTA: + title: Thorax - Tumor encasing aorta and/or major branches + description: Tumor encasing aorta and/or major branches. + THORAX_COMPRESSING_TRACHEA_BRONCHI: + title: Thorax - Tumor compressing trachea and/or principal bronchi + description: Tumor compressing trachea and/or principal bronchi. + THORAX_LOWER_MEDIASTINUM_INFILTRATING: + title: Thorax - Lower mediastinal tumor infiltrating costo-vertebral junction + description: Lower mediastinal tumor infiltrating the costo-vertebral junction between T9 and T12. + THORACOABDOMINAL_ENCASING_AORTA_CELIAC: + title: Thoraco-abdominal - Tumor encasing aorta and/or vena cava + description: Tumor encasing the aorta and/or vena cava. + ABDOMEN_PELVIS_ENCASING_CELIAC_SMA: + title: Abdomen/pelvis - Tumor encasing celiac axis and/or SMA + description: Tumor encasing celiac axis and/or superior mesenteric artery. + ABDOMEN_PELVIS_ENCASING_RENAL_VESSELS: + title: Abdomen/pelvis - Tumor encasing origin of renal vessels + description: Tumor encasing origin of renal vessels. + ABDOMEN_PELVIS_ENCASING_AORTA_IVC: + title: Abdomen/pelvis - Tumor encasing aorta and/or IVC + description: Tumor encasing aorta and/or inferior vena cava. + ABDOMEN_PELVIS_ENCASING_ILIAC_VESSELS: + title: Abdomen/pelvis - Tumor encasing iliac vessels + description: Tumor encasing iliac vessels. + ABDOMEN_PELVIS_PELVIC_CROSSING_SCIATIC_NOTCH: + title: Abdomen/pelvis - Pelvic tumor crossing sciatic notch + description: Pelvic tumor crossing the sciatic notch. + INTRASPINAL_EXTENSION: + title: Intraspinal tumor extension + description: Intraspinal tumor extension provided that more than one third of the spinal canal in the axial plane + is invaded and/or the perimedullary leptomeningeal spaces are not visible and/or spinal cord signal is abnormal. + ADJACENT_ORGAN_INFILTRATION: + title: Infiltration of adjacent organs/structures + description: Infiltration of adjacent organs/structures such as pericardium, diaphragm, kidney, liver, duodeno-pancreatic + block, and mesentery. + is_a: NeuroblastomaSchemaEnum + PhysicsDomainEnum: + description: Domain-level enum for physics value sets + is_a: ValueSetEnum + abstract: true + ParticlePhysicsSchemaEnum: + description: Schema-level enum for particle_physics in physics + is_a: PhysicsDomainEnum + abstract: true + annotations: + source_file: physics/particle_physics.yaml + ParticleAcceleratorType: + title: Particle Accelerator Type + description: Types of particle accelerator facilities used in high-energy physics research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LINEAR_ACCELERATOR: + description: Linear accelerator (linac) that accelerates particles along a straight path + title: Linear Accelerator + meaning: NCIT:C28169 + SYNCHROTRON: + description: Circular accelerator with increasing magnetic field to maintain constant orbit radius + title: Synchrotron + meaning: NCIT:C48205 + CYCLOTRON: + description: Circular accelerator using constant magnetic field and alternating electric field + title: Cyclotron + meaning: NCIT:C94881 + STORAGE_RING: + description: Circular ring that stores particles at constant energy for extended periods + FREE_ELECTRON_LASER: + description: Accelerator-based light source using relativistic electrons in a magnetic undulator + COLLIDER: + description: Accelerator that directs two counter-rotating beams into head-on collisions + SPALLATION_SOURCE: + description: Accelerator-driven neutron source where protons strike a heavy metal target + BETATRON: + description: Circular accelerator that uses a changing magnetic field to accelerate electrons + is_a: ParticlePhysicsSchemaEnum + annotations: + source_domain: physics + source_schema: particle_physics + FundamentalParticleType: + title: Fundamental Particle Type + description: Standard Model fundamental particles classified by type + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ELECTRON: + description: First-generation charged lepton with mass 0.511 MeV + title: electron + meaning: CHEBI:10545 + MUON: + description: Second-generation charged lepton with mass 105.66 MeV + title: muon + meaning: CHEBI:36356 + TAU: + description: Third-generation charged lepton with mass 1777 MeV + title: tau lepton + meaning: CHEBI:36355 + ELECTRON_NEUTRINO: + description: First-generation neutrino associated with the electron + title: electron neutrino + meaning: CHEBI:30223 + MUON_NEUTRINO: + description: Second-generation neutrino associated with the muon + title: muon neutrino + meaning: CHEBI:36353 + TAU_NEUTRINO: + description: Third-generation neutrino associated with the tau lepton + title: tau neutrino + meaning: CHEBI:36354 + UP_QUARK: + description: First-generation quark with charge +2/3 + title: up quark + meaning: CHEBI:36366 + DOWN_QUARK: + description: First-generation quark with charge -1/3 + title: down quark + meaning: CHEBI:36367 + CHARM_QUARK: + description: Second-generation quark with charge +2/3 + title: charm quark + meaning: CHEBI:36369 + STRANGE_QUARK: + description: Second-generation quark with charge -1/3 + title: strange quark + meaning: CHEBI:36368 + TOP_QUARK: + description: Third-generation quark with charge +2/3 + title: top quark + meaning: CHEBI:36371 + BOTTOM_QUARK: + description: Third-generation quark with charge -1/3 + title: bottom quark + meaning: CHEBI:36370 + PHOTON: + description: Massless gauge boson mediating the electromagnetic force + title: photon + meaning: CHEBI:30212 + GLUON: + description: Massless gauge boson mediating the strong force between quarks + W_BOSON: + description: Massive gauge boson mediating the charged weak interaction + Z_BOSON: + description: Massive gauge boson mediating the neutral weak interaction + HIGGS_BOSON: + description: Scalar boson associated with the Higgs field and mass generation mechanism + title: Higgs boson + meaning: CHEBI:146278 + is_a: ParticlePhysicsSchemaEnum annotations: - source_domain: medical - source_schema: clinical - BMIClassificationEnum: - title: Body Mass Index classifications - permissible_values: - UNDERWEIGHT: - title: BMI less than 18.5 - annotations: - bmi_range: <18.5 - NORMAL_WEIGHT: - title: BMI 18.5-24.9 - annotations: - bmi_range: 18.5-24.9 - OVERWEIGHT: - title: BMI 25.0-29.9 - annotations: - bmi_range: 25.0-29.9 - OBESE_CLASS_I: - title: BMI 30.0-34.9 - annotations: - bmi_range: 30.0-34.9 - OBESE_CLASS_II: - title: BMI 35.0-39.9 - annotations: - bmi_range: 35.0-39.9 - OBESE_CLASS_III: - title: BMI 40.0 or greater - annotations: - bmi_range: ≥40.0 - aliases: morbid obesity - is_a: ClinicalSchemaEnum - description: 'Enum: BMIClassificationEnum' + source_domain: physics + source_schema: particle_physics + DetectorType: + title: Detector Type + description: Types of detectors used in particle physics experiments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CALORIMETER: + description: Detector that measures the total energy of incident particles by absorbing them + TRACKING_DETECTOR: + description: Detector that records the trajectories of charged particles + TIME_PROJECTION_CHAMBER: + description: Gas-filled detector that provides three-dimensional particle track reconstruction + CHERENKOV_DETECTOR: + description: Detector that identifies particles by measuring Cherenkov radiation emitted in a medium + SCINTILLATOR: + description: Detector using scintillating material that emits light when traversed by ionizing radiation + SILICON_STRIP_DETECTOR: + description: Semiconductor detector using finely segmented silicon strips for precise position measurement + DRIFT_CHAMBER: + description: Gas-filled wire chamber that measures particle positions from electron drift times + MUON_SPECTROMETER: + description: Large detector system designed to identify and measure the momentum of muons + is_a: ParticlePhysicsSchemaEnum annotations: - source_domain: medical - source_schema: clinical - NeuroimagingSchemaEnum: - description: Schema-level enum for neuroimaging in medical - is_a: MedicalDomainEnum + source_domain: physics + source_schema: particle_physics + RadiationSchemaEnum: + description: Schema-level enum for radiation in physics + is_a: PhysicsDomainEnum abstract: true annotations: - source_file: medical/neuroimaging.yaml - MRIModalityEnum: - description: MRI imaging modalities and techniques + source_file: physics/radiation.yaml + RadiationTypeEnum: + title: Radiation Type + description: High-level classification of radiation types including electromagnetic, acoustic, and particle radiation. + Dynamically populated from ENVO. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + reachable_from: + source_ontology: obo:envo + source_nodes: + - ENVO:01001023 + include_self: true + relationship_types: + - rdfs:subClassOf + is_a: RadiationSchemaEnum + annotations: + source_domain: physics + source_schema: radiation + ElectromagneticRadiationTypeEnum: + title: Electromagnetic Radiation Type + description: Types of electromagnetic radiation across the spectrum, from radio waves to gamma rays, including ionizing + and non-ionizing radiation. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ELECTROMAGNETIC_RADIATION: + title: electromagnetic radiation + description: Radiation during which waves of the electromagnetic field propagate through space + meaning: ENVO:01001026 + IONIZING_RADIATION: + title: ionizing radiation + description: Electromagnetic radiation with sufficient energy to disrupt molecular bonds or alter electron numbers + meaning: ENVO:21001219 + GAMMA_RAY_RADIATION: + title: gamma-ray radiation + description: Penetrating electromagnetic radiation emitted from radioactive decay of atomic nuclei + meaning: ENVO:21001218 + X_RAY_RADIATION: + title: X-ray radiation + description: Penetrating electromagnetic radiation emitted by high-energy electrons falling to lower energy states + meaning: ENVO:21001217 + ULTRAVIOLET_RADIATION: + title: ultraviolet radiation + description: Electromagnetic radiation at wavelengths between 10 nm and 400 nm + meaning: ENVO:21001216 + VISIBLE_SPECTRUM_RADIATION: + title: visible spectrum radiation + description: Electromagnetic radiation at wavelengths between 380 nm and 760 nm + meaning: ENVO:21001215 + INFRARED_RADIATION: + title: infrared radiation + description: Electromagnetic radiation emitted by molecular rotational-vibrational movements, wavelengths 760 nm to + 1 mm + meaning: ENVO:21001214 + MICROWAVE_RADIATION: + title: microwave radiation + description: Electromagnetic radiation that travels line-of-sight and may produce molecular rotation on contact + meaning: ENVO:21001212 + RADIO_WAVE_RADIATION: + title: radio wave radiation + description: Electromagnetic radiation at wavelengths ranging from millimetre to kilometer scales + meaning: ENVO:21001213 + PHOTOSYNTHETICALLY_ACTIVE_RADIATION: + title: photosynthetically active radiation + description: Radiant energy in the 400-700 nm wave band usable by organisms for photosynthesis + meaning: ENVO:01001864 + SHORTWAVE_RADIATION: + title: shortwave radiation + description: Radiant energy in visible, near-ultraviolet, or near-infrared spectra + meaning: ENVO:01001861 + OUTGOING_LONGWAVE_RADIATION: + title: outgoing longwave radiation + description: Infrared radiation emitted from a planet and atmosphere to space as thermal radiation + meaning: ENVO:01001857 + is_a: RadiationSchemaEnum + annotations: + source_domain: physics + source_schema: radiation + InfraredRadiationTypeEnum: + title: Infrared Radiation Type + description: Subtypes of infrared radiation based on wavelength ranges. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NEAR_INFRARED: + title: near-infrared radiation + description: Infrared radiation with frequencies 120-400 THz, wavelengths 750 nm to 2.5 micrometers + meaning: ENVO:03500014 + MID_INFRARED: + title: mid-infrared radiation + description: Infrared radiation with frequencies 30-120 THz, wavelengths 2.5-10 micrometers + meaning: ENVO:03500013 + FAR_INFRARED: + title: far-infrared radiation + description: Infrared radiation with frequencies 300 GHz to 30 THz, wavelengths 10 micrometers to 1 mm + meaning: ENVO:03500015 + is_a: RadiationSchemaEnum + annotations: + source_domain: physics + source_schema: radiation + AcousticRadiationTypeEnum: + title: Acoustic Radiation Type + description: Types of acoustic (mechanical wave) radiation including ultrasound and infrasound. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ACOUSTIC_RADIATION: + title: acoustic radiation + description: Mechanical waves generated by oscillations that radiate through environmental material + meaning: ENVO:01001027 + ULTRASOUND_RADIATION: + title: ultrasound radiation + description: Acoustic radiation at frequencies above 20 kHz + meaning: ENVO:03500012 + INFRASOUND: + title: infrasound + description: Acoustic radiation at frequencies below the range of human hearing + meaning: ENVO:01001566 + is_a: RadiationSchemaEnum + annotations: + source_domain: physics + source_schema: radiation + StatesOfMatterSchemaEnum: + description: Schema-level enum for states_of_matter in physics + is_a: PhysicsDomainEnum + abstract: true + annotations: + source_file: physics/states_of_matter.yaml + StateOfMatterEnum: + title: State Of Matter + description: The physical state or phase of matter + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - STRUCTURAL_T1: - title: T1-weighted structural MRI - description: High-resolution anatomical imaging with T1 contrast - meaning: NCIT:C116455 + SOLID: + description: A state of matter where particles are closely packed together with fixed positions + meaning: AFO:AFQ_0000112 + LIQUID: + description: A nearly incompressible fluid that conforms to the shape of its container + meaning: AFO:AFQ_0000113 + GAS: + description: A compressible fluid that expands to fill its container + meaning: AFO:AFQ_0000114 + PLASMA: + description: An ionized gas with freely moving charged particles + meaning: AFO:AFQ_0000115 + BOSE_EINSTEIN_CONDENSATE: + description: A state of matter formed at extremely low temperatures where particles occupy the same quantum state + FERMIONIC_CONDENSATE: + description: A superfluid phase formed by fermionic particles at extremely low temperatures + SUPERCRITICAL_FLUID: + description: A state where distinct liquid and gas phases do not exist + SUPERFLUID: + description: A phase of matter with zero viscosity + SUPERSOLID: + description: A spatially ordered material with superfluid properties + QUARK_GLUON_PLASMA: + description: An extremely hot phase where quarks and gluons are not confined + is_a: StatesOfMatterSchemaEnum + annotations: + source_domain: physics + source_schema: states_of_matter + PreservationDomainEnum: + description: Domain-level enum for preservation value sets + is_a: ValueSetEnum + abstract: true + DigitalObjectsSchemaEnum: + description: Schema-level enum for digital_objects in preservation + is_a: PreservationDomainEnum + abstract: true + annotations: + source_file: preservation/digital_objects.yaml + DigitalObjectCategory: + title: Digital Object Category + description: 'The category of object to which preservation metadata applies. + + Based on PREMIS object categories. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://id.loc.gov/vocabulary/preservation/objectCategory.html + permissible_values: + BITSTREAM: + description: 'Contiguous or non-contiguous data within a file that has meaningful + + properties for preservation purposes. A bitstream cannot be transformed + + into a standalone file without the addition of file structure. + + ' + meaning: premis:objectCategory/bit + FILE: + description: 'A named and ordered sequence of bytes that is known to an operating + + system. A file can be zero or more bytes and has a file format, + + access permissions, and other file system characteristics. + + ' + meaning: premis:objectCategory/fil + INTELLECTUAL_ENTITY: + title: Intellectual Entity + description: 'A coherent set of content that is reasonably described as a unit. + + Examples include a book, a photograph, a database, or a software + + application. An intellectual entity may contain other intellectual + + entities. + + ' + meaning: premis:objectCategory/int + REPRESENTATION: + description: 'The set of files, including structural metadata, needed for a + + complete and reasonable rendition of an intellectual entity. + + A digital object may have multiple representations. + + ' + meaning: premis:objectCategory/rep + is_a: DigitalObjectsSchemaEnum + annotations: + source_domain: preservation + source_schema: digital_objects + CopyrightStatus: + title: Copyright Status + description: 'A designation for the copyright status of an object at the time + + the rights statement is recorded. Based on PREMIS. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://id.loc.gov/vocabulary/preservation/copyrightStatus.html + permissible_values: + COPYRIGHTED: + description: The object is protected by copyright. + meaning: premis:copyrightStatus/cpr + PUBLIC_DOMAIN: + title: Public Domain + description: 'The object is not protected by copyright, either because copyright + + has expired, was never applicable, or has been waived. + + ' + meaning: premis:copyrightStatus/pub + UNKNOWN: + description: The copyright status cannot be determined. + meaning: premis:copyrightStatus/unk + is_a: DigitalObjectsSchemaEnum + annotations: + source_domain: preservation + source_schema: digital_objects + RightsBasis: + title: Rights Basis + description: 'The basis for the right or permission granted for an object. + + Based on PREMIS rights basis vocabulary. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://id.loc.gov/vocabulary/preservation/rightsBasis.html + permissible_values: + COPYRIGHT: + description: Rights based on copyright law. + meaning: premis:rightsBasis/cop + INSTITUTIONAL_POLICY: + title: Institutional Policy + description: Rights based on the policies of the holding institution. + meaning: premis:rightsBasis/ins + LICENSE: + description: Rights based on a license agreement. + meaning: premis:rightsBasis/lic + STATUTE: + description: Rights based on statutory law other than copyright. + meaning: premis:rightsBasis/sta + OTHER: + description: Rights based on another basis not listed. + meaning: premis:rightsBasis/oth + is_a: DigitalObjectsSchemaEnum + annotations: + source_domain: preservation + source_schema: digital_objects + PreservationLevelRole: + title: Preservation Level Role + description: 'The context in which a preservation level value is specified. + + Based on PREMIS preservation level role vocabulary. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://id.loc.gov/vocabulary/preservation/preservationLevelRole.html + permissible_values: + CAPABILITY: + description: 'The preservation level that the repository is capable of providing + + based on its technical infrastructure and resources. + + ' + meaning: premis:preservationLevelRole/cap + INTENTION: + description: 'The preservation level that the repository intends to provide + + for the object, based on policy decisions. + + ' + meaning: premis:preservationLevelRole/int + REQUIREMENT: + description: 'The preservation level required by the depositor or + + other stakeholder for the object. + + ' + meaning: premis:preservationLevelRole/req + is_a: DigitalObjectsSchemaEnum + annotations: + source_domain: preservation + source_schema: digital_objects + PreservationLevelValue: + title: Preservation Level Value + description: 'Common preservation level tiers indicating the degree of preservation + + commitment. These are not from PREMIS directly but represent common + + practice in digital preservation. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://ndsa.org/publications/levels-of-digital-preservation/ + permissible_values: + BIT_LEVEL: + title: Bit-level Preservation + description: 'Ensures the exact bit sequence is maintained. Includes fixity checks + + and secure storage but no format migration or access provision. + + ' aliases: - - High Field Strength Magnetic Resonance Imaging - annotations: - contrast_mechanism: T1 relaxation - typical_use: anatomical reference, volumetric analysis - tissue_contrast: good gray/white matter contrast - STRUCTURAL_T2: - title: T2-weighted structural MRI - description: Structural imaging with T2 contrast - meaning: NCIT:C116456 + - Level 1 + LOGICAL_PRESERVATION: + title: Logical Preservation + description: 'Maintains the ability to render or use the content. May include + + format migration to ensure long-term accessibility. + + ' aliases: - - Low Field Strength Magnetic Resonance Imaging - annotations: - contrast_mechanism: T2 relaxation - typical_use: pathology detection, CSF visualization - tissue_contrast: good fluid contrast - FLAIR: - title: Fluid-attenuated inversion recovery - description: T2-weighted sequence with CSF signal suppressed - meaning: NCIT:C82392 - annotations: - contrast_mechanism: T2 with fluid suppression - typical_use: lesion detection, periventricular pathology - advantage: suppresses CSF signal - BOLD_FMRI: - title: Blood oxygen level dependent fMRI - description: Functional MRI based on blood oxygenation changes - meaning: NCIT:C17958 + - Level 2 + - Content Preservation + SEMANTIC_PRESERVATION: + title: Semantic Preservation + description: 'Preserves the meaning and context of content, including relationships + + between objects and their intellectual context. + + ' aliases: - - Functional Magnetic Resonance Imaging - annotations: - contrast_mechanism: BOLD signal - typical_use: brain activation mapping - temporal_resolution: seconds - ASL: - title: Arterial spin labeling - description: Perfusion imaging using magnetically labeled blood - meaning: NCIT:C116450 + - Level 3 + - Full Preservation + FULL_PRESERVATION: + title: Full Preservation + description: 'Comprehensive preservation including all aspects: bit-level integrity, + + format migration, semantic context, and provenance tracking. + + ' aliases: - - Arterial Spin Labeling Magnetic Resonance Imaging - annotations: - contrast_mechanism: arterial blood labeling - typical_use: cerebral blood flow measurement - advantage: no contrast agent required - DWI: - title: Diffusion-weighted imaging - description: Imaging sensitive to water molecule diffusion - meaning: mesh:D038524 - annotations: - contrast_mechanism: water diffusion - typical_use: stroke detection, fiber tracking - parameter: apparent diffusion coefficient - DTI: - title: Diffusion tensor imaging - description: Advanced diffusion imaging with directional information - meaning: NCIT:C64862 + - Level 4 + is_a: DigitalObjectsSchemaEnum + annotations: + source_domain: preservation + source_schema: digital_objects + EventsSchemaEnum: + description: Schema-level enum for events in preservation + is_a: PreservationDomainEnum + abstract: true + annotations: + source_file: preservation/events.yaml + PreservationEventType: + title: Preservation Event Type + description: 'Actions performed within or outside a repository that affect the long-term + + preservation of digital objects. Based on PREMIS 3.0 event types. