diff --git a/docs/subsets/genesis-mission.md b/docs/subsets/genesis-mission.md new file mode 100644 index 00000000..5d97c82a --- /dev/null +++ b/docs/subsets/genesis-mission.md @@ -0,0 +1,234 @@ +# DOE Genesis Mission Value Sets + +The U.S. Department of Energy's [Genesis Mission](https://www.energy.gov/genesis) defines +26 national science and technology challenges spanning clean energy, advanced computing, +manufacturing, earth systems, and national security. This project provides standardized +value sets (enums with ontology mappings) that support data interoperability across +these challenge areas. + +The 19 schema modules below cover topics from grid modernization and fusion energy to +quantum computing and autonomous laboratories. Each enum is mapped to established +ontologies wherever possible, enabling integration with broader scientific data ecosystems. + +## Coverage Summary + +| Domain | Schema | Enums | Ontologies | +|--------|--------|------:|------------| +| [Energy and Grid](#energy-and-grid) | grid, subsurface_energy | 6 | OEO, ENVO, CHEBI | +| [Nuclear](#nuclear) | fusion, nuclear_cleanup, nuclear_forensics | 8 | CHEBI, NCIT, CHMO, ENVO | +| [Earth Science](#earth-science) | subsurface, hydrogeology, remote_sensing, water_resources | 12 | ENVO, PATO, CHEBI, OBI | +| [Computing](#computing) | data_centers, microelectronics, quantum | 6 | Brick, CHEBI, NCIT | +| [Industry](#industry) | manufacturing, construction, unconventional_resources | 7 | OBI, CHMO, ENVO, Brick | +| [Materials and Physics](#materials-and-physics) | computational_materials, particle_physics | 5 | NCIT, CHEBI, PATO, SWO | +| [Bioprocessing and Labs](#bioprocessing-and-labs) | biomanufacturing, autonomous_labs | 6 | OBI, CHEBI, NCIT, BAO | + +--- + +## Energy and Grid + +Grid modernization and subsurface energy are central to the Genesis challenges on +decarbonization and energy security. These value sets standardize terminology for +grid components, storage technologies, and subsurface resources. + +### Enums + +- [GridComponentType](../elements/GridComponentType.md) -- transmission lines, transformers, substations, inverters +- [GridEnergyStorageType](../elements/GridEnergyStorageType.md) -- battery chemistries, pumped hydro, hydrogen storage +- [GridManagementStrategyType](../elements/GridManagementStrategyType.md) -- demand response, load balancing, virtual power plants +- [SubsurfaceEnergyResourceType](../elements/SubsurfaceEnergyResourceType.md) -- geothermal, oil, gas hydrate reservoirs +- [SubsurfaceStorageType](../elements/SubsurfaceStorageType.md) -- CCS, underground hydrogen, compressed air +- [ReservoirCharacterizationMethodType](../elements/ReservoirCharacterizationMethodType.md) -- well tests, seismic, core analysis + +### Example Mappings + +| Permissible Value | Enum | Ontology Mapping | +|-------------------|------|------------------| +| LITHIUM_ION_BATTERY | GridEnergyStorageType | OEO:00000248 | +| GEOTHERMAL_RESERVOIR | SubsurfaceEnergyResourceType | ENVO:2000034 | +| CARBON_CAPTURE_AND_STORAGE | SubsurfaceStorageType | OEO:00010141 | +| TRANSFORMER | GridComponentType | OEO:00000420 | + +--- + +## Nuclear + +Fusion energy, environmental cleanup of legacy nuclear sites, and nuclear forensics +each present distinct vocabulary needs. These enums cover confinement approaches, +plasma parameters, remediation techniques, and analytical methods. + +### Enums + +- [FusionConfinementType](../elements/FusionConfinementType.md) -- tokamak, stellarator, inertial confinement +- [FusionFuelType](../elements/FusionFuelType.md) -- D-T, D-D, D-He3, p-B11 fuel cycles +- [FusionPlasmaParameterType](../elements/FusionPlasmaParameterType.md) -- temperature, density, beta value +- [NuclearRemediationType](../elements/NuclearRemediationType.md) -- soil excavation, vitrification, phytoremediation +- [DecommissioningPhaseType](../elements/DecommissioningPhaseType.md) -- characterization through long-term monitoring +- [RadioactiveContaminantType](../elements/RadioactiveContaminantType.md) -- Cs-137, Sr-90, Tc-99, Pu, U +- [NuclearForensicsMethodType](../elements/NuclearForensicsMethodType.md) -- isotope ratios, mass spec, gamma spectroscopy +- [NuclearThreatCategoryType](../elements/NuclearThreatCategoryType.md) -- IND, RDD, material