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://id.loc.gov/vocabulary/preservation/eventType.html + - https://www.loc.gov/standards/premis/v3/ + permissible_values: + ACCESSION: + description: The process of adding objects to a repository's holdings. + meaning: premis:eventType/acc + APPRAISAL: + description: The process of evaluating objects for long-term retention. + meaning: premis:eventType/app + CAPTURE: + description: The process of recording or acquiring digital content. + meaning: premis:eventType/cap + COMPILING: + description: The process of converting source code into executable code. + meaning: premis:eventType/com + COMPRESSION: + description: The process of reducing file size through encoding. + meaning: premis:eventType/cmp + CREATION: + description: The act of creating a new digital object. + meaning: premis:eventType/cre + DEACCESSION: + description: The process of removing objects from a repository's holdings. + meaning: premis:eventType/dea + DECOMPRESSION: + description: The process of restoring compressed data to its original form. + meaning: premis:eventType/dec + DECRYPTION: + description: The process of converting encrypted data back to plaintext. + meaning: premis:eventType/der + DELETION: + description: The act of removing a digital object. + meaning: premis:eventType/del + DIGITAL_SIGNATURE_GENERATION: + title: Digital Signature Generation + description: The process of creating a digital signature for authentication. + meaning: premis:eventType/dig + DIGITAL_SIGNATURE_VALIDATION: + title: Digital Signature Validation + description: The process of verifying the authenticity of a digital signature. + meaning: premis:eventType/dsv + DISPLAYING: + description: The process of presenting content for viewing. + meaning: premis:eventType/dip + DISSEMINATION: + description: The process of making content available to users. + meaning: premis:eventType/dis + ENCRYPTION: + description: The process of converting plaintext to ciphertext. + meaning: premis:eventType/enc + EXECUTION: + description: The process of running software or scripts. + meaning: premis:eventType/exe + EXPORTING: + description: The process of extracting content from a system. + meaning: premis:eventType/exp + EXTRACTION: + description: The process of retrieving content from a container or archive. + meaning: premis:eventType/ext + FILENAME_CHANGE: + title: Filename Change + description: The act of modifying a file's name. + meaning: premis:eventType/fil + FIXITY_CHECK: + title: Fixity Check + description: The process of verifying data integrity using checksums or hashes. + meaning: premis:eventType/fix + FORENSIC_FEATURE_ANALYSIS: + title: Forensic Feature Analysis + description: Analysis of digital objects for authenticity or provenance evidence. + meaning: premis:eventType/for + FORMAT_IDENTIFICATION: + title: Format Identification + description: The process of determining the file format of a digital object. + meaning: premis:eventType/fmi + IMAGING: + description: The process of creating a bit-level copy of storage media. + meaning: premis:eventType/ima + INFORMATION_PACKAGE_CREATION: + title: Information Package Creation + description: Creating a packaged unit of content and metadata (SIP, AIP, DIP). + meaning: premis:eventType/ipc + INFORMATION_PACKAGE_MERGING: + title: Information Package Merging + description: Combining multiple information packages into one. + meaning: premis:eventType/ipm + INFORMATION_PACKAGE_SPLITTING: + title: Information Package Splitting + description: Dividing an information package into multiple packages. + meaning: premis:eventType/ips + INGESTION: + description: The process of accepting and processing submitted content. + meaning: premis:eventType/ing + INGESTION_END: + title: Ingestion End + description: The completion of the ingestion process. + meaning: premis:eventType/ine + INGESTION_START: + title: Ingestion Start + description: The beginning of the ingestion process. + meaning: premis:eventType/ins + INTERPRETING: + description: The process of rendering or executing interpretable content. + meaning: premis:eventType/int + MESSAGE_DIGEST_CALCULATION: + title: Message Digest Calculation + description: The process of computing a hash or checksum value. + meaning: premis:eventType/mes + METADATA_EXTRACTION: + title: Metadata Extraction + description: The process of extracting metadata from digital objects. + meaning: premis:eventType/mee + METADATA_MODIFICATION: + title: Metadata Modification + description: The process of changing metadata associated with an object. + meaning: premis:eventType/mem + MIGRATION: + description: 'The process of converting content from one format to another + + to ensure continued accessibility. + + ' + meaning: premis:eventType/mig + MODIFICATION: + description: The act of changing the content of a digital object. + meaning: premis:eventType/mod + NORMALIZATION: + description: 'The process of converting content to a standard format + + for preservation or access. + + ' + meaning: premis:eventType/nor + PACKING: + description: The process of combining files into a container format. + meaning: premis:eventType/pac + POLICY_ASSIGNMENT: + title: Policy Assignment + description: The act of associating preservation policies with objects. + meaning: premis:eventType/poa + PRINTING: + description: The process of producing a physical copy of digital content. + meaning: premis:eventType/pri + QUARANTINE: + description: Isolating objects suspected of containing malware or corruption. + meaning: premis:eventType/qua + RECOVERY: + description: The process of restoring objects from backup or damaged media. + meaning: premis:eventType/rec + REDACTION: + description: The process of removing sensitive content from objects. + meaning: premis:eventType/red + REFRESHMENT: + description: Copying data to new storage media without format change. + meaning: premis:eventType/ref + RENDERING: + description: The process of generating a viewable representation. + meaning: premis:eventType/ren + REPLICATION: + description: Creating exact copies for redundancy or distribution. + meaning: premis:eventType/rep + TRANSFER: + description: Moving objects between systems or locations. + meaning: premis:eventType/tra + UNPACKING: + description: Extracting files from a container format. + meaning: premis:eventType/unp + UNQUARANTINE: + description: Releasing objects from quarantine after verification. + meaning: premis:eventType/unq + VALIDATION: + description: Verifying that objects conform to expected specifications. + meaning: premis:eventType/val + VIRUS_CHECK: + title: Virus Check + description: Scanning objects for malware or viruses. + meaning: premis:eventType/vir + is_a: EventsSchemaEnum + annotations: + source_domain: preservation + source_schema: events + PreservationEventOutcome: + title: Preservation Event Outcome + description: The outcome or result of a preservation event. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://id.loc.gov/vocabulary/preservation/eventOutcome.html + permissible_values: + SUCCESS: + description: The event completed successfully. + meaning: premis:eventOutcome/suc + FAILURE: + description: The event failed to complete. + meaning: premis:eventOutcome/fai + WARNING: + description: The event completed with warnings or issues. + meaning: premis:eventOutcome/war + is_a: EventsSchemaEnum + annotations: + source_domain: preservation + source_schema: events + FixitySchemaEnum: + description: Schema-level enum for fixity in preservation + is_a: PreservationDomainEnum + abstract: true + annotations: + source_file: preservation/fixity.yaml + CryptographicHashFunction: + title: Cryptographic Hash Function + description: 'Algorithms that take an input and return a fixed-size string (hash value). + + Used for verifying data integrity and creating digital signatures. + + Based on PREMIS cryptographic hash functions vocabulary. + + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions.html + - https://spdx.github.io/spdx-spec/v2.3/file-information/#89-file-checksum-field + permissible_values: + ADLER_32: + title: Adler-32 + description: 'A checksum algorithm developed by Mark Adler. Faster than CRC32 + + but with weaker error detection. Used in zlib compression. + + ' + meaning: premis:cryptographicHashFunctions/adl + exact_mappings: + - spdx:checksumAlgorithm_adler32 annotations: - contrast_mechanism: directional diffusion - typical_use: white matter tractography - parameters: fractional anisotropy, mean diffusivity - PERFUSION_DSC: - title: Dynamic susceptibility contrast perfusion - description: Perfusion imaging using contrast agent bolus - meaning: NCIT:C116459 - aliases: - - Secretin-Enhanced Magnetic Resonance Imaging + output_bits: 32 + security_level: non-cryptographic + CRC32: + title: CRC32 + description: 'Cyclic Redundancy Check with 32-bit output. Used for error detection + + in network transmissions and storage. Not cryptographically secure. + + ' + meaning: premis:cryptographicHashFunctions/crc annotations: - contrast_mechanism: contrast agent dynamics - typical_use: cerebral blood flow, blood volume - requires: gadolinium contrast - PERFUSION_DCE: - title: Dynamic contrast-enhanced perfusion - description: Perfusion imaging with pharmacokinetic modeling - meaning: NCIT:C116458 - aliases: - - Multiparametric Magnetic Resonance Imaging + output_bits: 32 + security_level: non-cryptographic + HAVAL: + title: HAVAL + description: 'A cryptographic hash function that can produce hash values of + + 128, 160, 192, 224, or 256 bits. Variable number of rounds. + + ' + meaning: premis:cryptographicHashFunctions/hav annotations: - contrast_mechanism: contrast enhancement kinetics - typical_use: blood-brain barrier permeability - analysis: pharmacokinetic modeling - SWI: - title: Susceptibility-weighted imaging - description: High-resolution venography and iron detection - meaning: NCIT:C121377 + output_bits: variable + security_level: deprecated + MD2: + title: MD2 + description: 'Message Digest 2 algorithm producing a 128-bit hash value. + + Designed for 8-bit computers. Considered cryptographically broken. + + ' + meaning: premis:cryptographicHashFunctions/md2 + exact_mappings: + - spdx:checksumAlgorithm_md2 annotations: - contrast_mechanism: magnetic susceptibility - typical_use: venography, microbleeds, iron deposits - strength: high field preferred - TASK_FMRI: - title: Task-based functional MRI - description: fMRI during specific cognitive or motor tasks - meaning: NCIT:C178023 - aliases: - - Task Functional Magnetic Resonance Imaging + output_bits: 128 + security_level: broken + MD4: + title: MD4 + description: 'Message Digest 4 algorithm producing a 128-bit hash value. + + Predecessor to MD5. Considered cryptographically broken. + + ' + exact_mappings: + - spdx:checksumAlgorithm_md4 annotations: - paradigm: stimulus-response - typical_use: localization of brain functions - analysis: statistical parametric mapping - RESTING_STATE_FMRI: - title: Resting-state functional MRI - description: fMRI acquired at rest without explicit tasks - meaning: NCIT:C178024 - aliases: - - Resting Functional Magnetic Resonance Imaging + output_bits: 128 + security_level: broken + MD5: + title: MD5 + description: 'Message Digest 5 algorithm producing a 128-bit hash value. + + Widely used but vulnerable to collision attacks. Acceptable + + for non-security integrity checks only. + + ' + meaning: premis:cryptographicHashFunctions/md5 + exact_mappings: + - spdx:checksumAlgorithm_md5 annotations: - paradigm: no task - typical_use: functional connectivity analysis - networks: default mode, attention, executive - FUNCTIONAL_CONNECTIVITY: - title: Functional connectivity MRI - description: Analysis of temporal correlations between brain regions - meaning: NCIT:C116454 - aliases: - - Functional Connectivity Magnetic Resonance Imaging + output_bits: 128 + security_level: weak + MD6: + title: MD6 + description: 'Message Digest 6 algorithm with variable output size. + + Designed as a candidate for SHA-3 but not selected. + + ' + exact_mappings: + - spdx:checksumAlgorithm_md6 annotations: - analysis_type: connectivity mapping - typical_use: network analysis - metric: correlation coefficients - is_a: NeuroimagingSchemaEnum - annotations: - source_domain: medical - source_schema: neuroimaging - MRISequenceTypeEnum: - description: MRI pulse sequence types - permissible_values: - GRADIENT_ECHO: - title: Gradient echo sequence - description: Fast imaging sequence using gradient reversal - meaning: NCIT:C154542 + output_bits: variable + security_level: adequate + SHA_1: + title: SHA-1 + description: 'Secure Hash Algorithm 1 producing a 160-bit hash value. + + Deprecated for security applications due to collision vulnerabilities. + + Still acceptable for integrity verification in some contexts. + + ' + meaning: premis:cryptographicHashFunctions/sha1 + exact_mappings: + - spdx:checksumAlgorithm_sha1 aliases: - - Gradient Echo MRI + - SHA1 annotations: - speed: fast - typical_use: T2*, functional imaging - artifact_sensitivity: susceptible to magnetic field inhomogeneity - SPIN_ECHO: - title: Spin echo sequence - description: Sequence using 180-degree refocusing pulse - meaning: CHMO:0001868 + output_bits: 160 + security_level: weak + SHA_224: + title: SHA-224 + description: 'SHA-2 variant producing a 224-bit hash value. + + Truncated version of SHA-256. + + ' + exact_mappings: + - spdx:checksumAlgorithm_sha224 aliases: - - spin echo pulse sequence + - SHA224 annotations: - speed: slower - typical_use: T2 imaging, reduced artifacts - artifact_resistance: good - EPI: - title: Echo planar imaging - description: Ultrafast imaging sequence - meaning: NCIT:C17558 - annotations: - speed: very fast - typical_use: functional MRI, diffusion imaging - temporal_resolution: subsecond - MPRAGE: - title: Magnetization prepared rapid gradient echo - description: T1-weighted 3D sequence with preparation pulse - meaning: NCIT:C118462 + output_bits: 224 + security_level: secure + SHA_256: + title: SHA-256 + description: 'SHA-2 variant producing a 256-bit hash value. + + Widely used and considered secure for most applications. + + Recommended for digital preservation. + + ' + meaning: premis:cryptographicHashFunctions/sha256 + exact_mappings: + - spdx:checksumAlgorithm_sha256 aliases: - - Magnetization-Prepared Rapid Gradient Echo MRI - annotations: - image_type: T1-weighted - typical_use: high-resolution anatomical imaging - dimension: 3D - SPACE: - title: Sampling perfection with application optimized contrasts - description: 3D turbo spin echo sequence + - SHA256 annotations: - image_type: T2-weighted - typical_use: high-resolution T2 imaging - dimension: 3D - TRUFI: - title: True fast imaging with steady-state precession - description: Balanced steady-state free precession sequence - meaning: NCIT:C200534 + output_bits: 256 + security_level: secure + SHA_384: + title: SHA-384 + description: 'SHA-2 variant producing a 384-bit hash value. + + Truncated version of SHA-512. + + ' + meaning: premis:cryptographicHashFunctions/sha384 + exact_mappings: + - spdx:checksumAlgorithm_sha384 aliases: - - Constructive Interference In Steady State + - SHA384 annotations: - contrast: mixed T1/T2 - typical_use: cardiac imaging, fast scanning - signal: high - is_a: NeuroimagingSchemaEnum - annotations: - source_domain: medical - source_schema: neuroimaging - MRIContrastTypeEnum: - description: MRI image contrast mechanisms - permissible_values: - T1_WEIGHTED: - title: T1-weighted contrast - description: Image contrast based on T1 relaxation times - meaning: NCIT:C180727 + output_bits: 384 + security_level: secure + SHA_512: + title: SHA-512 + description: 'SHA-2 variant producing a 512-bit hash value. + + Highest security level in the SHA-2 family. + + ' + meaning: premis:cryptographicHashFunctions/sha512 + exact_mappings: + - spdx:checksumAlgorithm_sha512 aliases: - - T1-Weighted Magnetic Resonance Imaging + - SHA512 annotations: - tissue_contrast: gray matter darker than white matter - typical_use: anatomical structure - T2_WEIGHTED: - title: T2-weighted contrast - description: Image contrast based on T2 relaxation times - meaning: NCIT:C180729 - aliases: - - T2-Weighted Magnetic Resonance Imaging + output_bits: 512 + security_level: secure + SHA3_224: + title: SHA3-224 + description: 'SHA-3 variant producing a 224-bit hash value. + + Based on the Keccak algorithm. + + ' + exact_mappings: + - spdx:checksumAlgorithm_sha3_224 annotations: - tissue_contrast: CSF bright, gray matter brighter than white - typical_use: pathology detection - T2_STAR: - title: T2*-weighted contrast - description: Image contrast sensitive to magnetic susceptibility - meaning: NCIT:C156447 - aliases: - - T2 (Observed)-Weighted Imaging + output_bits: 224 + security_level: secure + SHA3_256: + title: SHA3-256 + description: 'SHA-3 variant producing a 256-bit hash value. + + Based on the Keccak algorithm. Provides defense against + + length extension attacks. + + ' + exact_mappings: + - spdx:checksumAlgorithm_sha3_256 annotations: - sensitivity: blood, iron, air-tissue interfaces - typical_use: functional imaging, venography - PROTON_DENSITY: - title: Proton density weighted - description: Image contrast based on hydrogen density - meaning: NCIT:C170797 - aliases: - - Proton Density MRI + output_bits: 256 + security_level: secure + SHA3_384: + title: SHA3-384 + description: 'SHA-3 variant producing a 384-bit hash value. + + Based on the Keccak algorithm. + + ' + exact_mappings: + - spdx:checksumAlgorithm_sha3_384 annotations: - tissue_contrast: proportional to water content - typical_use: joint imaging, some brain pathology - DIFFUSION_WEIGHTED: - title: Diffusion-weighted contrast - description: Image contrast based on water diffusion - meaning: NCIT:C111116 - aliases: - - Diffusion Weighted Imaging + output_bits: 384 + security_level: secure + SHA3_512: + title: SHA3-512 + description: 'SHA-3 variant producing a 512-bit hash value. + + Based on the Keccak algorithm. + + ' + exact_mappings: + - spdx:checksumAlgorithm_sha3_512 annotations: - sensitivity: molecular motion - typical_use: stroke, tumor cellularity - PERFUSION_WEIGHTED: - title: Perfusion-weighted contrast - description: Image contrast based on blood flow dynamics - meaning: mesh:D000098642 + output_bits: 512 + security_level: secure + BLAKE2B_256: + title: BLAKE2b-256 + description: 'BLAKE2b variant producing a 256-bit hash value. + + Faster than MD5 and SHA-1 while being more secure. + + ' + exact_mappings: + - spdx:checksumAlgorithm_blake2b256 annotations: - measurement: cerebral blood flow/volume - typical_use: stroke, tumor vascularity - is_a: NeuroimagingSchemaEnum - annotations: - source_domain: medical - source_schema: neuroimaging - FMRIParadigmTypeEnum: - description: fMRI experimental paradigm types - permissible_values: - BLOCK_DESIGN: - title: Block design paradigm - description: Alternating blocks of task and rest conditions - meaning: STATO:0000046 + output_bits: 256 + security_level: secure + BLAKE2B_384: + title: BLAKE2b-384 + description: 'BLAKE2b variant producing a 384-bit hash value. + + ' + exact_mappings: + - spdx:checksumAlgorithm_blake2b384 annotations: - duration: typically 15-30 seconds per block - advantage: high statistical power - typical_use: robust activation detection - EVENT_RELATED: - title: Event-related design - description: Brief stimuli presented at varying intervals - meaning: EDAM:topic_3678 - aliases: - - Experimental design and studies + output_bits: 384 + security_level: secure + BLAKE2B_512: + title: BLAKE2b-512 + description: 'BLAKE2b variant producing a 512-bit hash value. + + Optimized for 64-bit platforms. + + ' + exact_mappings: + - spdx:checksumAlgorithm_blake2b512 annotations: - duration: single events (seconds) - advantage: flexible timing, event separation - typical_use: studying cognitive processes - MIXED_DESIGN: - title: Mixed block and event-related design - description: Combination of block and event-related elements - meaning: EDAM:topic_3678 - aliases: - - Experimental design and studies + output_bits: 512 + security_level: secure + BLAKE3: + title: BLAKE3 + description: 'Latest BLAKE variant, extremely fast with 256-bit output. + + Supports parallelization and incremental hashing. + + ' + exact_mappings: + - spdx:checksumAlgorithm_blake3 annotations: - flexibility: high - advantage: sustained and transient responses - complexity: high - RESTING_STATE: - title: Resting state paradigm - description: No explicit task, spontaneous brain activity - meaning: NCIT:C178024 - aliases: - - Resting Functional Magnetic Resonance Imaging + output_bits: 256 + security_level: secure + TIGER: + title: Tiger + description: 'A cryptographic hash function designed for 64-bit platforms. + + Produces a 192-bit hash value. + + ' + meaning: premis:cryptographicHashFunctions/tig annotations: - instruction: rest, eyes open/closed - duration: typically 5-10 minutes - analysis: functional connectivity - NATURALISTIC: - title: Naturalistic paradigm - description: Ecologically valid stimuli (movies, stories) - meaning: EDAM:topic_3678 - aliases: - - Experimental design and studies + output_bits: 192 + security_level: adequate + WHIRLPOOL: + title: Whirlpool + description: 'A cryptographic hash function producing a 512-bit hash value. + + Based on a modified AES block cipher. + + ' + meaning: premis:cryptographicHashFunctions/whi annotations: - stimulus_type: complex, realistic - advantage: ecological validity - analysis: inter-subject correlation - is_a: NeuroimagingSchemaEnum + output_bits: 512 + security_level: secure + UNKNOWN: + description: The hash algorithm is not known or not specified. + meaning: premis:cryptographicHashFunctions/unk + is_a: FixitySchemaEnum + annotations: + source_domain: preservation + source_schema: fixity + ProvenanceDomainEnum: + description: Domain-level enum for provenance value sets + is_a: ValueSetEnum + abstract: true + EvidenceSchemaEnum: + description: Schema-level enum for evidence in provenance + is_a: ProvenanceDomainEnum + abstract: true annotations: - source_domain: medical - source_schema: neuroimaging - PhysicsDomainEnum: - description: Domain-level enum for physics value sets + source_file: provenance/evidence.yaml + EvidenceType: + title: Evidence Type + description: Types of evidence used to support assertions, dynamically populated from the Evidence and Conclusion Ontology + (ECO). Includes experimental evidence, computational evidence, author statements, and other evidence types. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://evidenceontology.org + publishers: https://evidenceontology.org + source_domain: provenance + source_schema: evidence + reachable_from: + source_nodes: + - ECO:0000000 + is_direct: false + relationship_types: + - rdfs:subClassOf + is_a: EvidenceSchemaEnum + PublishingDomainEnum: + description: Domain-level enum for publishing value sets is_a: ValueSetEnum abstract: true - StatesOfMatterSchemaEnum: - description: Schema-level enum for states_of_matter in physics - is_a: PhysicsDomainEnum + ArxivCategoriesSchemaEnum: + description: Schema-level enum for arxiv_categories in publishing + is_a: PublishingDomainEnum abstract: true annotations: - source_file: physics/states_of_matter.yaml - StateOfMatterEnum: - description: The physical state or phase of matter - permissible_values: - SOLID: - description: A state of matter where particles are closely packed together with fixed positions - meaning: AFO:AFQ_0000112 - LIQUID: - description: A nearly incompressible fluid that conforms to the shape of its container - meaning: AFO:AFQ_0000113 - GAS: - description: A compressible fluid that expands to fill its container - meaning: AFO:AFQ_0000114 - PLASMA: - description: An ionized gas with freely moving charged particles - meaning: AFO:AFQ_0000115 - BOSE_EINSTEIN_CONDENSATE: - description: A state of matter formed at extremely low temperatures where particles occupy the same quantum state - FERMIONIC_CONDENSATE: - description: A superfluid phase formed by fermionic particles at extremely low temperatures - SUPERCRITICAL_FLUID: - description: A state where distinct liquid and gas phases do not exist - SUPERFLUID: - description: A phase of matter with zero viscosity - SUPERSOLID: - description: A spatially ordered material with superfluid properties - QUARK_GLUON_PLASMA: - description: An extremely hot phase where quarks and gluons are not confined - is_a: StatesOfMatterSchemaEnum + source_file: publishing/arxiv_categories.yaml + ArxivCategory: + title: arXiv Category + description: arXiv subject categories for classifying preprints and publications. Categories are organized by major subject + groups. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + cs: + title: Computer Science + description: Computer science research areas + close_mappings: + - NCIT:C18145 + econ: + title: Economics + description: Economics research areas + close_mappings: + - NCIT:C61331 + - mesh:D004467 + eess: + title: Electrical Engineering and Systems Science + description: Electrical engineering and systems science research areas + close_mappings: + - NCIT:C19349 + math: + title: Mathematics + description: Mathematics research areas + close_mappings: + - NCIT:C16825 + - mesh:D008433 + astro-ph: + title: Astrophysics + description: Astrophysics research areas + cond-mat: + title: Condensed Matter + description: Condensed matter physics research areas + hep: + title: High Energy Physics + description: High energy physics research areas + nlin: + title: Nonlinear Sciences + description: Nonlinear sciences research areas + nucl: + title: Nuclear Physics + description: Nuclear physics research areas + close_mappings: + - mesh:D009686 + physics: + title: Physics + description: General physics research areas + close_mappings: + - NCIT:C16989 + - mesh:D010825 + q-bio: + title: Quantitative Biology + description: Quantitative biology research areas + close_mappings: + - NCIT:C16345 + - mesh:D001695 + q-fin: + title: Quantitative Finance + description: Quantitative finance research areas + stat: + title: Statistics + description: Statistics research areas + close_mappings: + - NCIT:C17167 + cs.AI: + title: Artificial Intelligence + description: Covers all areas of AI except Vision, Robotics, Machine Learning, Multiagent Systems, and NLP. Includes + Expert Systems, Theorem Proving, Knowledge Representation, Planning, and Uncertainty in AI. + is_a: cs + close_mappings: + - NCIT:C16309 + - mesh:D001185 + cs.AR: + title: Hardware Architecture + description: Covers systems organization and hardware architecture. Roughly includes material in ACM Subject Class + C.0, C.1, and C.5. + is_a: cs + cs.CC: + title: Computational Complexity + description: Covers models of computation, complexity classes, structural complexity, complexity tradeoffs, upper + and lower bounds. + is_a: cs + cs.CE: + title: Computational Engineering, Finance, and Science + description: Covers applications of computer science to the mathematical modeling of complex systems in science, engineering, + and finance. + is_a: cs + cs.CG: + title: Computational Geometry + description: Geometric algorithms, discrete differential geometry, and directly related problems. + is_a: cs + cs.CL: + title: Computation and Language + description: Covers natural language processing. Includes computational linguistics, speech processing, text retrieval + and processing. + is_a: cs + close_mappings: + - NCIT:C176260 + - mesh:D009323 + cs.CR: + title: Cryptography and Security + description: Covers all areas of cryptography and security including authentication, public key cryptosystems, proof-carrying + code, etc. + is_a: cs + cs.CV: + title: Computer Vision and Pattern Recognition + description: Covers image processing, computer vision, pattern recognition, and scene understanding. + is_a: cs + cs.CY: + title: Computers and Society + description: Covers impact of computers on society, computer ethics, information technology and public policy, legal + aspects of computing. + is_a: cs + cs.DB: + title: Databases + description: Covers database management, datamining, and data processing. Roughly includes material in ACM Subject + Classes H.2, H.3, and H.4. + is_a: cs + cs.DC: + title: Distributed, Parallel, and Cluster Computing + description: Covers fault-tolerance, distributed algorithms, stabilization, parallel computation, and cluster computing. + is_a: cs + cs.DL: + title: Digital Libraries + description: Covers all aspects of digital library design and document creation. Note this may overlap with other + areas. + is_a: cs + cs.DM: + title: Discrete Mathematics + description: Covers combinatorics, graph theory, applications of probability. Roughly includes material in ACM Subject + Classes G.2 and G.3. + is_a: cs + cs.DS: + title: Data Structures and Algorithms + description: Covers data structures and analysis of algorithms. Roughly includes material in ACM Subject Classes E.1, + E.2, F.2.1, and F.2.2. + is_a: cs + cs.ET: + title: Emerging Technologies + description: Covers approaches to computing based on emerging technologies such as quantum computing, DNA computing, + optical computing. + is_a: cs + cs.FL: + title: Formal Languages and Automata Theory + description: Covers automata theory, formal language theory, grammars, and combinatorics on words. + is_a: cs + cs.GL: + title: General Literature + description: Covers introductory material, survey material, predictions of future trends, biographies, and miscellaneous + computer-science related material. + is_a: cs + cs.GR: + title: Graphics + description: Covers all aspects of computer graphics. Roughly includes material in ACM Subject Classes I.3.0-I.3.8. + is_a: cs + close_mappings: + - NCIT:C16460 + cs.GT: + title: Computer Science and Game Theory + description: Covers all theoretical and applied aspects at the intersection of computer science and game theory. + is_a: cs + cs.HC: + title: Human-Computer Interaction + description: Covers human factors, user interfaces, and collaborative computing. Roughly includes material in ACM + Subject Classes H.1.2 and H.5. + is_a: cs + cs.IR: + title: Information Retrieval + description: Covers indexing, dictionaries, retrieval, content and analysis. Roughly includes material in ACM Subject + Classes H.3.0-H.3.4. + is_a: cs + cs.IT: + title: Information Theory + description: Covers theoretical and experimental aspects of information theory and coding. + is_a: cs + cs.LG: + title: Machine Learning + description: Papers on all aspects of machine learning research, including supervised, unsupervised, reinforcement + learning, bandit algorithms. + is_a: cs + close_mappings: + - NCIT:C176231 + - mesh:D000069550 + cs.LO: + title: Logic in Computer Science + description: Covers all aspects of logic in computer science, including finite model theory, logics of programs, modal + logic, and program verification. + is_a: cs + cs.MA: + title: Multiagent Systems + description: Covers multiagent systems, distributed artificial intelligence, intelligent agents, coordinated interactions. + is_a: cs + cs.MM: + title: Multimedia + description: Covers all aspects of multimedia systems, including hypermedia and information systems design. + is_a: cs + cs.MS: + title: Mathematical Software + description: Covers aspects of mathematical software for mathematical computation and related support. + is_a: cs + cs.NA: + title: Numerical Analysis + description: Covers numerical algorithms for problems in analysis and algebra. Includes numerical linear algebra, + optimization, and interpolation. + is_a: cs + cs.NE: + title: Neural and Evolutionary Computing + description: Covers neural networks, connectionism, genetic algorithms, artificial life, adaptive behavior. + is_a: cs + cs.NI: + title: Networking and Internet Architecture + description: Covers all aspects of computer communication networks, including network architecture and design. + is_a: cs + cs.OH: + title: Other Computer Science + description: Covers topics not fitting other computer science categories. + is_a: cs + cs.OS: + title: Operating Systems + description: Covers aspects of operating systems including structure, design, management, and synchronization. + is_a: cs + cs.PF: + title: Performance + description: Covers performance measurement, simulation, and evaluation methodology. + is_a: cs + cs.PL: + title: Programming Languages + description: Covers programming language semantics, language features, programming approaches, compilers. + is_a: cs + cs.RO: + title: Robotics + description: Covers all aspects of robotics, including control, manipulation, planning, and robot learning. + is_a: cs + close_mappings: + - mesh:D012371 + cs.SC: + title: Symbolic Computation + description: Covers symbolics, including computer algebra systems, implementation, and applications. + is_a: cs + cs.SD: + title: Sound + description: Covers all aspects of computing with sound, and sound as an information channel. + is_a: cs + cs.SE: + title: Software Engineering + description: Covers design tools, software metrics, testing and debugging, programming environments, requirements, + specifications. + is_a: cs + cs.SI: + title: Social and Information Networks + description: Covers design, analysis, and modeling of social and information networks, including their applications + for online systems. + is_a: cs + cs.SY: + title: Systems and Control + description: Covers theoretical and practical aspects of systems and control, including control system design. + is_a: cs + econ.EM: + title: Econometrics + description: Econometric theory and practice, including estimation, hypothesis testing, and forecasting. + is_a: econ + econ.GN: + title: General Economics + description: General methodological, applied, and empirical contributions to economics. + is_a: econ + econ.TH: + title: Theoretical Economics + description: Includes decision theory, game theory, mechanism design, and mathematical modeling in economics. + is_a: econ + eess.AS: + title: Audio and Speech Processing + description: Theory and methods for processing signals representing audio, speech, and language, and their applications. + is_a: eess + eess.IV: + title: Image and Video Processing + description: Theory, algorithms, and applications for the formation, capture, processing, communication, analysis, + and display of images. + is_a: eess + eess.SP: + title: Signal Processing + description: Theory, algorithms, performance analysis and applications of signal and data analysis. + is_a: eess + eess.SY: + title: Systems and Control + description: Analysis and design of control systems, covering mathematical modeling and automatic control. + is_a: eess + math.AC: + title: Commutative Algebra + description: Commutative rings, modules, ideals, homological algebra, computational aspects, local rings. + is_a: math + math.AG: + title: Algebraic Geometry + description: Algebraic varieties, stacks, sheaves, schemes, moduli spaces, complex geometry, quantum cohomology. + is_a: math + math.AP: + title: Analysis of PDEs + description: Existence and uniqueness, boundary conditions, linear and non-linear operators, stability, soliton theory. + is_a: math + math.AT: + title: Algebraic Topology + description: Homotopy theory, homological algebra, algebraic treatments of manifolds. + is_a: math + math.CA: + title: Classical Analysis and ODEs + description: Special functions, orthogonal polynomials, harmonic analysis, ODEs, differential relations. + is_a: math + math.CO: + title: Combinatorics + description: Discrete mathematics, graph theory, enumeration, combinatorial optimization. + is_a: math + math.CT: + title: Category Theory + description: Enriched categories, topoi, abelian categories, monoidal categories, homological algebra. + is_a: math + math.CV: + title: Complex Variables + description: Holomorphic functions, automorphic group actions, and their generalizations, complex geometry. + is_a: math + math.DG: + title: Differential Geometry + description: Complex, contact, Riemannian, pseudo-Riemannian, symplectic geometry, relativity, gauge theory. + is_a: math + math.DS: + title: Dynamical Systems + description: Dynamics of differential equations and flows, mechanics, classical few-body problems. + is_a: math + math.FA: + title: Functional Analysis + description: Banach spaces, function spaces, real functions, distributions, measures, integration. + is_a: math + math.GM: + title: General Mathematics + description: Mathematical material of general interest, broadly accessible expositions of research results. + is_a: math + math.GN: + title: General Topology + description: Continuum theory, point-set topology, spaces with algebraic structure, topological dynamics. + is_a: math + math.GR: + title: Group Theory + description: Finite groups, topological groups, representation theory, cohomology, classification. + is_a: math + math.GT: + title: Geometric Topology + description: Manifolds, orbifolds, polyhedra, cell complexes, foliations, geometric structures. + is_a: math + math.HO: + title: History and Overview + description: Biographies, philosophy of mathematics, mathematics education, recreational mathematics. + is_a: math + math.IT: + title: Information Theory + description: Math methods in information theory and coding theory. + is_a: math + math.KT: + title: K-Theory and Homology + description: Algebraic and topological K-theory, relations with topology, commutative algebra, index theories. + is_a: math + math.LO: + title: Logic + description: Logic, set theory, point-set topology, formal mathematics. + is_a: math + math.MG: + title: Metric Geometry + description: Euclidean, hyperbolic, discrete, convex, coarse geometry, comparisons in Riemannian geometry. + is_a: math + math.MP: + title: Mathematical Physics + description: Articles in which math methods are used to study physics problems, or math questions arising from physics. + is_a: math + math.NA: + title: Numerical Analysis + description: Numerical algorithms for problems in analysis and algebra, scientific computation. + is_a: math + math.NT: + title: Number Theory + description: Prime numbers, diophantine equations, analytic number theory, algebraic number theory, arithmetic geometry. + is_a: math + math.OA: + title: Operator Algebras + description: Algebras of operators on Hilbert space, C*-algebras, von Neumann algebras, non-commutative geometry. + is_a: math + math.OC: + title: Optimization and Control + description: Operations research, linear programming, control theory, systems theory, optimal control. + is_a: math + math.PR: + title: Probability + description: Theory and applications of probability and stochastic processes, including stochastic differential equations. + is_a: math + math.QA: + title: Quantum Algebra + description: Quantum groups, skein theories, operadic and diagrammatic algebra, quantum field theory. + is_a: math + math.RA: + title: Rings and Algebras + description: Non-commutative rings and algebras, non-associative algebras, universal algebra. + is_a: math + math.RT: + title: Representation Theory + description: Linear representations of algebras and groups, Lie theory, associative algebras. + is_a: math + math.SG: + title: Symplectic Geometry + description: Hamiltonian systems, symplectic flows, classical integrable systems. + is_a: math + math.SP: + title: Spectral Theory + description: Schrodinger operators, differential operators, spectral measures, scattering theory. + is_a: math + math.ST: + title: Statistics Theory + description: Applied, computational and theoretical statistics including probability, coverage, learning theory. + is_a: math + astro-ph.CO: + title: Cosmology and Nongalactic Astrophysics + description: Phenomenology of early universe, cosmic microwave background, cosmological parameters, primordial element + abundances. + is_a: astro-ph + astro-ph.EP: + title: Earth and Planetary Astrophysics + description: Interplanetary medium, planetary physics, terrestrial planets, extrasolar planets, irregular satellites. + is_a: astro-ph + astro-ph.GA: + title: Astrophysics of Galaxies + description: Phenomena pertaining to galaxies or combinations of galaxies, interstellar medium, star clusters. + is_a: astro-ph + astro-ph.HE: + title: High Energy Astrophysical Phenomena + description: Cosmic ray production, gamma rays, X-rays, charged particles, supernovae, neutron stars, pulsars. + is_a: astro-ph + astro-ph.IM: + title: Instrumentation and Methods for Astrophysics + description: Detector and calculation design, space and laboratory observatories, data analysis methods. + is_a: astro-ph + astro-ph.SR: + title: Solar and Stellar Astrophysics + description: White dwarfs, brown dwarfs, stars, solar system, helioseismology, stellar evolution. + is_a: astro-ph + cond-mat.dis-nn: + title: Disordered Systems and Neural Networks + description: Glasses and spin glasses; random systems; information theory in physics; neural networks. + is_a: cond-mat + cond-mat.mes-hall: + title: Mesoscale and Nanoscale Physics + description: Quantum dots and wires, nanotubes, graphene, ballistic transport, mesoscale and nanoscale systems. + is_a: cond-mat + cond-mat.mtrl-sci: + title: Materials Science + description: Techniques, synthesis, characterization, structure; mechanical and structural phase transitions. + is_a: cond-mat + cond-mat.other: + title: Other Condensed Matter + description: Work in condensed matter that does not fit into other cond-mat classifications. + is_a: cond-mat + cond-mat.quant-gas: + title: Quantum Gases + description: Ultracold atomic gases, Bose-Einstein condensation, Feshbach resonances, spinor condensates. + is_a: cond-mat + cond-mat.soft: + title: Soft Condensed Matter + description: Membranes, emulsions, gels, foams, nematic phases, polymers, liquid crystals. + is_a: cond-mat + cond-mat.stat-mech: + title: Statistical Mechanics + description: Phase transitions, thermodynamics, field theory, non-equilibrium phenomena, renormalization. + is_a: cond-mat + cond-mat.str-el: + title: Strongly Correlated Electrons + description: Quantum magnetism, non-Fermi liquid, spin liquids, stripe phases, electron-phonon interactions. + is_a: cond-mat + cond-mat.supr-con: + title: Superconductivity + description: Superconductivity