theft scenarios + +### Example Mappings + +| Permissible Value | Enum | Ontology Mapping | +|-------------------|------|------------------| +| CESIUM_137 | RadioactiveContaminantType | CHEBI:196959 | +| ISOTOPE_RATIO_ANALYSIS | NuclearForensicsMethodType | CHMO:0000506 | +| DECONTAMINATION | DecommissioningPhaseType | NCIT:C68769 | +| PLASMA_TEMPERATURE | FusionPlasmaParameterType | PATO:0000146 | + +--- + +## Earth Science + +Subsurface characterization, hydrogeology, remote sensing, and water resources span +multiple Genesis challenges related to environmental stewardship, critical minerals, +and climate resilience. + +### Enums + +- [SubsurfaceFormationType](../elements/SubsurfaceFormationType.md) -- aquifers, fault zones, permafrost, shale +- [GeophysicalMethodType](../elements/GeophysicalMethodType.md) -- seismic, GPR, resistivity tomography +- [SubsurfacePropertyType](../elements/SubsurfacePropertyType.md) -- porosity, permeability, geothermal gradient +- [AquiferType](../elements/AquiferType.md) -- unconfined, confined, artesian, karst +- [GroundwaterProcessType](../elements/GroundwaterProcessType.md) -- recharge, discharge, saltwater intrusion +- [HydrogeologyWellType](../elements/HydrogeologyWellType.md) -- monitoring, production, injection wells +- [RemoteSensingPlatformType](../elements/RemoteSensingPlatformType.md) -- satellite, airborne, UAV, ground-based +- [RemoteSensingDataType](../elements/RemoteSensingDataType.md) -- multispectral, hyperspectral, SAR, LiDAR +- [WaterResourceType](../elements/WaterResourceType.md) -- surface water, groundwater, produced water +- [WaterUseCategoryType](../elements/WaterUseCategoryType.md) -- irrigation, industrial cooling, environmental flow +- [WaterQualityParameterType](../elements/WaterQualityParameterType.md) -- pH, dissolved oxygen, turbidity, nitrate +- [WaterContaminantEnum](../elements/WaterContaminantEnum.md) -- water contaminant classification + +### Example Mappings + +| Permissible Value | Enum | Ontology Mapping | +|-------------------|------|------------------| +| AQUIFER | SubsurfaceFormationType | ENVO:00012408 | +| POROSITY | SubsurfacePropertyType | PATO:0000973 | +| SURFACE_WATER | WaterResourceType | ENVO:00002042 | +| DISSOLVED_OXYGEN | WaterQualityParameterType | CHEBI:15379 | + +--- + +## Computing + +Data center infrastructure, semiconductor fabrication, and quantum computing are +addressed by Genesis challenges on advanced computing and microelectronics supply chains. + +### Enums + +- [DataCenterCoolingType](../elements/DataCenterCoolingType.md) -- air, liquid, immersion, geothermal cooling +- [DataCenterTierLevel](../elements/DataCenterTierLevel.md) -- Tier I through Tier IV reliability +- [SemiconductorMaterialType](../elements/SemiconductorMaterialType.md) -- silicon, GaN, SiC, diamond +- [ChipFabricationNodeType](../elements/ChipFabricationNodeType.md) -- 3 nm through mature node processes +- [QubitType](../elements/QubitType.md) -- superconducting, trapped ion, photonic, topological +- [QuantumAlgorithmCategoryType](../elements/QuantumAlgorithmCategoryType.md) -- optimization, simulation, ML, cryptography + +### Example Mappings + +| Permissible Value | Enum | Ontology Mapping | +|-------------------|------|------------------| +| SILICON | SemiconductorMaterialType | CHEBI:27573 | +| SILICON_CARBIDE | SemiconductorMaterialType | CHEBI:29390 | +| PHOTONIC | QubitType | CHEBI:30212 | +| SYNCHROTRON | ParticleAcceleratorType | NCIT:C48205 | + +--- + +## Industry + +Advanced manufacturing, building energy performance, and unconventional mineral +resources reflect Genesis challenges on industrial competitiveness, infrastructure +resilience, and critical material supply chains. + +### Enums + +- [ManufacturingProcessType](../elements/ManufacturingProcessType.md) -- additive, subtractive, casting, CVD, PVD +- [SmartManufacturingTechnologyType](../elements/SmartManufacturingTechnologyType.md) -- digital twins, IIoT, predictive maintenance +- [BuildingSystemType](../elements/BuildingSystemType.md) -- HVAC, electrical, structural, fire protection +- [BuildingEnergyPerformanceLevel](../elements/BuildingEnergyPerformanceLevel.md) -- net zero, passive house, LEED tiers +- [UnconventionalMineralResourceType](../elements/UnconventionalMineralResourceType.md) -- mine tailings, red mud, fly ash, geothermal brine +- [BioextractionMethodType](../elements/BioextractionMethodType.md) -- bioleaching, phytomining, biosorption +- [TailingCharacterizationType](../elements/TailingCharacterizationType.md) -- particle size, mineralogy, metal content + +### Example Mappings + +| Permissible Value | Enum | Ontology Mapping | +|-------------------|------|------------------| +| INJECTION_MOLDING | ManufacturingProcessType | CHMO:0001430 | +| HVAC | BuildingSystemType | brick:HVAC_System | +| MINE_TAILINGS | UnconventionalMineralResourceType | ENVO:00000003 | +| HEAP_BIOLEACHING | BioextractionMethodType | CHMO:0001681 | + +--- + +## Materials and Physics + +Computational materials discovery and particle physics instrumentation underpin +Genesis challenges on scientific discovery and next-generation materials. + +### Enums + +- [MaterialsSimulationType](../elements/MaterialsSimulationType.md) -- DFT, molecular dynamics, Monte Carlo, phase field +- [MaterialPropertyPredictionType](../elements/MaterialPropertyPredictionType.md) -- band gap, elastic modulus, thermal conductivity +- [ParticleAcceleratorType](../elements/ParticleAcceleratorType.md) -- linac, synchrotron, cyclotron, FEL +- [FundamentalParticleType](../elements/FundamentalParticleType.md) -- Standard Model particles (quarks, leptons, bosons) +- [DetectorType](../elements/DetectorType.md) -- calorimeters, tracking, Cherenkov, muon spectrometers + +### Example Mappings + +| Permissible Value | Enum | Ontology Mapping | +|-------------------|------|------------------| +| MOLECULAR_DYNAMICS | MaterialsSimulationType | NCIT:C18097 | +| ELASTIC_MODULUS | MaterialPropertyPredictionType | PATO:0001031 | +| ELECTRON | FundamentalParticleType | CHEBI:10545 | +| HIGGS_BOSON | FundamentalParticleType | CHEBI:146278 | + +--- + +## Bioprocessing and Labs + +Biomanufacturing scale-up and autonomous/self-driving laboratories address Genesis +challenges on the bioeconomy and accelerated scientific discovery. + +### Enums + +- [BiomanufacturingScaleType](../elements/BiomanufacturingScaleType.md) -- micro through commercial scale +- [BioproductCategoryType](../elements/BioproductCategoryType.md) -- biofuels, biochemicals, enzymes, biopharmaceuticals +- [BioprocessOptimizationType](../elements/BioprocessOptimizationType.md) -- media optimization, strain engineering, PAT +- [AutonomousLabComponentType](../elements/AutonomousLabComponentType.md) -- robotic handlers, synthesizers, HTS platforms +- [ExperimentalDesignMethodType](../elements/ExperimentalDesignMethodType.md) -- Bayesian optimization, active learning, DOE +- [LabAutomationWorkflowType](../elements/LabAutomationWorkflowType.md) -- closed-loop optimization, self-driving experimentation + +### Example Mappings + +| Permissible Value | Enum | Ontology Mapping | +|-------------------|------|------------------| +| BIOFUEL | BioproductCategoryType | CHEBI:33292 | +| ROBOTIC_SAMPLE_HANDLER | AutonomousLabComponentType | OBI:0400112 | +| HIGH_THROUGHPUT_SCREENING | LabAutomationWorkflowType | BAO:0010074 | +| DOWNSTREAM_PURIFICATION | BioprocessOptimizationType | OBI:0001505 | + +--- + +## Ontology Coverage + +The Genesis value sets draw on 15 ontologies: + +| Ontology | Full Name | Used In | +|----------|-----------|---------| +| CHEBI | Chemical Entities of Biological Interest | 9 modules | +| ENVO | Environment Ontology | 8 modules | +| NCIT | NCI Thesaurus | 8 modules | +| PATO | Phenotype and Trait Ontology | 6 modules | +| OBI | Ontology for Biomedical Investigations | 4 modules | +| CHMO | Chemical Methods Ontology | 4 modules | +| OEO | Open Energy Ontology | 3 modules | +| Brick | Brick Schema for Buildings | 2 modules | +| MS | Mass Spectrometry Ontology | 1 module | +| SWO | Software Ontology | 1 module | +| AGRO | Agronomy Ontology | 1 module | +| FOODON | Food Ontology | 1 module | +| PROCO | Process Chemistry Ontology | 1 module | +| BAO | BioAssay Ontology | 1 module | +| STATO | Statistics Ontology | 1 module | diff --git a/mkdocs.yml b/mkdocs.yml index 467bd074..5157128f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -33,6 +33,8 @@ 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 - Slides: slides/index.md - About: about.md