theory, models, phenomenology, experimental results. + is_a: cond-mat + hep-ex: + title: High Energy Physics - Experiment + description: Results from high-energy/particle physics experiments at accelerators and observatories. + is_a: hep + hep-lat: + title: High Energy Physics - Lattice + description: Lattice field theory results with desired precision and algorithmic advances. + is_a: hep + hep-ph: + title: High Energy Physics - Phenomenology + description: Theoretical particle physics and its relation to experiment. Covers Standard Model and beyond. + is_a: hep + hep-th: + title: High Energy Physics - Theory + description: Formal aspects of quantum field theory, string theory, quantum gravity. + is_a: hep + gr-qc: + title: General Relativity and Quantum Cosmology + description: General relativity, gravitational physics, cosmological models, relativistic astrophysics. + is_a: physics + math-ph: + title: Mathematical Physics + description: Applications of mathematics to problems in physics and development of mathematical methods for such applications. + is_a: physics + quant-ph: + title: Quantum Physics + description: Quantum foundations, quantum information, quantum computation, quantum mechanics. + is_a: physics + close_mappings: + - NCIT:C19650 + - mesh:D000098222 + nlin.AO: + title: Adaptation and Self-Organizing Systems + description: Self-organization, adaptation, and autonomous systems. + is_a: nlin + nlin.CD: + title: Chaotic Dynamics + description: Dynamical systems with chaotic behavior, routes to chaos, spectral analysis, Lyapunov exponents. + is_a: nlin + nlin.CG: + title: Cellular Automata and Lattice Gases + description: Cellular automata, lattice Boltzmann, lattice gas automata, signal processing with cellular automata. + is_a: nlin + nlin.PS: + title: Pattern Formation and Solitons + description: Pattern formation, coherent structures, solitons, waves. + is_a: nlin + nlin.SI: + title: Exactly Solvable and Integrable Systems + description: Integrable PDEs, integrable ODEs, Painleve analysis, integrable discrete systems. + is_a: nlin + nucl-ex: + title: Nuclear Experiment + description: Experimental results from nuclear physics laboratories, such as heavy-ion collisions. + is_a: nucl + nucl-th: + title: Nuclear Theory + description: Theory of nuclear structure and low-energy reactions, including heavy-ion physics. + is_a: nucl + physics.acc-ph: + title: Accelerator Physics + description: Accelerator theory and target design, beam physics, secondary beams, photon sources. + is_a: physics + physics.ao-ph: + title: Atmospheric and Oceanic Physics + description: Atmospheric and oceanic processes, climate dynamics, waves, boundary layer physics. + is_a: physics + physics.app-ph: + title: Applied Physics + description: Applications of physics to new technology, medical physics, instrumentation. + is_a: physics + physics.atm-clus: + title: Atomic and Molecular Clusters + description: Binding, structure, and properties of clusters, nanoparticles. + is_a: physics + physics.atom-ph: + title: Atomic Physics + description: Atomic and molecular structure, spectra, collisions, and data. Ultrafast physics, molecular physics. + is_a: physics + physics.bio-ph: + title: Biological Physics + description: Molecular biophysics, cellular biophysics, single molecule biophysics. + is_a: physics + close_mappings: + - NCIT:C16349 + - mesh:D001703 + physics.chem-ph: + title: Chemical Physics + description: Experimental, methods, and results in chemical physics and molecular dynamics. + is_a: physics + physics.class-ph: + title: Classical Physics + description: Newtonian and Lagrangian mechanics, electromagnetism, thermodynamics, special relativity. + is_a: physics + physics.comp-ph: + title: Computational Physics + description: All aspects of computational science applied to physics problems. + is_a: physics + physics.data-an: + title: Data Analysis, Statistics and Probability + description: Methods, software, and results in physics data analysis. + is_a: physics + physics.ed-ph: + title: Physics Education + description: Physics teaching and learning research. + is_a: physics + physics.flu-dyn: + title: Fluid Dynamics + description: Turbulence, instabilities, incompressible and compressible flows, boundary layers. + is_a: physics + physics.gen-ph: + title: General Physics + description: General physics that does not fit elsewhere. + is_a: physics + physics.geo-ph: + title: Geophysics + description: Computational and theoretical geophysics including seismology, potential theory. + is_a: physics + physics.hist-ph: + title: History and Philosophy of Physics + description: History and philosophy of all aspects of physics. + is_a: physics + physics.ins-det: + title: Instrumentation and Detectors + description: Instrumentation and detectors for accelerator, astro-, geo-, or particle physics. + is_a: physics + physics.med-ph: + title: Medical Physics + description: Radiation therapy, biomedical imaging, health physics. + is_a: physics + close_mappings: + - NCIT:C16667 + physics.optics: + title: Optics + description: Adaptive optics, polarimetry, quantum optics, ultrafast optics, photonics. + is_a: physics + physics.plasm-ph: + title: Plasma Physics + description: Fundamental plasma physics, magnetic and inertial confinement, astrophysical plasmas. + is_a: physics + physics.pop-ph: + title: Popular Physics + description: General physics topics for a broad audience. + is_a: physics + physics.soc-ph: + title: Physics and Society + description: Sociophysics, structure and dynamics of societies, opinion dynamics. + is_a: physics + physics.space-ph: + title: Space Physics + description: Space plasma physics, magnetospheric physics, solar wind, cosmic rays. + is_a: physics + q-bio.BM: + title: Biomolecules + description: DNA, RNA, proteins, lipids, small molecules; molecular structure and dynamics; molecular engineering. + is_a: q-bio + q-bio.CB: + title: Cell Behavior + description: Cell-cell signaling, morphogenesis, development; cell division/cycle; immunology. + is_a: q-bio + q-bio.GN: + title: Genomics + description: DNA sequencing and assembly; gene finding; genome structure, organization, and regulation. + is_a: q-bio + close_mappings: + - NCIT:C84343 + - mesh:D023281 + q-bio.MN: + title: Molecular Networks + description: Gene regulation, signal transduction, metabolic networks, kinetics, synthetic biology. + is_a: q-bio + q-bio.NC: + title: Neurons and Cognition + description: Synapse, receptor dynamics, learning, neural coding, neuroinformatics. + is_a: q-bio + q-bio.OT: + title: Other Quantitative Biology + description: Work in quantitative biology that does not fit in the other q-bio classifications. + is_a: q-bio + q-bio.PE: + title: Populations and Evolution + description: Population dynamics, spatio-temporal evolution, migration, phylogeny, biodiversity. + is_a: q-bio + q-bio.QM: + title: Quantitative Methods + description: Research papers with experimental, numerical, or statistical contributions of value to biologists. + is_a: q-bio + q-bio.SC: + title: Subcellular Processes + description: Subcellular structures, molecular motors, organelle transport, packaging. + is_a: q-bio + q-bio.TO: + title: Tissues and Organs + description: Blood flow, biomechanics, tumor growth, tissue morphogenesis. + is_a: q-bio + q-fin.CP: + title: Computational Finance + description: Monte Carlo, PDE, and other numerical methods with applications to quantitative finance. + is_a: q-fin + q-fin.EC: + title: Economics + description: General economics topics with quantitative approaches. + is_a: q-fin + q-fin.GN: + title: General Finance + description: General quantitative financial methodologies covering multiple sub-fields. + is_a: q-fin + q-fin.MF: + title: Mathematical Finance + description: Mathematical and analytical methods in finance, stochastic methods, hedging strategies. + is_a: q-fin + q-fin.PM: + title: Portfolio Management + description: Security selection and optimization, capital allocation, investment strategies. + is_a: q-fin + q-fin.PR: + title: Pricing of Securities + description: Valuation and hedging of financial securities, their derivatives, and structured products. + is_a: q-fin + q-fin.RM: + title: Risk Management + description: Measurement and management of financial risks in trading, banking, insurance. + is_a: q-fin + q-fin.ST: + title: Statistical Finance + description: Statistical, econometric methods applied to financial markets. + is_a: q-fin + q-fin.TR: + title: Trading and Market Microstructure + description: Market microstructure, algorithmic trading, order book dynamics. + is_a: q-fin + stat.AP: + title: Applications + description: Biology, education, epidemiology, engineering, environmental sciences, medical, physical sciences. + is_a: stat + stat.CO: + title: Computation + description: Algorithms, computational methods, simulation, visualization. + is_a: stat + stat.ME: + title: Methodology + description: Design, surveys, model selection, regression, testing, time series. + is_a: stat + stat.ML: + title: Machine Learning + description: Covers machine learning papers with a statistical or theoretical grounding. + is_a: stat + close_mappings: + - NCIT:C176231 + - mesh:D000069550 + stat.OT: + title: Other Statistics + description: Work in statistics that does not fit into the other stat-* classifications. + is_a: stat + stat.TH: + title: Statistics Theory + description: Asymptotics, Bayesian inference, decision theory, estimation, foundations, inference. + is_a: stat + is_a: ArxivCategoriesSchemaEnum + annotations: + source_domain: publishing + source_schema: arxiv_categories + OstiRecordSchemaEnum: + description: Schema-level enum for osti_record in publishing + is_a: PublishingDomainEnum + abstract: true annotations: - source_domain: physics - source_schema: states_of_matter + source_file: publishing/osti_record.yaml + OstiWorkflowStatus: + title: OSTI Workflow Status + description: Workflow status codes for OSTI record revisions. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + R: {} + SA: {} + SR: {} + SO: {} + SF: {} + SX: {} + SV: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiAccessLimitation: + title: OSTI Access Limitation + description: Access and distribution limitation codes from OSTI. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + UNL: {} + OPN: {} + CPY: {} + OUO: {} + PROT: {} + PDOUO: {} + ECI: {} + PDSH: {} + USO: {} + LRD: {} + NAT: {} + NNPI: {} + INTL: {} + PROP: {} + PAT: {} + OTHR: {} + CUI: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiCollectionType: + title: OSTI Collection Type + description: Collection type codes used by OSTI for record origin. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + CHORUS: {} + DOE_GRANT: {} + DOE_LAB: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiSensitivityFlag: + title: OSTI Sensitivity Flag + description: Sensitivity flags calculated by OSTI for released records. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + H: {} + S: {} + U: {} + X: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiOrganizationIdentifierType: + title: OSTI Organization Identifier Type + description: Identifier types for OSTI organizations. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + AWARD_DOI: {} + CN_DOE: {} + CN_NONDOE: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiProductType: + title: OSTI Product Type + description: Product type codes from OSTI record metadata. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + AR: {} + B: {} + CO: {} + DA: {} + FS: {} + JA: {} + MI: {} + OT: {} + P: {} + PD: {} + SM: {} + TD: {} + TR: {} + PA: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiOrganizationType: + title: OSTI Organization Type + description: Organization role types used by OSTI. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + AUTHOR: {} + CONTRIBUTING: {} + RESEARCHING: {} + SPONSOR: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiPersonType: + title: OSTI Person Type + description: Person role types used by OSTI. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + AUTHOR: {} + RELEASE: {} + CONTACT: {} + CONTRIBUTING: {} + PROT_CE: {} + PROT_RO: {} + SBIZ_PI: {} + SBIZ_BO: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiContributorType: + title: OSTI Contributor Type + description: Contributor role types used by OSTI. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + Chair: {} + DataCollector: {} + DataCurator: {} + DataManager: {} + Distributor: {} + Editor: {} + HostingInstitution: {} + Producer: {} + ProjectLeader: {} + ProjectManager: {} + ProjectMember: {} + RegistrationAgency: {} + RegistrationAuthority: {} + RelatedPerson: {} + Reviewer: {} + ReviewAssistant: {} + ReviewerExternal: {} + RightsHolder: {} + StatsReviewer: {} + Supervisor: {} + Translator: {} + WorkPackageLeader: {} + Other: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiRelatedIdentifierType: + title: OSTI Related Identifier Type + description: Identifier types for related resources in OSTI. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + ARK: {} + arXiv: {} + bibcode: {} + DOI: {} + EAN13: {} + EISSN: {} + IGSN: {} + ISBN: {} + ISSN: {} + ISTC: {} + Handle: {} + LISSN: {} + LSID: {} + OTHER: {} + PMCID: {} + PMID: {} + PURL: {} + UPC: {} + URI: {} + URL: {} + URN: {} + UUID: {} + w3id: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiRelationType: + title: OSTI Relation Type + description: Relationship types between records in OSTI. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + BasedOnData: {} + Cites: {} + Compiles: {} + Continues: {} + Describes: {} + Documents: {} + Finances: {} + HasComment: {} + HasDerivation: {} + HasMetadata: {} + HasPart: {} + HasRelatedMaterial: {} + HasReply: {} + HasReview: {} + HasVersion: {} + IsBasedOn: {} + IsBasisFor: {} + IsCitedBy: {} + IsCommentOn: {} + IsCompiledBy: {} + IsContinuedBy: {} + IsDataBasisFor: {} + IsDerivedFrom: {} + IsDescribedBy: {} + IsDocumentedBy: {} + IsFinancedBy: {} + IsIdenticalTo: {} + IsMetadataFor: {} + IsNewVersionOf: {} + IsObsoletedBy: {} + IsOriginalFormOf: {} + IsPartOf: {} + IsPreviousVersionOf: {} + IsReferencedBy: {} + IsRelatedMaterial: {} + IsReplyTo: {} + IsRequiredBy: {} + IsReviewedBy: {} + IsReviewOf: {} + IsSourceOf: {} + IsSupplementedBy: {} + IsSupplementTo: {} + IsVariantFormOf: {} + IsVersionOf: {} + Obsoletes: {} + References: {} + Requires: {} + Reviews: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiIdentifierType: + title: OSTI Identifier Type + description: Identifier type codes from OSTI record metadata. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + AUTH_REV: {} + CN_DOE: {} + CN_NONDOE: {} + CODEN: {} + DOE_DOCKET: {} + EDB: {} + ETDE_RN: {} + INIS_RN: {} + ISBN: {} + ISSN: {} + LEGACY: {} + NSA: {} + OPN_ACC: {} + OTHER_ID: {} + PATENT: {} + PROJ_ID: {} + PROP_REV: {} + REF: {} + REL_TRN: {} + RN: {} + TRN: {} + TVI: {} + USER_VER: {} + WORK_AUTH: {} + WORK_PROP: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiGeolocationType: + title: OSTI Geolocation Type + description: Geolocation shape types in OSTI record metadata. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + POINT: {} + BOX: {} + POLYGON: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record + OstiMediaLocationType: + title: OSTI Media Location Type + description: Location indicators for OSTI media files and sets. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.osti.gov/elink2api/record-schema + permissible_values: + L: {} + O: {} + is_a: OstiRecordSchemaEnum + annotations: + source_domain: publishing + source_schema: osti_record RootDomainEnum: description: Domain-level enum for root value sets is_a: ValueSetEnum @@ -23236,8 +47237,15 @@ enums: annotations: source_file: confidence_levels.yaml ConfidenceLevel: + title: Confidence Level description: Standard confidence levels based on NCIT (NCI Thesaurus) definitions. Used to express the degree of confidence in evidence, data, or assertions. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/ncit.owl conforms_to: NCI Thesaurus permissible_values: @@ -23260,8 +47268,15 @@ enums: source_domain: root source_schema: confidence_levels CIOConfidenceLevel: + title: CIO Confidence Level description: Confidence levels from the Confidence Information Ontology (CIO), representing different levels of trust in evidence. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HIGH: description: A confidence level representing a high trust in an evidence. @@ -23289,8 +47304,15 @@ enums: source_domain: root source_schema: confidence_levels OBCSCertaintyLevel: + title: OBCS Certainty Level description: Certainty levels from the Ontology of Biological and Clinical Statistics (OBCS). These terms are used to express degrees of certainty in statistical and clinical contexts. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DEFINITIVE: description: Definitive certainty level - the highest degree of certainty. @@ -23318,8 +47340,15 @@ enums: source_domain: root source_schema: confidence_levels IPCCLikelihoodScale: + title: IPCC Likelihood Scale description: IPCC (Intergovernmental Panel on Climate Change) standardized likelihood scale used to communicate the assessed probability of an outcome or result. Widely used in climate science and environmental assessments. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VIRTUALLY_CERTAIN: description: 99-100% probability of occurrence/truth. @@ -23366,8 +47395,15 @@ enums: source_domain: root source_schema: confidence_levels IPCCConfidenceLevel: + title: IPCC Confidence Level description: IPCC confidence qualifiers used to express the degree of confidence in a finding based on the type, amount, quality, and consistency of evidence and the degree of agreement. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VERY_HIGH_CONFIDENCE: description: Very high confidence in the validity of a finding. @@ -23394,8 +47430,15 @@ enums: source_domain: root source_schema: confidence_levels NCITFivePointConfidenceScale: + title: NCIT Five Point Confidence Scale description: NCIT 5-point subjective confidence scale ranging from "Not at all confident" (1) to "Very confident" (5). Used in clinical assessments and questionnaires. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NOT_AT_ALL_CONFIDENT: description: A subjective score of 1 - Not at all confident. @@ -23433,7 +47476,14 @@ enums: annotations: source_file: contributor.yaml ContributorType: + title: Contributor Type description: The type of contributor being represented. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PERSON: description: A person. @@ -23454,16 +47504,34 @@ enums: annotations: source_file: core.yaml RelativeTimeEnum: - permissible_values: - BEFORE: null - AFTER: null - AT_SAME_TIME_AS: null + title: Relative Time + description: Temporal relationships between events or time points + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BEFORE: + description: Occurs before the reference time point + AFTER: + description: Occurs after the reference time point + AT_SAME_TIME_AS: + description: Occurs at the same time as the reference time point is_a: CoreSchemaEnum - description: 'Enum: RelativeTimeEnum' annotations: source_domain: root source_schema: core PresenceEnum: + title: Presence Status + description: Classification of whether an entity is present, absent, or at detection limits + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRESENT: description: The entity is present @@ -23474,7 +47542,6 @@ enums: ABOVE_DETECTION_LIMIT: description: The entity is above the detection limit is_a: CoreSchemaEnum - description: 'Enum: PresenceEnum' annotations: source_domain: root source_schema: core @@ -23485,7 +47552,14 @@ enums: annotations: source_file: demographics.yaml EducationLevel: + title: Education Level description: Years of education that a person has completed + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://terminology.hl7.org/CodeSystem-v3-EducationLevel.html permissible_values: ELEM: @@ -23520,7 +47594,14 @@ enums: source_domain: root source_schema: demographics MaritalStatus: + title: Marital Status description: The domestic partnership status of a person + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.hl7.org/fhir/valueset-marital-status.html permissible_values: ANNULLED: @@ -23564,7 +47645,14 @@ enums: source_domain: root source_schema: demographics EmploymentStatus: + title: Employment Status description: Employment status of a person + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://terminology.hl7.org/CodeSystem-v2-0066.html permissible_values: FULL_TIME_EMPLOYED: @@ -23608,7 +47696,14 @@ enums: source_domain: root source_schema: demographics HousingStatus: + title: Housing Status description: Housing status of patients per UDS Plus HRSA standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.fhir.org/guides/hrsa/uds-plus/CodeSystem-udsplus-housing-status-codes.html permissible_values: HOMELESS_SHELTER: @@ -23637,7 +47732,14 @@ enums: source_domain: root source_schema: demographics GenderIdentity: + title: Gender Identity description: Gender identity codes indicating an individual's personal sense of gender + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://terminology.hl7.org/ValueSet-gender-identity.html permissible_values: FEMALE: @@ -23660,7 +47762,14 @@ enums: source_domain: root source_schema: demographics OmbRaceCategory: + title: Omb Race Category description: Office of Management and Budget (OMB) race category codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.hl7.org/fhir/us/core/ValueSet-omb-race-category.html permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: @@ -23692,7 +47801,14 @@ enums: source_domain: root source_schema: demographics OmbEthnicityCategory: + title: Omb Ethnicity Category description: Office of Management and Budget (OMB) ethnicity category codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.hl7.org/fhir/us/core/ValueSet-omb-ethnicity-category.html permissible_values: HISPANIC_OR_LATINO: @@ -23711,6 +47827,26 @@ enums: annotations: source_domain: root source_schema: demographics + OccupationEnum: + title: Occupation + description: The principal activity that a person does to earn money. Dynamic enum populated from NCIT occupation hierarchy + including medical, professional, service, and military occupations. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + reachable_from: + source_nodes: + - NCIT:C25193 + is_direct: false + relationship_types: + - rdfs:subClassOf + is_a: DemographicsSchemaEnum + annotations: + source_domain: root + source_schema: demographics EcologicalInteractionsSchemaEnum: description: Schema-level enum for ecological_interactions in root is_a: RootDomainEnum @@ -23718,10 +47854,17 @@ enums: annotations: source_file: ecological_interactions.yaml BioticInteractionType: + title: Biotic Interaction Type description: 'Types of biotic interactions between organisms, based on RO:0002437 (biotically interacts with). These represent ecological relationships where at least one partner is an organism. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BIOTICALLY_INTERACTS_WITH: description: 'An interaction relationship in which at least one of the partners is an organism and the other is either @@ -24001,7 +48144,14 @@ enums: annotations: source_file: health.yaml VitalStatusEnum: + title: Vital Status description: The vital status of a person or organism + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ALIVE: description: The person is living @@ -24028,6 +48178,13 @@ enums: annotations: source_file: healthcare.yaml HealthcareEncounterClassification: + title: Healthcare Encounter Classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: Inpatient Visit: description: Person visiting hospital, at a Care Site, in bed, for duration of more than one day, with physicians @@ -24070,6 +48227,13 @@ enums: annotations: source_file: investigation.yaml CaseOrControlEnum: + title: Case Or Control + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CASE: title: case role in case-control study @@ -24083,6 +48247,13 @@ enums: source_domain: root source_schema: investigation StudyDesignEnum: + title: Study Design + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - OBI:0500000 @@ -24095,6 +48266,13 @@ enums: source_domain: root source_schema: investigation InvestigativeProtocolEnum: + title: Investigative Protocol + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - OBI:0000272 @@ -24107,6 +48285,13 @@ enums: source_domain: root source_schema: investigation SampleProcessingEnum: + title: Sample Processing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - OBI:0000094 @@ -24118,6 +48303,49 @@ enums: annotations: source_domain: root source_schema: investigation + PlannedProcessCompletionStatus: + title: Planned Process Completion Status + description: The completion status of a planned process, indicating whether the process was successfully executed or failed. + Based on COB (Core Ontology for Biology) planned process hierarchy. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + COMPLETELY_EXECUTED: + title: completely executed planned process + description: A planned process that was successfully completed as intended + meaning: COB:0000035 + FAILED: + title: failed planned process + description: A planned process that did not complete successfully + meaning: COB:0000083 + is_a: InvestigationSchemaEnum + annotations: + source_domain: root + source_schema: investigation + StudyTypeEnum: + title: Study Type + description: Types of studies, including clinical trials, observational studies, and other research investigations. Dynamically + populated from NCIT descendants of Study (NCIT:C63536). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + reachable_from: + source_nodes: + - NCIT:C63536 + is_direct: false + relationship_types: + - rdfs:subClassOf + is_a: InvestigationSchemaEnum + annotations: + source_domain: root + source_schema: investigation MiningProcessingSchemaEnum: description: Schema-level enum for mining_processing in root is_a: RootDomainEnum @@ -24125,10 +48353,17 @@ enums: annotations: source_file: mining_processing.yaml MineralogyFeedstockClass: + title: Mineralogy Feedstock Class description: 'Types of mineral feedstock sources for extraction and processing operations, including primary and secondary sources. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HARDROCK_PRIMARY: title: HARDROCK_PRIMARY @@ -24153,9 +48388,16 @@ enums: source_domain: root source_schema: mining_processing BeneficiationPathway: + title: Beneficiation Pathway description: 'Methods for mineral separation and concentration aligned with advanced ore processing initiatives (AOI-2). ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ORE_SORTING: description: Sensor-based sorting of ore particles @@ -24180,10 +48422,17 @@ enums: source_domain: root source_schema: mining_processing InSituChemistryRegime: + title: In Situ Chemistry Regime description: 'Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, temperature, and ionic strength. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACIDIC_SULFATE: title: ACIDIC_SULFATE @@ -24205,76 +48454,148 @@ enums: source_domain: root source_schema: mining_processing ExtractableTargetElement: - description: 'Target elements for extraction, particularly rare earth elements (REE) and critical minerals. - - ' + title: Extractable Target Elements + description: Target elements for extraction in mining operations, including rare earth elements (REE), critical minerals, + and battery metals. These elements are strategically important for clean energy technologies, electronics, and defense + applications. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - REE_LA: - title: REE_LA - description: Lanthanum - REE_CE: - title: REE_CE - description: Cerium - REE_PR: - title: REE_PR - description: Praseodymium - REE_ND: - title: REE_ND - description: Neodymium - REE_PM: - title: REE_PM - description: Promethium - REE_SM: - title: REE_SM - description: Samarium - REE_EU: - title: REE_EU - description: Europium - REE_GD: - title: REE_GD - description: Gadolinium - REE_TB: - title: REE_TB - description: Terbium - REE_DY: - title: REE_DY - description: Dysprosium - REE_HO: - title: REE_HO - description: Holmium - REE_ER: - title: REE_ER - description: Erbium - REE_TM: - title: REE_TM - description: Thulium - REE_YB: - title: REE_YB - description: Ytterbium - REE_LU: - title: REE_LU - description: Lutetium + LA: + title: Lanthanum + aliases: + - lanthanum atom + description: Light rare earth element (atomic number 57) used in catalysts, optics, and battery electrodes + meaning: CHEBI:33336 + CE: + title: Cerium + aliases: + - cerium + description: Light rare earth element (atomic number 58) used in catalytic converters, glass polishing, and metallurgy + meaning: CHEBI:33369 + PR: + title: Praseodymium + aliases: + - praseodymium atom + description: Light rare earth element (atomic number 59) used in magnets, lasers, and aircraft engines + meaning: CHEBI:49828 + ND: + title: Neodymium + aliases: + - neodymium atom + description: Light rare earth element (atomic number 60) essential for high-strength permanent magnets in wind turbines + and EVs + meaning: CHEBI:33372 + PM: + title: Promethium + aliases: + - promethium atom + description: Radioactive rare earth element (atomic number 61) used in nuclear batteries and luminous paint + meaning: CHEBI:33373 + SM: + title: Samarium + aliases: + - samarium atom + description: Light rare earth element (atomic number 62) used in samarium-cobalt magnets and cancer treatment + meaning: CHEBI:33374 + EU: + title: Europium + aliases: + - europium atom + description: Rare earth element (atomic number 63) used in phosphors for displays and fluorescent lighting + meaning: CHEBI:32999 + GD: + title: Gadolinium + aliases: + - gadolinium atom + description: Heavy rare earth element (atomic number 64) used in MRI contrast agents and nuclear reactor control rods + meaning: CHEBI:33375 + TB: + title: Terbium + aliases: + - terbium atom + description: Heavy rare earth element (atomic number 65) used in solid-state devices and green phosphors + meaning: CHEBI:33376 + DY: + title: Dysprosium + aliases: + - dysprosium atom + description: Heavy rare earth element (atomic number 66) critical for high-temperature permanent magnets + meaning: CHEBI:33377 + HO: + title: Holmium + aliases: + - holmium atom + description: Heavy rare earth element (atomic number 67) used in lasers and magnetic flux concentrators + meaning: CHEBI:49648 + ER: + title: Erbium + aliases: + - erbium + description: Heavy rare earth element (atomic number 68) used in fiber optic amplifiers and lasers + meaning: CHEBI:33379 + TM: + title: Thulium + aliases: + - thulium atom + description: Heavy rare earth element (atomic number 69) used in portable X-ray devices and lasers + meaning: CHEBI:33380 + YB: + title: Ytterbium + aliases: + - ytterbium + description: Heavy rare earth element (atomic number 70) used in metallurgy, lasers, and atomic clocks + meaning: CHEBI:33381 + LU: + title: Lutetium + aliases: + - lutetium atom + description: Heavy rare earth element (atomic number 71) used in PET scan detectors and cancer treatment + meaning: CHEBI:33382 SC: - title: SC - description: Scandium + title: Scandium + aliases: + - scandium atom + description: Transition metal (atomic number 21) used in aluminum alloys for aerospace and sports equipment + meaning: CHEBI:33330 CO: - title: CO - description: Cobalt + title: Cobalt + aliases: + - cobalt atom + description: Transition metal (atomic number 27) essential for lithium-ion battery cathodes and superalloys + meaning: CHEBI:27638 NI: - title: NI - description: Nickel + title: Nickel + aliases: + - nickel atom + description: Transition metal (atomic number 28) used in stainless steel, batteries, and electroplating + meaning: CHEBI:28112 LI: - title: LI - description: Lithium + title: Lithium + aliases: + - lithium atom + description: Alkali metal (atomic number 3) essential for lithium-ion batteries and energy storage systems + meaning: CHEBI:30145 is_a: MiningProcessingSchemaEnum annotations: source_domain: root source_schema: mining_processing SensorWhileDrillingFeature: + title: Sensor While Drilling Feature description: 'Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering applications. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: WOB: description: Weight on bit measurement @@ -24297,10 +48618,17 @@ enums: source_domain: root source_schema: mining_processing ProcessPerformanceMetric: + title: Process Performance Metric description: 'Key performance indicators for mining and processing operations tied to SMART milestones and sustainability goals. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RECOVERY_PCT: description: Percentage recovery of target material @@ -24321,9 +48649,16 @@ enums: source_domain: root source_schema: mining_processing BioleachOrganism: + title: Bioleach Organism description: 'Microorganisms used in bioleaching and biomining operations, including engineered strains. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACIDITHIOBACILLUS_FERROOXIDANS: description: Iron and sulfur oxidizing bacterium @@ -24341,9 +48676,16 @@ enums: source_domain: root source_schema: mining_processing BioleachMode: + title: Bioleach Mode description: 'Mechanisms of bioleaching including indirect and direct bacterial action. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INDIRECT_BIOLEACH_ORGANIC_ACIDS: description: Indirect bioleaching through organic acid production @@ -24356,10 +48698,17 @@ enums: source_domain: root source_schema: mining_processing AutonomyLevel: + title: Autonomy Level description: 'Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for Topic 1 initiatives). ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ASSISTIVE: description: Human operator with assistive technologies @@ -24374,45 +48723,302 @@ enums: source_domain: root source_schema: mining_processing RegulatoryConstraint: + title: Regulatory Constraint description: 'Regulatory and community constraints affecting mining operations, particularly for in-situ extraction and community engagement. - ' - permissible_values: - AQUIFER_PROTECTION: - title: AQUIFER_PROTECTION - description: Requirements for groundwater and aquifer protection - EMISSIONS_CAP: - description: Limits on atmospheric emissions - CULTURAL_HERITAGE_ZONE: - description: Protection of cultural heritage sites - WATER_RIGHTS_LIMIT: - description: Restrictions based on water usage rights - is_a: MiningProcessingSchemaEnum - annotations: - source_domain: root - source_schema: mining_processing - StatisticsSchemaEnum: - description: Schema-level enum for statistics in root - is_a: RootDomainEnum - abstract: true - annotations: - source_file: statistics.yaml - PredictionOutcomeType: - permissible_values: - TP: - description: True Positive - FP: - description: False Positive - TN: - description: True Negative - FN: - description: False Negative - is_a: StatisticsSchemaEnum - description: 'Enum: PredictionOutcomeType' + ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + AQUIFER_PROTECTION: + title: AQUIFER_PROTECTION + description: Requirements for groundwater and aquifer protection + EMISSIONS_CAP: + description: Limits on atmospheric emissions + CULTURAL_HERITAGE_ZONE: + description: Protection of cultural heritage sites + WATER_RIGHTS_LIMIT: + description: Restrictions based on water usage rights + is_a: MiningProcessingSchemaEnum + annotations: + source_domain: root + source_schema: mining_processing + StatisticsSchemaEnum: + description: Schema-level enum for statistics in root + is_a: RootDomainEnum + abstract: true + annotations: + source_file: statistics.yaml + PredictionOutcomeType: + title: Prediction Outcome Type + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TP: + description: True Positive + FP: + description: False Positive + TN: + description: True Negative + FN: + description: False Negative + is_a: StatisticsSchemaEnum + description: 'Enum: PredictionOutcomeType' + annotations: + source_domain: root + source_schema: statistics + StewardshipSchemaEnum: + description: Schema-level enum for stewardship in root + is_a: RootDomainEnum + abstract: true + annotations: + source_file: stewardship.yaml + ValueSetStewardEnum: + title: Value Set Steward + description: 'Organizations and consortia that may serve as stewards, publishers, or + + endorsers for value sets. Includes standards bodies, bioinformatics + + consortia, and data coordination centers. + + + Use ROR IDs where available; otherwise use canonical organization URLs. + + ' + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + see_also: + - https://ror.org/ + - https://build.fhir.org/metadataresource.html + permissible_values: + GA4GH: + title: Global Alliance for Genomics and Health + description: 'International consortium developing standards for responsible sharing + + of genomic and health-related data. Develops standards including + + Phenopackets, VRS, DRS, and Beacon. + + ' + meaning: https://ga4gh.org + aliases: + - Global Alliance for Genomics and Health + annotations: + established: '2013' + headquarters: Multiple host institutions + website: https://ga4gh.org + GENE_ONTOLOGY_CONSORTIUM: + title: Gene Ontology Consortium + description: 'International consortium developing and maintaining the Gene Ontology, + + the world''s largest source of information on gene function. Provides + + GO annotations and the GO ontology itself. + + ' + meaning: https://geneontology.org + aliases: + - GO Consortium + - GOC + annotations: + established: '1998' + website: https://geneontology.org + GENOMIC_STANDARDS_CONSORTIUM: + title: Genomic Standards Consortium + description: 'Open-membership community developing standards for describing genomes, + + metagenomes, and related data. Develops MIxS checklists and related + + metadata standards. + + ' + meaning: https://gensc.org + aliases: + - GSC + annotations: + established: '2005' + website: https://gensc.org + MONARCH_INITIATIVE: + title: Monarch Initiative + description: 'International consortium integrating genotype-phenotype data across + + species. Develops and maintains ontologies including HPO, Mondo, + + and Upheno, and provides data integration services. + + ' + meaning: https://monarchinitiative.org + aliases: + - Monarch + annotations: + website: https://monarchinitiative.org + OBO_FOUNDRY: + title: OBO Foundry + description: 'Collaborative effort to develop interoperable ontologies for the + + life sciences. Coordinates ontology development and establishes + + principles for ontology best practices. + + ' + meaning: https://obofoundry.org + aliases: + - Open Biological and Biomedical Ontologies Foundry + annotations: + established: '2007' + website: https://obofoundry.org + OHDSI: + title: OHDSI + description: 'Observational Health Data Sciences and Informatics program. + + International collaborative developing open-source analytics solutions + + for observational health data. Maintains the OMOP Common Data Model. + + ' + meaning: https://ohdsi.org + aliases: + - Observational Health Data Sciences and Informatics + annotations: + established: '2014' + website: https://ohdsi.org + coordinating_center: Columbia University + PHENOPACKETS: + title: Phenopackets + description: 'GA4GH work stream developing standards for sharing disease and + + phenotype information. Develops the Phenopacket Schema for + + representing clinical and phenotypic data. + + ' + meaning: https://phenopackets.org + aliases: + - GA4GH Phenopackets + annotations: + parent_organization: GA4GH + website: https://phenopackets.org + EMBL_EBI: + title: European Bioinformatics Institute + description: 'EMBL''s European Bioinformatics Institute, a global leader in + + bioinformatics services, databases, and tools. Hosts major resources + + including UniProt, Ensembl, and the Ontology Lookup Service. + + ' + meaning: ROR:02catss52 + aliases: + - EMBL-EBI + - EBI + annotations: + parent_organization: European Molecular Biology Laboratory + website: https://www.ebi.ac.uk/ + location: Hinxton, UK + NCBI: + title: National Center for Biotechnology Information + description: 'Part of the United States National Library of Medicine. Develops + + databases and tools for molecular biology including GenBank, + + PubMed, and the NCBI Taxonomy. + + ' + meaning: ROR:02meqm098 + aliases: + - National Center for Biotechnology Information + annotations: + parent_organization: National Library of Medicine + website: https://www.ncbi.nlm.nih.gov/ + location: Bethesda, MD, USA + CDISC: + title: CDISC + description: 'Clinical Data Interchange Standards Consortium. Develops global + + data standards for clinical research including CDASH, SDTM, + + and ADaM. + + ' + meaning: https://cdisc.org + aliases: + - Clinical Data Interchange Standards Consortium + annotations: + established: '1997' + website: https://cdisc.org + HL7: + title: Health Level Seven International + description: 'Standards development organization for healthcare information + + exchange. Develops FHIR, CDA, and HL7 v2 messaging standards. + + ' + meaning: ROR:029ga8k16 + aliases: + - Health Level Seven + - HL7 International + annotations: + established: '1987' + website: https://www.hl7.org/ + headquarters: Ann Arbor, Michigan + ISO: + title: International Organization for Standardization + description: 'International standard-setting body for industrial and commercial + + standards. Develops standards across many domains including + + terminology (ISO 704) and healthcare. + + ' + meaning: ROR:004s85t07 + annotations: + established: '1947' + website: https://www.iso.org/ + headquarters: Geneva, Switzerland + W3C: + title: World Wide Web Consortium + description: 'International standards organization for the World Wide Web. + + Develops standards including RDF, OWL, SPARQL, and accessibility + + guidelines. + + ' + meaning: ROR:0059y1582 + annotations: + established: '1994' + website: https://www.w3.org/ + VALUESETS_PROJECT: + title: Valuesets Project + description: 'The valuesets repository itself, for value sets that are community + + contributions without a specific external steward. Use sparingly; + + prefer identifying an appropriate domain consortium. + + ' + meaning: https://github.com/linkml/valuesets + aliases: + - LinkML Valuesets + annotations: + website: https://w3id.org/valuesets/ + is_a: StewardshipSchemaEnum annotations: source_domain: root - source_schema: statistics + source_schema: stewardship SocialDomainEnum: description: Domain-level enum for social value sets is_a: ValueSetEnum @@ -24424,7 +49030,14 @@ enums: annotations: source_file: social/person_status.yaml PersonStatusEnum: + title: Person Status description: Vital status of a person (living or deceased) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ALIVE: description: The person is living @@ -24442,6 +49055,163 @@ enums: annotations: source_domain: social source_schema: person_status + SdohSchemaEnum: + description: Schema-level enum for sdoh in social + is_a: SocialDomainEnum + abstract: true + annotations: + source_file: social/sdoh.yaml + GravitySdohDomainEnum: + title: Gravity Project SDOH Domains + description: Social Determinants of Health domains as defined by the Gravity Project. These domains represent key areas + of social need that impact health outcomes. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://thegravityproject.net/ + - https://hl7.org/fhir/us/sdoh-clinicalcare/ + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + FOOD_INSECURITY: + description: Limited or uncertain availability of nutritionally adequate and safe foods + meaning: NCIT:C171542 + aliases: + - Food Insecurity + HOUSING_INSTABILITY: + description: Challenges with housing including trouble paying rent or frequent moves + meaning: SNOMED:1156191002 + aliases: + - Housing instability + HOMELESSNESS: + description: The condition of lacking stable, safe, and adequate housing + meaning: SNOMED:32911000 + aliases: + - Homeless + INADEQUATE_HOUSING: + description: Housing that does not meet basic standards for safety and habitability + meaning: SNOMED:105531004 + aliases: + - Unsatisfactory housing conditions + TRANSPORTATION_INSECURITY: + description: Lack of reliable, safe, and affordable transportation + FINANCIAL_INSECURITY: + description: Inability to meet basic financial needs and obligations + MATERIAL_HARDSHIP: + description: Difficulty affording basic necessities such as food, housing, and utilities + EMPLOYMENT_STATUS: + description: Current employment situation and stability + meaning: NCIT:C179143 + aliases: + - Employment Status + EDUCATIONAL_ATTAINMENT: + description: Highest level of education completed + meaning: EFO:0011015 + aliases: + - educational attainment + VETERAN_STATUS: + description: Military veteran status and related needs + STRESS: + description: Psychological stress affecting health and wellbeing + meaning: NCIT:C35041 + aliases: + - Stress + SOCIAL_CONNECTION: + description: Quality and quantity of social relationships and support networks + INTIMATE_PARTNER_VIOLENCE: + description: Abuse occurring between people in a close relationship + meaning: MESH:D000066511 + aliases: + - IPV + - domestic violence + - Intimate Partner Violence + ELDER_ABUSE: + description: Abuse, neglect, or exploitation of older adults + meaning: MESH:D004552 + aliases: + - Elder Abuse + HEALTH_LITERACY: + description: Ability to obtain, process, and understand health information + meaning: MESH:D057220 + aliases: + - Health Literacy + MEDICAL_COST_BURDEN: + description: Financial strain from healthcare costs + HEALTH_INSURANCE_COVERAGE_STATUS: + description: Status of health insurance coverage + meaning: NCIT:C157356 + aliases: + - Health Insurance + DIGITAL_LITERACY: + description: Ability to use digital technology and access digital resources + DIGITAL_ACCESS: + description: Access to internet and digital devices + UTILITY_INSECURITY: + description: Difficulty paying for utilities such as electricity, gas, or water + is_a: SdohSchemaEnum + annotations: + source_domain: social + source_schema: sdoh + EducationalAttainmentEnum: + title: Educational Attainment Levels + description: Levels of educational attainment for survey and demographic purposes. Based on standard US educational categories. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + EIGHTH_GRADE_OR_LESS: + description: Completed 8th grade or less + aliases: + - 8TH_GRADE_OR_LESS + - elementary + HIGH_SCHOOL_NO_DIPLOMA: + description: Some high school but no diploma + meaning: NCIT:C76123 + aliases: + - some high school + - Not High School Graduate + HIGH_SCHOOL_GRADUATE_GED: + description: High school graduate or GED equivalent + meaning: NCIT:C67136 + aliases: + - high school diploma + - GED + - High School Completion + SOME_COLLEGE_NO_DEGREE: + description: Some college or technical school but no degree + aliases: + - SOME_COLLEGE_OR_TECH_NO_DEGREE + ASSOCIATE_DEGREE: + description: Associate degree (2-year college) + meaning: NCIT:C71344 + aliases: + - Associate of Science + BACHELORS_DEGREE: + description: Bachelor's degree (4-year college) + meaning: NCIT:C71345 + aliases: + - COLLEGE_OR_TECH_WITH_DEGREE + - Bachelor of Arts + MASTERS_DEGREE: + description: Master's degree + meaning: NCIT:C39452 + aliases: + - Master of Science + DOCTORAL_DEGREE: + description: Doctoral or professional degree (PhD, MD, JD, etc.) + meaning: NCIT:C39387 + aliases: + - MASTERS_OR_DOCTORAL_DEGREE + - Doctor of Philosophy + is_a: SdohSchemaEnum + annotations: + source_domain: social + source_schema: sdoh SpatialDomainEnum: description: Domain-level enum for spatial value sets is_a: ValueSetEnum @@ -24453,7 +49223,14 @@ enums: annotations: source_file: spatial/spatial_qualifiers.yaml SimpleSpatialDirection: + title: Simple Spatial Direction description: Basic spatial directional terms for general use + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEFT: description: To the left side @@ -24500,9 +49277,16 @@ enums: source_domain: spatial source_schema: spatial_qualifiers AnatomicalSide: + title: Anatomical Side description: 'Anatomical sides as defined in the Biological Spatial Ontology (BSPO). An anatomical region bounded by a plane perpendicular to an axis through the middle.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEFT: title: Left side of a bilaterally symmetric organism @@ -24638,7 +49422,14 @@ enums: source_domain: spatial source_schema: spatial_qualifiers AnatomicalRegion: + title: Anatomical Region description: Anatomical regions based on spatial position + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANTERIOR_REGION: title: Region in the anterior portion @@ -24705,7 +49496,14 @@ enums: source_domain: spatial source_schema: spatial_qualifiers AnatomicalAxis: + title: Anatomical Axis description: Anatomical axes defining spatial organization + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANTERIOR_POSTERIOR: title: Anterior-posterior axis (head-tail axis) @@ -24747,7 +49545,14 @@ enums: source_domain: spatial source_schema: spatial_qualifiers AnatomicalPlane: + title: Anatomical Plane description: Standard anatomical planes for sectioning + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SAGITTAL: title: Vertical plane dividing body into left and right @@ -24796,7 +49601,14 @@ enums: source_domain: spatial source_schema: spatial_qualifiers SpatialRelationship: + title: Spatial Relationship description: Spatial relationships between anatomical structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ADJACENT_TO: title: Next to or adjoining @@ -24871,7 +49683,14 @@ enums: source_domain: spatial source_schema: spatial_qualifiers CellPolarity: + title: Cell Polarity description: Spatial polarity in cells and tissues + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: APICAL: description: The free surface of an epithelial cell @@ -24909,6 +49728,109 @@ enums: annotations: source_domain: spatial source_schema: spatial_qualifiers + AnatomicalOrientation: + description: Directional orientation between anatomical positions based on OME NGFF specification + permissible_values: + LEFT_TO_RIGHT: + title: Left to right orientation + description: Directional orientation from left to right lateral side of an anatomical structure + annotations: + source: OME NGFF + RIGHT_TO_LEFT: + title: Right to left orientation + description: Directional orientation from right to left lateral side of an anatomical structure + annotations: + source: OME NGFF + ANTERIOR_TO_POSTERIOR: + title: Anterior to posterior orientation + description: Directional orientation from front to back of an anatomical structure + annotations: + source: OME NGFF + POSTERIOR_TO_ANTERIOR: + title: Posterior to anterior orientation + description: Directional orientation from back to front of an anatomical structure + annotations: + source: OME NGFF + INFERIOR_TO_SUPERIOR: + title: Inferior to superior orientation + description: Directional orientation from below to above in an anatomical structure + annotations: + source: OME NGFF + SUPERIOR_TO_INFERIOR: + title: Superior to inferior orientation + description: Directional orientation from above to below in an anatomical structure + annotations: + source: OME NGFF + DORSAL_TO_VENTRAL: + title: Dorsal to ventral orientation + description: Directional orientation from top/upper to belly/lower in an anatomical structure + annotations: + source: OME NGFF + VENTRAL_TO_DORSAL: + title: Ventral to dorsal orientation + description: Directional orientation from belly/lower to top/upper in an anatomical structure + annotations: + source: OME NGFF + DORSAL_TO_PALMAR: + title: Dorsal to palmar orientation + description: Directional orientation from top/upper to palm of hand + annotations: + source: OME NGFF + context: hand anatomy + PALMAR_TO_DORSAL: + title: Palmar to dorsal orientation + description: Directional orientation from palm of hand to top/upper + annotations: + source: OME NGFF + context: hand anatomy + DORSAL_TO_PLANTAR: + title: Dorsal to plantar orientation + description: Directional orientation from top/upper to sole of foot + annotations: + source: OME NGFF + context: foot anatomy + PLANTAR_TO_DORSAL: + title: Plantar to dorsal orientation + description: Directional orientation from sole of foot to top/upper + annotations: + source: OME NGFF + context: foot anatomy + ROSTRAL_TO_CAUDAL: + title: Rostral to caudal orientation + description: Directional orientation from nasal to tail end, typically for central nervous system + annotations: + source: OME NGFF + context: central nervous system + CAUDAL_TO_ROSTRAL: + title: Caudal to rostral orientation + description: Directional orientation from tail to nasal end, typically for central nervous system + annotations: + source: OME NGFF + context: central nervous system + CRANIAL_TO_CAUDAL: + title: Cranial to caudal orientation + description: Directional orientation from head to tail end of a structure + annotations: + source: OME NGFF + CAUDAL_TO_CRANIAL: + title: Caudal to cranial orientation + description: Directional orientation from tail to head end of a structure + annotations: + source: OME NGFF + PROXIMAL_TO_DISTAL: + title: Proximal to distal orientation + description: Directional orientation from body center to periphery of a structure + annotations: + source: OME NGFF + DISTAL_TO_PROXIMAL: + title: Distal to proximal orientation + description: Directional orientation from periphery to body center of a structure + annotations: + source: OME NGFF + is_a: SpatialQualifiersSchemaEnum + annotations: + source_domain: spatial + source_schema: spatial_qualifiers StatisticsDomainEnum: description: Domain-level enum for statistics value sets is_a: ValueSetEnum @@ -24920,7 +49842,14 @@ enums: annotations: source_file: statistics/prediction_outcomes.yaml OutcomeTypeEnum: + title: Outcome Type description: Types of prediction outcomes for classification tasks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TP: description: True Positive @@ -24949,7 +49878,14 @@ enums: annotations: source_file: time/temporal.yaml DayOfWeek: + title: Day Of Week description: Days of the week following ISO 8601 standard (Monday = 1) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MONDAY: description: Monday (first day of week in ISO 8601) @@ -25019,126 +49955,133 @@ enums: source_domain: time source_schema: temporal Month: + title: Month description: Months of the year + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JANUARY: description: January meaning: greg:January + rank: 1 exact_mappings: - OPMI:0000071 - NCIT:C106180 annotations: - month_number: 1 abbreviation: Jan days: 31 FEBRUARY: description: February meaning: greg:February + rank: 2 exact_mappings: - OPMI:0000072 - NCIT:C106181 annotations: - month_number: 2 abbreviation: Feb days: 28/29 MARCH: description: March meaning: greg:March + rank: 3 exact_mappings: - OPMI:0000073 - NCIT:C106182 annotations: - month_number: 3 abbreviation: Mar days: 31 APRIL: description: April meaning: greg:April + rank: 4 exact_mappings: - OPMI:0000074 - NCIT:C106183 annotations: - month_number: 4 abbreviation: Apr days: 30 MAY: description: May meaning: greg:May + rank: 5 exact_mappings: - OPMI:0000075 - NCIT:C106184 annotations: - month_number: 5 abbreviation: May days: 31 JUNE: description: June meaning: greg:June + rank: 6 exact_mappings: - OPMI:0000076 - NCIT:C106185 annotations: - month_number: 6 abbreviation: Jun days: 30 JULY: description: July meaning: greg:July + rank: 7 exact_mappings: - OPMI:0000077 - NCIT:C106186 annotations: - month_number: 7 abbreviation: Jul days: 31 AUGUST: description: August meaning: greg:August + rank: 8 exact_mappings: - OPMI:0000078 - NCIT:C106187 annotations: - month_number: 8 abbreviation: Aug days: 31 SEPTEMBER: description: September meaning: greg:September + rank: 9 exact_mappings: - OPMI:0000079 - NCIT:C106188 annotations: - month_number: 9 abbreviation: Sep days: 30 OCTOBER: description: October meaning: greg:October + rank: 10 exact_mappings: - OPMI:0000080 - NCIT:C106189 annotations: - month_number: 10 abbreviation: Oct days: 31 NOVEMBER: description: November meaning: greg:November + rank: 11 exact_mappings: - OPMI:0000081 - NCIT:C106191 annotations: - month_number: 11 abbreviation: Nov days: 30 DECEMBER: description: December meaning: greg:December + rank: 12 exact_mappings: - OPMI:0000082 - NCIT:C106192 annotations: - month_number: 12 abbreviation: Dec days: 31 is_a: TemporalSchemaEnum @@ -25146,7 +50089,14 @@ enums: source_domain: time source_schema: temporal Quarter: + title: Quarter description: Calendar quarters + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: Q1: description: First quarter (January-March) @@ -25169,7 +50119,14 @@ enums: source_domain: time source_schema: temporal Season: + title: Season description: Seasons of the year (Northern Hemisphere) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SPRING: description: Spring season @@ -25201,7 +50158,14 @@ enums: source_domain: time source_schema: temporal TimePeriod: + title: Time Period description: Common time periods and intervals + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HOURLY: description: Every hour @@ -25244,7 +50208,14 @@ enums: source_domain: time source_schema: temporal TimeOfDay: + title: Time Of Day description: Common times of day + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DAWN: description: Dawn (first light) @@ -25279,7 +50250,14 @@ enums: source_domain: time source_schema: temporal BusinessTimeFrame: + title: Business Time Frame description: Common business and financial time frames + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: REAL_TIME: description: Real-time/instantaneous @@ -25334,7 +50312,14 @@ enums: source_domain: time source_schema: temporal GeologicalEra: + title: Geological Era description: Major geological eras + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRECAMBRIAN: description: Precambrian (4.6 billion - 541 million years ago) @@ -25349,7 +50334,14 @@ enums: source_domain: time source_schema: temporal HistoricalPeriod: + title: Historical Period description: Major historical periods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PREHISTORIC: description: Before written records @@ -25386,7 +50378,14 @@ enums: annotations: source_file: units/measurements.yaml LengthUnitEnum: + title: Length Unit description: Units of length/distance measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: METER: title: meter @@ -25476,7 +50475,14 @@ enums: source_domain: units source_schema: measurements MassUnitEnum: + title: Mass Unit description: Units of mass measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: KILOGRAM: description: Kilogram (SI base unit) @@ -25552,7 +50558,14 @@ enums: source_domain: units source_schema: measurements VolumeUnitEnum: + title: Volume Unit description: Units of volume measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LITER: description: Liter (SI derived) @@ -25657,7 +50670,14 @@ enums: source_domain: units source_schema: measurements TemperatureUnitEnum: + title: Temperature Unit description: Units of temperature measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: KELVIN: description: Kelvin (SI base unit) @@ -25691,78 +50711,15 @@ enums: annotations: source_domain: units source_schema: measurements - TimeUnitEnum: - description: Units of time measurement - permissible_values: - SECOND: - description: Second (SI base unit) - meaning: UO:0000010 - annotations: - symbol: s - system: SI - MILLISECOND: - description: Millisecond (0.001 second) - meaning: UO:0000028 - annotations: - symbol: ms - conversion_to_second: '0.001' - MICROSECOND: - description: Microsecond (10^-6 second) - meaning: UO:0000029 - annotations: - symbol: μs - conversion_to_second: 1e-6 - NANOSECOND: - title: nanosecond - description: Nanosecond (10^-9 second) - meaning: UO:0000150 - annotations: - symbol: ns - conversion_to_second: 1e-9 - MINUTE: - description: Minute (60 seconds) - meaning: UO:0000031 - annotations: - symbol: min - conversion_to_second: '60' - HOUR: - description: Hour (3600 seconds) - meaning: UO:0000032 - annotations: - symbol: h - conversion_to_second: '3600' - DAY: - description: Day (86400 seconds) - meaning: UO:0000033 - annotations: - symbol: d - conversion_to_second: '86400' - WEEK: - description: Week (7 days) - meaning: UO:0000034 - annotations: - symbol: wk - conversion_to_second: '604800' - MONTH: - description: Month (approximately 30 days) - meaning: UO:0000035 - annotations: - symbol: mo - conversion_to_second: '2592000' - note: approximate, varies by month - YEAR: - description: Year (365.25 days) - meaning: UO:0000036 - annotations: - symbol: yr - conversion_to_second: '31557600' - note: accounts for leap years - is_a: MeasurementsSchemaEnum - annotations: - source_domain: units - source_schema: measurements PressureUnitEnum: + title: Pressure Unit description: Units of pressure measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PASCAL: description: Pascal (SI derived unit) @@ -25823,83 +50780,15 @@ enums: annotations: source_domain: units source_schema: measurements - ConcentrationUnitEnum: - description: Units of concentration measurement - permissible_values: - MOLAR: - description: Molar (moles per liter) - meaning: UO:0000062 - annotations: - symbol: M - definition: mol/L - MILLIMOLAR: - description: Millimolar (10^-3 molar) - meaning: UO:0000063 - annotations: - symbol: mM - conversion_to_molar: '0.001' - MICROMOLAR: - description: Micromolar (10^-6 molar) - meaning: UO:0000064 - annotations: - symbol: μM - conversion_to_molar: 1e-6 - NANOMOLAR: - description: Nanomolar (10^-9 molar) - meaning: UO:0000065 - annotations: - symbol: nM - conversion_to_molar: 1e-9 - PICOMOLAR: - description: Picomolar (10^-12 molar) - meaning: UO:0000066 - annotations: - symbol: pM - conversion_to_molar: 1e-12 - MG_PER_ML: - title: milligram per milliliter - description: Milligrams per milliliter - meaning: UO:0000176 - annotations: - symbol: mg/mL - UG_PER_ML: - title: microgram per milliliter - description: Micrograms per milliliter - meaning: UO:0000274 - annotations: - symbol: μg/mL - NG_PER_ML: - title: nanogram per milliliter - description: Nanograms per milliliter - meaning: UO:0000275 - annotations: - symbol: ng/mL - PERCENT: - description: Percent (parts per hundred) - meaning: UO:0000187 - annotations: - symbol: '%' - conversion_to_fraction: '0.01' - PPM: - title: parts per million - description: Parts per million - meaning: UO:0000169 - annotations: - symbol: ppm - conversion_to_fraction: 1e-6 - PPB: - title: parts per billion - description: Parts per billion - meaning: UO:0000170 - annotations: - symbol: ppb - conversion_to_fraction: 1e-9 - is_a: MeasurementsSchemaEnum - annotations: - source_domain: units - source_schema: measurements FrequencyUnitEnum: + title: Frequency Unit description: Units of frequency measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HERTZ: description: Hertz (cycles per second) @@ -25940,7 +50829,14 @@ enums: source_domain: units source_schema: measurements AngleUnitEnum: + title: Angle Unit description: Units of angle measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RADIAN: description: Radian (SI derived unit) @@ -25979,7 +50875,14 @@ enums: source_domain: units source_schema: measurements DataSizeUnitEnum: + title: Data Size Unit description: Units of digital data size + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BIT: description: Bit (binary digit) @@ -26052,6 +50955,391 @@ enums: annotations: source_domain: units source_schema: measurements + QuantityKindsSchemaEnum: + description: Schema-level enum for quantity_kinds in units + is_a: UnitsDomainEnum + abstract: true + annotations: + source_file: units/quantity_kinds.yaml + QuantityKindEnum: + title: Quantity Kind + description: Physical quantity kinds based on QUDT. These represent abstract types of physical quantities independent + of the units used to measure them. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.qudt.org/doc/DOC_VOCAB-QUANTITY-KINDS.html + permissible_values: + LENGTH: + title: length + description: A 1-D extent quality representing distance between two points + meaning: quantitykind:Length + exact_mappings: + - PATO:0000122 + annotations: + si_base: 'true' + dimension: L + MASS: + title: mass + description: The amount of matter in an object + meaning: quantitykind:Mass + exact_mappings: + - PATO:0000125 + annotations: + si_base: 'true' + dimension: M + TIME: + title: time + description: Duration or temporal extent + meaning: quantitykind:Time + exact_mappings: + - PATO:0001309 + annotations: + si_base: 'true' + dimension: T + pato_label: duration + THERMODYNAMIC_TEMPERATURE: + title: thermodynamic temperature + description: The thermal energy of a system + meaning: quantitykind:ThermodynamicTemperature + exact_mappings: + - PATO:0000146 + annotations: + si_base: 'true' + dimension: Θ + pato_label: temperature + AMOUNT_OF_SUBSTANCE: + title: amount of substance + description: The number of elementary entities (atoms, molecules, etc.) + meaning: quantitykind:AmountOfSubstance + close_mappings: + - PATO:0000070 + annotations: + si_base: 'true' + dimension: N + pato_label: amount + ELECTRIC_CURRENT: + title: electric current + description: Flow of electric charge per unit time + meaning: quantitykind:ElectricCurrent + annotations: + si_base: 'true' + dimension: I + LUMINOUS_INTENSITY: + title: luminous intensity + description: Luminous power per unit solid angle emitted by a point light source + meaning: quantitykind:LuminousIntensity + close_mappings: + - PATO:0001718 + annotations: + si_base: 'true' + dimension: J + pato_label: luminance + AREA: + title: area + description: A 2-D extent representing the size of a surface + meaning: quantitykind:Area + exact_mappings: + - PATO:0001323 + annotations: + dimension: L² + VOLUME: + title: volume + description: A 3-D extent representing the amount of space occupied + meaning: quantitykind:Volume + exact_mappings: + - PATO:0000918 + annotations: + dimension: L³ + ANGLE: + title: plane angle + description: The figure formed by two rays sharing a common endpoint + meaning: quantitykind:Angle + exact_mappings: + - PATO:0002326 + annotations: + dimension: dimensionless + SOLID_ANGLE: + title: solid angle + description: A 3-D angular measure + meaning: quantitykind:SolidAngle + annotations: + dimension: dimensionless + VELOCITY: + title: velocity + description: Rate of change of position with direction + meaning: quantitykind:Velocity + exact_mappings: + - PATO:0002242 + annotations: + dimension: L·T⁻¹ + SPEED: + title: speed + description: Scalar rate of change of position + meaning: quantitykind:Speed + exact_mappings: + - PATO:0000008 + annotations: + dimension: L·T⁻¹ + ACCELERATION: + title: acceleration + description: Rate of change of velocity + meaning: quantitykind:Acceleration + exact_mappings: + - PATO:0001028 + annotations: + dimension: L·T⁻² + FORCE: + title: force + description: Rate of change of momentum + meaning: quantitykind:Force + exact_mappings: + - PATO:0001035 + annotations: + dimension: M·L·T⁻² + PRESSURE: + title: pressure + description: Force per unit area + meaning: quantitykind:Pressure + exact_mappings: + - PATO:0001025 + annotations: + dimension: M·L⁻¹·T⁻² + ENERGY: + title: energy + description: Capacity to do work + meaning: quantitykind:Energy + exact_mappings: + - PATO:0001021 + annotations: + dimension: M·L²·T⁻² + WORK: + title: work + description: Energy transferred by a force + meaning: quantitykind:Work + exact_mappings: + - PATO:0001026 + annotations: + dimension: M·L²·T⁻² + POWER: + title: power + description: Rate of doing work or transferring energy + meaning: quantitykind:Power + exact_mappings: + - PATO:0001024 + annotations: + dimension: M·L²·T⁻³ + MOMENTUM: + title: momentum + description: Product of mass and velocity + meaning: quantitykind:Momentum + exact_mappings: + - PATO:0001023 + annotations: + dimension: M·L·T⁻¹ + TORQUE: + title: torque + description: Rotational force or moment of force + meaning: quantitykind:Torque + annotations: + dimension: M·L²·T⁻² + ANGULAR_VELOCITY: + title: angular velocity + description: Rate of change of angular position + meaning: quantitykind:AngularVelocity + annotations: + dimension: T⁻¹ + ANGULAR_ACCELERATION: + title: angular acceleration + description: Rate of change of angular velocity + meaning: quantitykind:AngularAcceleration + exact_mappings: + - PATO:0001350 + annotations: + dimension: T⁻² + DENSITY: + title: density + description: Mass per unit volume + meaning: quantitykind:Density + exact_mappings: + - PATO:0001019 + annotations: + dimension: M·L⁻³ + pato_label: mass density + VISCOSITY: + title: dynamic viscosity + description: Internal resistance to flow + meaning: quantitykind:DynamicViscosity + exact_mappings: + - PATO:0000992 + annotations: + dimension: M·L⁻¹·T⁻¹ + KINEMATIC_VISCOSITY: + title: kinematic viscosity + description: Dynamic viscosity divided by density + meaning: quantitykind:KinematicViscosity + annotations: + dimension: L²·T⁻¹ + FREQUENCY: + title: frequency + description: Number of repetitive events per unit time + meaning: quantitykind:Frequency + exact_mappings: + - PATO:0000044 + annotations: + dimension: T⁻¹ + MASS_CONCENTRATION: + title: mass concentration + description: Mass of a substance per unit volume + meaning: quantitykind:MassConcentration + exact_mappings: + - PATO:0000033 + annotations: + dimension: M·L⁻³ + pato_label: concentration of + AMOUNT_CONCENTRATION: + title: amount concentration + description: Amount of substance per unit volume (molarity) + meaning: quantitykind:AmountConcentration + close_mappings: + - PATO:0000033 + annotations: + dimension: N·L⁻³ + ELECTRIC_CHARGE: + title: electric charge + description: Fundamental property of matter causing electromagnetic interaction + meaning: quantitykind:ElectricCharge + exact_mappings: + - PATO:0002193 + annotations: + dimension: I·T + ELECTRIC_POTENTIAL: + title: electric potential + description: Potential energy per unit charge (voltage) + meaning: quantitykind:ElectricPotential + exact_mappings: + - PATO:0001464 + aliases: + - voltage + annotations: + dimension: M·L²·T⁻³·I⁻¹ + ELECTRIC_RESISTANCE: + title: electric resistance + description: Opposition to electric current flow + meaning: quantitykind:Resistance + annotations: + dimension: M·L²·T⁻³·I⁻² + ELECTRICAL_CONDUCTIVITY: + title: electrical conductivity + description: Ability to conduct electric current + meaning: quantitykind:Conductivity + exact_mappings: + - PATO:0001757 + annotations: + dimension: I²·T³·M⁻¹·L⁻³ + CAPACITANCE: + title: capacitance + description: Ability to store electric charge + meaning: quantitykind:Capacitance + annotations: + dimension: I²·T⁴·M⁻¹·L⁻² + INDUCTANCE: + title: inductance + description: Property relating magnetic flux to electric current + meaning: quantitykind:Inductance + annotations: + dimension: M·L²·T⁻²·I⁻² + MAGNETIC_FLUX: + title: magnetic flux + description: Measure of total magnetic field passing through a surface + meaning: quantitykind:MagneticFlux + annotations: + dimension: M·L²·T⁻²·I⁻¹ + MAGNETIC_FLUX_DENSITY: + title: magnetic flux density + description: Magnetic flux per unit area + meaning: quantitykind:MagneticFluxDensity + annotations: + dimension: M·T⁻²·I⁻¹ + HEAT_CAPACITY: + title: heat capacity + description: Heat required to raise temperature by one unit + meaning: quantitykind:HeatCapacity + annotations: + dimension: M·L²·T⁻²·Θ⁻¹ + SPECIFIC_HEAT_CAPACITY: + title: specific heat capacity + description: Heat capacity per unit mass + meaning: quantitykind:SpecificHeatCapacity + annotations: + dimension: L²·T⁻²·Θ⁻¹ + THERMAL_CONDUCTIVITY: + title: thermal conductivity + description: Ability to conduct heat + meaning: quantitykind:ThermalConductivity + exact_mappings: + - PATO:0001756 + annotations: + dimension: M·L·T⁻³·Θ⁻¹ + pato_label: heat conductivity + LUMINOUS_FLUX: + title: luminous flux + description: Total perceived light power emitted + meaning: quantitykind:LuminousFlux + exact_mappings: + - PATO:0001296 + annotations: + dimension: J + ILLUMINANCE: + title: illuminance + description: Luminous flux per unit area + meaning: quantitykind:Illuminance + annotations: + dimension: J·L⁻² + RADIANT_INTENSITY: + title: radiant intensity + description: Radiant power per unit solid angle + meaning: quantitykind:RadiantIntensity + annotations: + dimension: M·L²·T⁻³ + ACTIVITY: + title: activity (radioactivity) + description: Number of nuclear disintegrations per unit time + meaning: quantitykind:Activity + annotations: + dimension: T⁻¹ + ABSORBED_DOSE: + title: absorbed dose + description: Energy deposited per unit mass by ionizing radiation + meaning: quantitykind:AbsorbedDose + annotations: + dimension: L²·T⁻² + DOSE_EQUIVALENT: + title: dose equivalent + description: Absorbed dose weighted by radiation type + meaning: quantitykind:DoseEquivalent + annotations: + dimension: L²·T⁻² + INFORMATION_ENTROPY: + title: information entropy + description: Measure of information content or uncertainty + meaning: quantitykind:InformationEntropy + annotations: + dimension: dimensionless + DATA_RATE: + title: data rate + description: Amount of data transferred per unit time + meaning: quantitykind:DataRate + annotations: + dimension: T⁻¹ + is_a: QuantityKindsSchemaEnum + annotations: + source_domain: units + source_schema: quantity_kinds VisualDomainEnum: description: Domain-level enum for visual value sets is_a: ValueSetEnum @@ -26063,7 +51351,14 @@ enums: annotations: source_file: visual/colors.yaml BasicColorEnum: + title: Basic Color description: Basic color names commonly used in everyday language + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED: description: Primary red color @@ -26143,7 +51438,14 @@ enums: source_domain: visual source_schema: colors WebColorEnum: + title: Web Color description: Standard HTML/CSS named colors (147 colors) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INDIAN_RED: description: Indian red @@ -26740,7 +52042,14 @@ enums: source_domain: visual source_schema: colors X11ColorEnum: + title: X11 Color description: X11/Unix system colors (extended set) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: X11_AQUA: description: X11 Aqua @@ -26801,7 +52110,14 @@ enums: source_domain: visual source_schema: colors ColorSpaceEnum: + title: Color Space description: Color space and model types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RGB: description: Red Green Blue color model diff --git a/src/valuesets/schema/bio/assays/bio_assay.yaml b/src/valuesets/schema/bio/assays/bio_assay.yaml new file mode 100644 index 00000000..41e839ac --- /dev/null +++ b/src/valuesets/schema/bio/assays/bio_assay.yaml @@ -0,0 +1,62 @@ +name: bio_assay +title: Biological Assay Dynamic Value Sets +description: >- + Dynamic enumerations for biological assays backed by OBI and BAO ontologies. + OBIAssayEnum covers assays from the Ontology for Biomedical Investigations, + while BAOBioassayEnum covers assays from the BioAssay Ontology. Together they + form a logical union of assay types. +id: https://w3id.org/valuesets/bio/assays/bio_assay +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + OBI: http://purl.obolibrary.org/obo/OBI_ + BAO: http://www.bioassayontology.org/bao#BAO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + obi_assay: + description: Any assay from the Ontology for Biomedical Investigations (OBI) + range: OBIAssayEnum + bao_bioassay: + description: Any bioassay from the BioAssay Ontology (BAO) + range: BAOBioassayEnum +enums: + OBIAssayEnum: + title: OBI Assay + description: >- + Dynamic enum covering all assays defined in the Ontology for + Biomedical Investigations (OBI), rooted at OBI:0000070 (assay). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + reachable_from: + source_ontology: obo:obi + source_nodes: + - OBI:0000070 + include_self: true + relationship_types: + - rdfs:subClassOf + BAOBioassayEnum: + title: BAO Bioassay + description: >- + Dynamic enum covering all bioassays defined in the BioAssay Ontology + (BAO), rooted at BAO:0000015 (bioassay). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + reachable_from: + source_ontology: obo:bao + source_nodes: + - BAO:0000015 + include_self: true + relationship_types: + - rdfs:subClassOf diff --git a/src/valuesets/schema/bio/assays/enzymology.yaml b/src/valuesets/schema/bio/assays/enzymology.yaml new file mode 100644 index 00000000..ce9d0a71 --- /dev/null +++ b/src/valuesets/schema/bio/assays/enzymology.yaml @@ -0,0 +1,81 @@ +name: enzymology +title: Enzymology Assay Value Sets +description: >- + Value sets for enzymology assays including enzyme activity, kinetics, + inhibition, and substrate specificity measurements. +id: https://w3id.org/valuesets/bio/assays/enzymology +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + BAO: http://www.bioassayontology.org/bao#BAO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + enzymology_assay: + description: Enzymology assay type + range: EnzymologyAssayEnum +enums: + EnzymologyAssayEnum: + title: Enzymology Assay Types + description: >- + Assays for characterizing enzyme function including activity, + kinetics, inhibition, and substrate specificity. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ENZYME_ACTIVITY_ASSAY: + description: Measures the effect of a perturbagen on enzyme activity + meaning: BAO:0002994 + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + companion_enum_readout: DetectionModeEnum + MICHAELIS_MENTEN_KINETICS: + description: Enzyme kinetics assay measuring Km and Vmax parameters + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + INHIBITION_ASSAY: + description: Assay to measure enzyme inhibition (IC50, Ki) + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + SUBSTRATE_SPECIFICITY: + description: Assay to determine enzyme substrate preference and specificity + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + FLUOROMETRIC_ENZYME_ASSAY: + description: Enzyme assay using fluorescent substrates or products for detection + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + companion_enum_readout: DetectionModeEnum + COLORIMETRIC_ENZYME_ASSAY: + description: Enzyme assay using chromogenic substrates for absorbance-based detection + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + companion_enum_readout: DetectionModeEnum + COUPLED_ENZYME_ASSAY: + description: Enzyme assay using a secondary enzyme reaction for signal generation + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + CONTINUOUS_ENZYME_ASSAY: + description: Real-time monitoring of enzyme reaction progress + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein + ENDPOINT_ENZYME_ASSAY: + description: Single time-point measurement of enzyme reaction product + annotations: + companion_enum_substrate: ChemicalEntity + companion_enum_enzyme: Protein diff --git a/src/valuesets/schema/bio/assays/immunology.yaml b/src/valuesets/schema/bio/assays/immunology.yaml new file mode 100644 index 00000000..37b0dd6b --- /dev/null +++ b/src/valuesets/schema/bio/assays/immunology.yaml @@ -0,0 +1,85 @@ +name: immunology +title: Immunology Assay Value Sets +description: >- + Value sets for immunological assays including ELISA, immunoprecipitation, + flow cytometry, western blot, and related methods. +id: https://w3id.org/valuesets/bio/assays/immunology +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + BAO: http://www.bioassayontology.org/bao#BAO_ + OBI: http://purl.obolibrary.org/obo/OBI_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + immunology_assay: + description: Immunology assay type + range: ImmunologyAssayEnum +enums: + ImmunologyAssayEnum: + title: Immunology Assay Types + description: >- + Assays for detecting and quantifying immune-related molecules + including antibody-based detection, cell sorting, and blotting methods. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ELISA: + description: Enzyme-linked immunosorbent assay for detecting antigens or antibodies + meaning: BAO:0000134 + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum + SANDWICH_ELISA: + description: Sandwich ELISA using capture and detection antibodies + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum + IMMUNOPRECIPITATION: + description: Precipitation of a protein antigen from solution using a specific antibody + meaning: BAO:0002508 + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum + FLOW_CYTOMETRY: + description: Analysis of cell populations using fluorescent antibodies and light scattering + meaning: BAO:0000005 + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum + WESTERN_BLOT: + description: Protein detection by gel electrophoresis, membrane transfer, and antibody staining + meaning: OBI:0000854 + aliases: + - western blot assay + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum + CYTOKINE_SECRETION_ASSAY: + description: Measurement of cytokine types and amounts released from cells + meaning: BAO:0003003 + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum + IMMUNOBLOT: + description: Detection of proteins using antibodies on a membrane + meaning: BAO:0002422 + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum + COMPLEMENT_FIXATION: + description: Serological assay detecting antibodies by complement consumption + annotations: + companion_enum_antibody_target: Protein + MULTIPLEX_BEAD_ASSAY: + description: Simultaneous detection of multiple analytes using antibody-conjugated beads + annotations: + companion_enum_antibody_target: Protein + companion_enum_detection_method: DetectionModeEnum diff --git a/src/valuesets/schema/bio/assays.yaml b/src/valuesets/schema/bio/assays/nf_osi_assays.yaml similarity index 99% rename from src/valuesets/schema/bio/assays.yaml rename to src/valuesets/schema/bio/assays/nf_osi_assays.yaml index 3ce65788..9652deb1 100644 --- a/src/valuesets/schema/bio/assays.yaml +++ b/src/valuesets/schema/bio/assays/nf_osi_assays.yaml @@ -1,10 +1,10 @@ -name: assays -title: Biological Assay Value Sets +name: nf_osi_assays +title: NF-OSI Biological Assay Value Sets description: >- Value sets for biological assays including sequencing, imaging, mass spectrometry, cell-based, and clinical/behavioral assays. Derived from NF-OSI metadata dictionary with ontology mappings to OBI, CHMO, BAO, and other relevant ontologies. -id: https://w3id.org/valuesets/bio/assays +id: https://w3id.org/valuesets/bio/assays/nf_osi_assays imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/assays/protein_engineering.yaml b/src/valuesets/schema/bio/assays/protein_engineering.yaml new file mode 100644 index 00000000..289fabac --- /dev/null +++ b/src/valuesets/schema/bio/assays/protein_engineering.yaml @@ -0,0 +1,79 @@ +name: protein_engineering +title: Protein Engineering Assay Value Sets +description: >- + Value sets for protein engineering and characterization assays including + binding kinetics, biophysical characterization, and display technologies. +id: https://w3id.org/valuesets/bio/assays/protein_engineering +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + BAO: http://www.bioassayontology.org/bao#BAO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + protein_engineering_assay: + description: Protein engineering assay type + range: ProteinEngineeringAssayEnum +enums: + ProteinEngineeringAssayEnum: + title: Protein Engineering Assay Types + description: >- + Assays for protein engineering including binding kinetics, + biophysical characterization, and display-based selection methods. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SURFACE_PLASMON_RESONANCE: + description: Real-time label-free measurement of biomolecular binding kinetics + meaning: BAO:0000054 + aliases: + - SPR + annotations: + companion_enum_target_protein: Protein + companion_enum_readout: DetectionModeEnum + BIOLAYER_INTERFEROMETRY: + description: Label-free measurement of biomolecular interactions via interference patterns + meaning: BAO:0000066 + aliases: + - BLI + - bio layer interferometry + annotations: + companion_enum_target_protein: Protein + companion_enum_readout: DetectionModeEnum + THERMAL_SHIFT_ASSAY: + description: Measurement of protein thermal stability via fluorescent dye binding + meaning: BAO:0010261 + aliases: + - differential scanning fluorimetry + - DSF + annotations: + companion_enum_target_protein: Protein + companion_enum_readout: DetectionModeEnum + CIRCULAR_DICHROISM: + description: Assessment of protein secondary and tertiary structure using polarized light + meaning: BAO:0000161 + aliases: + - CD + annotations: + companion_enum_target_protein: Protein + companion_enum_readout: DetectionModeEnum + PHAGE_DISPLAY: + description: Selection of peptides or proteins displayed on bacteriophage surface + annotations: + companion_enum_target_protein: Protein + YEAST_DISPLAY: + description: Selection of proteins displayed on yeast cell surface + annotations: + companion_enum_target_protein: Protein + DIRECTED_EVOLUTION_SCREEN: + description: High-throughput screening of mutant protein libraries for improved function + annotations: + companion_enum_target_protein: Protein + companion_enum_readout: DetectionModeEnum diff --git a/src/valuesets/schema/bio/assays/toxicology.yaml b/src/valuesets/schema/bio/assays/toxicology.yaml new file mode 100644 index 00000000..aff09673 --- /dev/null +++ b/src/valuesets/schema/bio/assays/toxicology.yaml @@ -0,0 +1,79 @@ +name: toxicology +title: Toxicology Assay Value Sets +description: >- + Value sets for toxicological assays including cytotoxicity, genotoxicity, + mutagenicity, and dose-response measurements. +id: https://w3id.org/valuesets/bio/assays/toxicology +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + BAO: http://www.bioassayontology.org/bao#BAO_ + OBI: http://purl.obolibrary.org/obo/OBI_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + toxicology_assay: + description: Toxicology assay type + range: ToxicologyAssayEnum +enums: + ToxicologyAssayEnum: + title: Toxicology Assay Types + description: >- + Assays for evaluating toxicity, genotoxicity, and safety of + compounds including cytotoxicity, mutagenicity, and ADME measurements. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + TOXICITY_ASSAY: + description: General assay measuring degree of substance toxicity to living cells + meaning: BAO:0002189 + annotations: + companion_enum_compound: ChemicalEntity + companion_enum_cell_line: CellType + MTT_ASSAY: + description: Colorimetric assay measuring cell metabolic activity via MTT reduction + meaning: BAO:0002457 + aliases: + - MTT reduction assay + annotations: + companion_enum_compound: ChemicalEntity + companion_enum_cell_line: CellType + LDH_RELEASE_ASSAY: + description: Cytotoxicity assay measuring lactate dehydrogenase release from damaged cells + meaning: BAO:0013056 + annotations: + companion_enum_compound: ChemicalEntity + companion_enum_cell_line: CellType + AMES_TEST: + description: Mutagenicity assay using bacterial reverse mutation in Salmonella strains + meaning: BAO:0013054 + annotations: + companion_enum_compound: ChemicalEntity + COMET_ASSAY: + description: Single cell gel electrophoresis assay measuring DNA strand breaks + meaning: OBI:0302736 + annotations: + companion_enum_compound: ChemicalEntity + companion_enum_cell_line: CellType + MICRONUCLEUS_ASSAY: + description: Genotoxicity assay detecting chromosomal damage via micronucleus formation + meaning: BAO:0013055 + annotations: + companion_enum_compound: ChemicalEntity + companion_enum_cell_line: CellType + DOSE_RESPONSE: + description: Measurement of biological response as a function of compound concentration + annotations: + companion_enum_compound: ChemicalEntity + companion_enum_cell_line: CellType + ADME_ASSAY: + description: Absorption, distribution, metabolism, and excretion profiling + annotations: + companion_enum_compound: ChemicalEntity diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index f1d198ef..fddac088 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -95,6 +95,12 @@ imports: - bio/lipid_categories - bio/proteomics_standards - bio/psi_mi +- bio/assays/nf_osi_assays +- bio/assays/bio_assay +- bio/assays/enzymology +- bio/assays/immunology +- bio/assays/protein_engineering +- bio/assays/toxicology - ecological_interactions - mining_processing - chemistry/chemical_entities From 444c68b95c280afd1b4a125f13634b7681671e85 Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Sun, 22 Feb 2026 15:53:38 -0500 Subject: [PATCH 2/2] Add view docs, design plan, update ontology caches - Rename docs/subsets/genesis-mission.md to docs/views/ - Add microbial-ecology and rare-disease view docs - Add genesis mission design plan - Update ontology term caches (chebi, chmo, envo, ncit, obi, pato) Co-Authored-By: Claude Opus 4.6 --- cache/chebi/terms.csv | 15 +++ cache/chmo/terms.csv | 7 ++ cache/envo/terms.csv | 19 ++++ cache/ncit/terms.csv | 13 +++ cache/obi/terms.csv | 2 + cache/pato/terms.csv | 4 + ...-02-12-genesis-mission-valuesets-design.md | 64 +++++++++++ docs/{subsets => views}/genesis-mission.md | 0 docs/views/microbial-ecology.md | 103 +++++++++++++++++ docs/views/rare-disease.md | 107 ++++++++++++++++++ 10 files changed, 334 insertions(+) create mode 100644 docs/plans/2026-02-12-genesis-mission-valuesets-design.md rename docs/{subsets => views}/genesis-mission.md (100%) create mode 100644 docs/views/microbial-ecology.md create mode 100644 docs/views/rare-disease.md diff --git a/cache/chebi/terms.csv b/cache/chebi/terms.csv index 04355bbb..67fa214c 100644 --- a/cache/chebi/terms.csv +++ b/cache/chebi/terms.csv @@ -238,3 +238,18 @@ CHEBI:29238,tritium atom,2025-12-14T23:20:37.648492 CHEBI:36927,carbon-14 atom,2025-12-14T23:20:37.649036 CHEBI:37340,polonium-210 atom,2025-12-14T23:20:37.649555 CHEBI:26188,polyketide,2025-12-14T23:34:13.539907 +CHEBI:33373,promethium atom,2026-01-30T18:48:58.387369 +CHEBI:33374,samarium atom,2026-01-30T18:48:58.387899 +CHEBI:33375,gadolinium atom,2026-01-30T18:48:58.388278 +CHEBI:49648,holmium atom,2026-01-30T18:48:58.389147 +CHEBI:33379,erbium,2026-01-30T18:48:58.389830 +CHEBI:33380,thulium atom,2026-01-30T18:48:58.390225 +CHEBI:33381,ytterbium,2026-01-30T18:48:58.390560 +CHEBI:33382,lutetium atom,2026-01-30T18:48:58.391037 +CHEBI:27573,silicon atom,2026-02-14T13:12:08.187733 +CHEBI:29390,silicon carbide,2026-02-14T13:12:08.189109 +CHEBI:82281,Indium phosphide,2026-02-14T13:12:08.190378 +CHEBI:33371,technetium-99,2026-02-14T13:12:45.429091 +CHEBI:33388,plutonium atom,2026-02-14T13:12:45.429768 +CHEBI:33389,americium atom,2026-02-14T13:12:45.430292 +CHEBI:52636,iodine-129 atom,2026-02-14T13:12:45.431463 diff --git a/cache/chmo/terms.csv b/cache/chmo/terms.csv index e38470e8..e9c0345d 100644 --- a/cache/chmo/terms.csv +++ b/cache/chmo/terms.csv @@ -63,3 +63,10 @@ CHMO:0000896,rotational-echo double-resonance spectroscopy,2025-12-19T10:23:50.4 CHMO:0000701,liquid chromatography-tandem mass spectrometry,2025-12-19T10:23:50.442059 CHMO:0000817,impedance spectrum,2025-12-19T10:23:50.442354 CHMO:0001009,high-performance liquid chromatography,2025-12-19T10:23:51.583446 +CHMO:0001430,injection moulding,2026-02-14T13:11:57.085965 +CHMO:0001613,extrusion,2026-02-14T13:11:57.086674 +CHMO:0000414,gamma-ray spectroscopy,2026-02-14T13:13:05.885585 +CHMO:0000230,alpha-particle spectroscopy,2026-02-14T13:13:05.886238 +CHMO:0000782,neutron activation analysis,2026-02-14T13:13:05.886825 +CHMO:0000068,electron microscopy,2026-02-14T13:13:05.887378 +CHMO:0002119,granulometry,2026-02-15T15:45:57.306305 diff --git a/cache/envo/terms.csv b/cache/envo/terms.csv index 7c8e5f0c..490a5487 100644 --- a/cache/envo/terms.csv +++ b/cache/envo/terms.csv @@ -93,3 +93,22 @@ ENVO:00002244,gleysol,2025-12-19T09:48:32.851266 ENVO:00002252,solonchak,2025-12-19T09:48:39.303320 ENVO:00002254,vertisol,2025-12-19T09:48:41.590102 ENVO:01001320,fresh water body,2025-12-19T09:48:43.832579 +ENVO:00012408,aquifer,2026-02-14T13:11:34.028669 +ENVO:00000175,karst,2026-02-14T13:11:34.029277 +ENVO:01000505,salt dome,2026-02-14T13:11:34.029563 +ENVO:00002056,shale,2026-02-14T13:11:34.029807 +ENVO:00002185,oil reservoir,2026-02-14T13:12:11.178064 +ENVO:01000851,methane clathrate,2026-02-14T13:12:11.179029 +ENVO:00000354,volcanic field,2026-02-14T13:12:11.179698 +ENVO:00002042,surface water,2026-02-14T13:12:25.875964 +ENVO:01001004,groundwater,2026-02-14T13:12:25.876965 +ENVO:00002019,brackish water,2026-02-14T13:12:25.877294 +ENVO:00002149,sea water,2026-02-14T13:12:25.877834 +ENVO:01001267,stormwater,2026-02-14T13:12:25.880279 +ENVO:01000722,meltwater,2026-02-14T13:12:25.880967 +ENVO:00000003,mine tailing,2026-02-14T13:12:45.427518 +ENVO:02000127,coal ash,2026-02-14T13:12:45.428552 +ENVO:02000130,boiler slag,2026-02-14T13:12:45.428924 +ENVO:02000128,fly ash,2026-02-14T13:12:45.429293 +ENVO:00003044,brine,2026-02-14T13:12:45.429918 +ENVO:01000470,building envelope,2026-02-14T13:12:52.142467 diff --git a/cache/ncit/terms.csv b/cache/ncit/terms.csv index 6a8a37c4..5db49c9d 100644 --- a/cache/ncit/terms.csv +++ b/cache/ncit/terms.csv @@ -415,3 +415,16 @@ NCIT:C8509,Primary Neoplasm,2025-12-22T08:19:09.518825 NCIT:C122534,Other Architecture and Engineering Workers,2025-12-22T08:19:09.519891 NCIT:C116701,Spectrophotometry,2025-12-22T08:19:09.525228 NCIT:C122936,Patient Derived Xenograft,2025-12-22T08:19:25.480593 +NCIT:C62378,Quantum Dot,2026-02-14T13:11:57.130239 +NCIT:C28169,Linear Accelerator,2026-02-14T13:12:45.427776 +NCIT:C48205,Synchrotron,2026-02-14T13:12:45.428917 +NCIT:C94881,Cyclotron,2026-02-14T13:12:45.430407 +NCIT:C307,Biological Agent,2026-02-15T15:41:30.218030 +NCIT:C18472,High Throughput Screening,2026-02-15T15:43:03.912026 +NCIT:C50227,Transformer Device,2026-02-15T15:45:56.748457 +NCIT:C156494,Magnetic Field Strength,2026-02-15T15:46:23.291483 +NCIT:C18097,Molecular Dynamics,2026-02-15T15:46:23.783307 +NCIT:C68769,Decontamination,2026-02-15T15:46:36.956886 +NCIT:C28239,Cobalt Co-60,2026-02-15T15:46:57.873654 +NCIT:C120576,Improvised Nuclear Device,2026-02-15T15:47:04.484150 +NCIT:C120580,Radiological Dispersal Device,2026-02-15T15:47:13.265115 diff --git a/cache/obi/terms.csv b/cache/obi/terms.csv index fe7a884b..7fdb8292 100644 --- a/cache/obi/terms.csv +++ b/cache/obi/terms.csv @@ -76,3 +76,5 @@ OBI:0001186,epitope protection from infectious challenge experiment based on pat OBI:0001937,has specified numeric value,2025-12-19T11:06:30.227493 OBI:0000659,specimen collection process,2025-12-22T08:16:54.248591 OBI:0000094,material processing,2025-12-22T08:16:54.249148 +OBI:0000854,western blot assay,2026-02-22T14:59:00.342925 +OBI:0302736,comet assay,2026-02-22T14:59:17.858350 diff --git a/cache/pato/terms.csv b/cache/pato/terms.csv index 87c6deb0..90e6da62 100644 --- a/cache/pato/terms.csv +++ b/cache/pato/terms.csv @@ -16,3 +16,7 @@ PATO:0002477,brittle,2025-10-19T07:20:50.014732 PATO:0040070,thermoplastic,2025-10-19T07:20:50.023960 PATO:0001421,alive,2025-10-19T07:20:51.275331 PATO:0001422,dead,2025-10-19T07:20:51.275821 +PATO:0000973,porosity,2026-02-14T13:11:36.077664 +PATO:0000970,permeability,2026-02-14T13:11:36.080996 +PATO:0000146,temperature,2026-02-14T13:12:25.889278 +PATO:0001756,heat conductivity,2026-02-14T13:12:51.425663 diff --git a/docs/plans/2026-02-12-genesis-mission-valuesets-design.md b/docs/plans/2026-02-12-genesis-mission-valuesets-design.md new file mode 100644 index 00000000..40bd8a80 --- /dev/null +++ b/docs/plans/2026-02-12-genesis-mission-valuesets-design.md @@ -0,0 +1,64 @@ +# Genesis Mission Valuesets Coverage Design + +## Context + +The DOE Genesis Mission defines 26 national science and technology challenges. +Four BER (Biological and Environmental Research) lighthouse concepts provide +deeper detail: GEO-AI, AI-Driven Living Mine, Change, and G2P. + +This design adds valuesets coverage for all 26 challenges using a tiered +depth approach, organized into the existing domain-based directory structure. + +## Tiering + +### Tier 1 (Deep) - BER lighthouses + adjacent + +| Challenge | New Schema Files | +|---|---| +| GEO-AI lighthouse | `earth_science/subsurface.yaml`, `earth_science/hydrogeology.yaml`, `earth_science/remote_sensing.yaml` | +| AI-Driven Living Mine lighthouse | `bio/biogeochemistry.yaml`, `industry/unconventional_resources.yaml` | +| Change lighthouse | `bio/stress_response.yaml`, `bio/microbial_ecology.yaml`, `bio/synthetic_biology.yaml` | +| G2P lighthouse | `bio/omics_data_types.yaml`, `bio/enzyme_function.yaml` | +| #3 Biotechnology Revolution | `bioprocessing/biomanufacturing.yaml` | +| #4 Critical Minerals Supply | (covered by Living Mine + existing mining enums) | +| #14 Autonomous Labs | `lab_automation/autonomous_labs.yaml` | +| #17 Water for Energy | `earth_science/water_resources.yaml` | +| #19 Subsurface Energy Assets | `energy/subsurface_energy.yaml` | + +### Tier 2 (Moderate) - extensions to existing domains + +| Challenge | New Schema Files | +|---|---| +| #1 Advanced Manufacturing | `industry/manufacturing.yaml` | +| #5 Nuclear Energy | (covered by existing 46 nuclear enums) | +| #6 Fusion Energy | `energy/nuclear/fusion.yaml` | +| #7 Nuclear Cleanup | `energy/nuclear/nuclear_cleanup.yaml` | +| #12 Materials Discovery | `materials_science/computational_materials.yaml` | +| #13 Materials Design | (covered by #12 + existing materials_science enums) | +| #18 Grid Scaling | `energy/grid.yaml` | + +### Tier 3 (Light) - 1-2 enums each + +| Challenge | New Schema Files | +|---|---| +| #2 Buildings | `industry/construction.yaml` | +| #8-9 Quantum | `computing/quantum.yaml` | +| #10 Microelectronics | `computing/microelectronics.yaml` | +| #11 Data Centers | `computing/data_centers.yaml` | +| #15-16 Physics | `physics/particle_physics.yaml` | +| #20-26 Nuclear Security | `energy/nuclear/nuclear_forensics.yaml` | + +## Estimated New Enums + +- Tier 1: ~40-50 new enums across 13 files +- Tier 2: ~15-20 new enums across 5 files +- Tier 3: ~8-12 new enums across 6 files +- Total: ~65-80 new enums + +## Conventions + +- Follow existing pattern: CamelCase enum names, UPPER_CASE permissible values +- Use `meaning:` with OBO CURIEs where possible (verify via OLS) +- All enums get `status: DRAFT`, contributor ORCID, and `valuesets_meta:ValueSetEnumDefinition` +- Schema IDs use `https://w3id.org/valuesets/{path}` +- New files must be added to `valuesets.yaml` imports diff --git a/docs/subsets/genesis-mission.md b/docs/views/genesis-mission.md similarity index 100% rename from docs/subsets/genesis-mission.md rename to docs/views/genesis-mission.md diff --git a/docs/views/microbial-ecology.md b/docs/views/microbial-ecology.md new file mode 100644 index 00000000..d9f649ba --- /dev/null +++ b/docs/views/microbial-ecology.md @@ -0,0 +1,103 @@ +# Microbial Ecology Value Sets + +Microbial ecology research spans taxonomy, physiology, environmental genomics, and +ecosystem interactions. This view collects value sets from across multiple schema +domains -- biology, earth science, and investigation -- that are commonly needed +when describing microbial communities and their environments. + +## Coverage Summary + +| Domain | Schema Sources | Enums | Ontologies | +|--------|---------------|------:|------------| +| [Taxonomy and Organisms](#taxonomy-and-organisms) | bio/taxonomy | 4 | NCBITaxon, ENVO | +| [Physiology and Metabolism](#physiology-and-metabolism) | bio/relationship_to_oxygen, bio/bio_entities | 3 | ENVO, GO | +| [Ecological Interactions](#ecological-interactions) | ecological_interactions, bio/bio_entities, industry/mining | 3 | RO, ENVO | +| [Sequencing and Genomics](#sequencing-and-genomics) | bio/sequencing_platforms, bio/genome_features | 5 | OBI, GENEPIO | +| [Aquatic and Subsurface Environments](#aquatic-and-subsurface-environments) | earth_science/water_resources, earth_science/hydrogeology, earth_science/subsurface | 5 | ENVO, CHEBI | +| [Study Design](#study-design) | investigation | 2 | OBI | + +--- + +## Taxonomy and Organisms + +Microbial community studies require precise taxonomic classification from domain +level through strain. These enums support both fixed lists of common taxa and +dynamic lookups against the NCBI Taxonomy. + +### Enums + +- [CommonOrganismTaxaEnum](../elements/CommonOrganismTaxaEnum.md) -- frequently studied bacteria, archaea, and proteobacteria +- [OrganismTaxonEnum](../elements/OrganismTaxonEnum.md) -- dynamic taxonomy lookup +- [TaxonomicRank](../elements/TaxonomicRank.md) -- domain through strain +- [BiologicalKingdom](../elements/BiologicalKingdom.md) -- high-level kingdoms of life + +--- + +## Physiology and Metabolism + +Oxygen tolerance and metabolic capabilities are fundamental to characterizing +microbial isolates and interpreting metagenome-assembled genomes. + +### Enums + +- [RelToOxygenEnum](../elements/RelToOxygenEnum.md) -- aerobe, anaerobe, facultative, microaerophilic +- [BiologicalProcess](../elements/BiologicalProcess.md) -- biological processes (dynamic, GO-backed) +- [BiologicalRole](../elements/BiologicalRole.md) -- functional roles of chemical entities + +--- + +## Ecological Interactions + +Microbes exist in complex webs of competition, mutualism, and parasitism. These +enums describe biotic interactions and the environmental materials and impacts +relevant to microbial ecology fieldwork. + +### Enums + +- [BioticInteractionType](../elements/BioticInteractionType.md) -- predation, parasitism, mutualism, symbiosis, commensalism +- [EnvironmentalMaterial](../elements/EnvironmentalMaterial.md) -- soil, sediment, water, biofilm, and other environmental materials +- [EnvironmentalImpact](../elements/EnvironmentalImpact.md) -- environmental impacts from industrial and natural processes + +--- + +## Sequencing and Genomics + +Amplicon sequencing (16S/18S/ITS), metagenomics, and metatranscriptomics are +core methods in microbial ecology. These enums standardize platform, chemistry, +library preparation, and genomic feature descriptions. + +### Enums + +- [SequencingPlatform](../elements/SequencingPlatform.md) -- Illumina, PacBio, Oxford Nanopore, Ion Torrent +- [SequencingChemistry](../elements/SequencingChemistry.md) -- platform-specific chemistries +- [LibraryPreparation](../elements/LibraryPreparation.md) -- amplicon, shotgun, Hi-C, and other library types +- [GeneFeature](../elements/GeneFeature.md) -- gene-level features (dynamic) +- [GenomeFeatureType](../elements/GenomeFeatureType.md) -- CDS, rRNA, tRNA, CRISPR, and other genome features + +--- + +## Aquatic and Subsurface Environments + +Many microbial ecology studies focus on aquatic systems, groundwater, or +subsurface formations. These enums from the earth science domain describe +water resources, aquifer types, and subsurface geological contexts. + +### Enums + +- [WaterResourceType](../elements/WaterResourceType.md) -- surface water, groundwater, produced water +- [WaterQualityParameterType](../elements/WaterQualityParameterType.md) -- pH, dissolved oxygen, turbidity, nitrate +- [AquiferType](../elements/AquiferType.md) -- unconfined, confined, artesian, karst +- [GroundwaterProcessType](../elements/GroundwaterProcessType.md) -- recharge, discharge, saltwater intrusion +- [SubsurfaceFormationType](../elements/SubsurfaceFormationType.md) -- permafrost, karst, shale, fault zones + +--- + +## Study Design + +Microbial ecology experiments range from controlled mesocosms to large-scale +field surveys. These investigation enums capture study-level metadata. + +### Enums + +- [StudyDesignEnum](../elements/StudyDesignEnum.md) -- observational, experimental, longitudinal, cross-sectional +- [StudyTypeEnum](../elements/StudyTypeEnum.md) -- field study, laboratory study, computational study diff --git a/docs/views/rare-disease.md b/docs/views/rare-disease.md new file mode 100644 index 00000000..850488dc --- /dev/null +++ b/docs/views/rare-disease.md @@ -0,0 +1,107 @@ +# Rare Disease Value Sets + +Rare disease research requires precise vocabulary for variant interpretation, +phenotyping, family history, and clinical management. This view collects value +sets from across the clinical, medical, and investigation schema domains that +are commonly needed in rare disease genomics and clinical care. + +## Coverage Summary + +| Domain | Schema Sources | Enums | Ontologies | +|--------|---------------|------:|------------| +| [Genetics and Variants](#genetics-and-variants) | clinical/phenopackets, clinical/genetics, medical/family_history, bio/bio_entities | 6 | GENO, LOINC, HP, OMIM | +| [Phenotyping and Clinical](#phenotyping-and-clinical) | clinical/phenopackets, medical/clinical, bio/bio_entities | 8 | HP, NCIT, UBERON | +| [Family History and Pedigree](#family-history-and-pedigree) | medical/family_history | 3 | NCIT | +| [Treatment and Response](#treatment-and-response) | clinical/phenopackets, medical/clinical | 3 | NCIT, RxNorm | +| [Diagnostics](#diagnostics) | medical/clinical, bio/sequencing_platforms | 3 | NCIT, OBI | +| [Demographics and Study](#demographics-and-study) | clinical/nih_demographics, investigation | 4 | NCIT, OBI | + +--- + +## Genetics and Variants + +Variant interpretation in rare disease follows ACMG/AMP guidelines. These enums +capture allelic state, pathogenicity classification, actionability, and the +interpretation workflow. + +### Enums + +- [AllelicStateEnum](../elements/AllelicStateEnum.md) -- heterozygous, homozygous, hemizygous +- [ACMGPathogenicityEnum](../elements/ACMGPathogenicityEnum.md) -- ACMG/AMP five-tier variant classification +- [TherapeuticActionabilityEnum](../elements/TherapeuticActionabilityEnum.md) -- clinical actionability of variants +- [InterpretationProgressEnum](../elements/InterpretationProgressEnum.md) -- variant interpretation workflow status +- [GeneticRelationship](../elements/GeneticRelationship.md) -- biological relationships (full sibling, half sibling) +- [GeneticDisease](../elements/GeneticDisease.md) -- genetic diseases (dynamic) + +--- + +## Phenotyping and Clinical + +Deep phenotyping is central to rare disease diagnosis. These enums support +structured capture of phenotypic features, anatomical systems, onset timing, +laterality, and severity -- aligned with the Human Phenotype Ontology and +Phenopacket standards. + +### Enums + +- [KaryotypicSexEnum](../elements/KaryotypicSexEnum.md) -- chromosomal sex determination +- [PhenotypicSexEnum](../elements/PhenotypicSexEnum.md) -- phenotypic sex +- [OnsetTimingEnum](../elements/OnsetTimingEnum.md) -- age of disease onset (congenital, infantile, juvenile, adult) +- [LateralityEnum](../elements/LateralityEnum.md) -- sidedness of clinical findings +- [SymptomSeverityEnum](../elements/SymptomSeverityEnum.md) -- mild, moderate, severe, profound +- [Phenotype](../elements/Phenotype.md) -- phenotypic features (dynamic, HP-backed) +- [Disease](../elements/Disease.md) -- diseases (dynamic, MONDO-backed) +- [AnatomicalSystemEnum](../elements/AnatomicalSystemEnum.md) -- affected organ systems + +--- + +## Family History and Pedigree + +Rare disease diagnosis depends heavily on family history. These enums support +pedigree construction and recording of family history completeness. + +### Enums + +- [FamilyRelationship](../elements/FamilyRelationship.md) -- pedigree relationships (parent, child, sibling, cousin) +- [FamilyHistoryStatus](../elements/FamilyHistoryStatus.md) -- completeness of family history collection +- [GeneticRelationship](../elements/GeneticRelationship.md) -- biological relationships + +--- + +## Treatment and Response + +Tracking drug response and treatment regimens is important for rare disease +management and clinical trials. + +### Enums + +- [DrugResponseEnum](../elements/DrugResponseEnum.md) -- patient response to drug therapy +- [DrugRouteEnum](../elements/DrugRouteEnum.md) -- route of drug administration +- [RegimenStatusEnum](../elements/RegimenStatusEnum.md) -- treatment regimen status + +--- + +## Diagnostics + +Rare disease workup involves a range of diagnostic modalities, from biochemical +tests to whole-genome sequencing. + +### Enums + +- [DiagnosticTestTypeEnum](../elements/DiagnosticTestTypeEnum.md) -- laboratory, imaging, and genetic tests +- [BloodTypeEnum](../elements/BloodTypeEnum.md) -- ABO and Rh blood type classification +- [SequencingPlatform](../elements/SequencingPlatform.md) -- WGS/WES platforms for rare disease diagnosis + +--- + +## Demographics and Study + +Rare disease studies require careful demographic characterization and study +design documentation, particularly for natural history studies and registries. + +### Enums + +- [AgeGroupEnum](../elements/AgeGroupEnum.md) -- pediatric, adolescent, adult, geriatric +- [BiologicalSexEnum](../elements/BiologicalSexEnum.md) -- biological sex at birth +- [StudyDesignEnum](../elements/StudyDesignEnum.md) -- observational, experimental, longitudinal +- [StudyPhaseEnum](../elements/StudyPhaseEnum.md) -- clinical trial phases