diff --git a/gdcdictionary/schemas/aliquot.yaml b/gdcdictionary/schemas/aliquot.yaml index 5f83b15..34c1739 100644 --- a/gdcdictionary/schemas/aliquot.yaml +++ b/gdcdictionary/schemas/aliquot.yaml @@ -3,9 +3,8 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "aliquot" title: Aliquot type: object -nodeTerms: null namespace: https://rerf.datacommons.org/ -category: biospecimen +category: clinical program: '*' project: '*' description: A portion taken from a sample used for analysis, including analytes extracted @@ -24,7 +23,7 @@ systemProperties: links: - name: samples backref: aliquots - label: derived_from + label: taken_from target_type: sample multiplicity: many_to_many required: true @@ -33,6 +32,7 @@ required: - submitter_id - type - samples + - sysid uniqueKeys: - [id] @@ -122,5 +122,9 @@ properties: and/or stored. type: number + sysid: + description: Unique subject identifier + type: integer + samples: $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/base_mortality.yaml b/gdcdictionary/schemas/base_mortality.yaml deleted file mode 100644 index 7dbae46..0000000 --- a/gdcdictionary/schemas/base_mortality.yaml +++ /dev/null @@ -1,66 +0,0 @@ -$schema: "http://json-schema.org/draft-04/schema#" - -id: "base_mortality" -title: Base Mortality -type: object -nodeTerms: null -namespace: https://rerf.datacommons.org/ -category: clinical -program: '*' -project: '*' -description: Cohort data related to study entry and death from cancer. -additionalProperties: false -submittable: true -validators: null - -systemProperties: - - id - - project_id - - state - - created_datetime - - updated_datetime - -links: - - name: subjects - backref: base_mortalities - label: describing - target_type: subject - multiplicity: many_to_one - required: true - -required: - - submitter_id - - type - - subjects - -uniqueKeys: - - [id] - - [project_id, submitter_id] - -properties: - - $ref: "_definitions.yaml#/ubiquitous_properties" - - age_in: - description: Age at entry date (entry_dt). From RERF 'base_mortality' table. - type: number - - age_out: - description: Age at last follow-up, age at death, or age at end of study. From - RERF 'base_mortality' table. - type: number - - cancerdeath: - description: Indicator for a death of interest. From RERF 'base_mortality' table. - type: integer - - col_dose: - description: Radiation dose received by colon. From RERF 'base_mortality' table. - type: number - - nic: - description: Not in City. From RERF 'base_mortality' table. - type: integer - - subjects: - $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/birth.yaml b/gdcdictionary/schemas/birth.yaml index 219c3a7..28594fe 100644 --- a/gdcdictionary/schemas/birth.yaml +++ b/gdcdictionary/schemas/birth.yaml @@ -3,12 +3,11 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "birth" title: Births type: object -nodeTerms: null namespace: https://rerf.datacommons.org/ category: clinical program: '*' project: '*' -description: Birth date data. +description: Birth data from multiple sources additionalProperties: false submittable: true validators: null @@ -32,6 +31,7 @@ required: - submitter_id - type - subjects + - sysid uniqueKeys: - [id] @@ -41,29 +41,62 @@ properties: $ref: "_definitions.yaml#/ubiquitous_properties" - bdy: - description: Birth day. From RERF 'births' table. - type: integer - birth_dt: - description: Birth date (DDmonYYYY, e.g., 21dec1912). From RERF 'births' table. + description: Date of birth + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + birth_updt: + description: Last update of subject's birth records type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - bmo: - description: Birth month. From RERF 'births' table. + sysid: + description: Globally unique identifier for subject type: integer - byr: - description: Birth year. From RERF 'births' table. + birth_ind: + description: Indicator of quality of birth data (1 - best information) + enum: + - 0 - Not use + - 1 - use + + birth_source: + description: Source of the information of subject's birth (ex. Birth certificate, + etc.) + enum: + - 60 - 1960 census + - AH - Adult Health Study + - BR - Birth record + - CN - Contact Card + - CR - Cross Index + - DE - Death Certification + - FU - Fuhyo + - G3 - Genetic study (GE-3) + - JS - Residence registry inquiry (regional cancer registry) + - KO - Koseki + - MC - Master File Code + - MF - Master File record + - MO - Mortality + - MQ - Master Sample Questionnaire + - OT - Other + - SK - Death certificate (regional cancer registry) + - TE - Hibakusha Techo + - TI - Tissue Registry Data Base + - TR - Tumor Registry Data Base + - YU - Mail Survey + + birth_dt_year: + description: Year of birth type: integer - ind: - description: Birthdate information can come from multiple sources. ind=1 indicates the "best" source of information. From RERF 'births' table. + birth_dt_month: + description: Month of birth type: integer - source: - description: Source (KO or MF). The source of the birthdate information. From RERF 'births' table. - type: string + birth_dt_day: + description: Day of birth + type: integer subjects: $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/cancer_diag.yaml b/gdcdictionary/schemas/cancer_diag.yaml new file mode 100644 index 0000000..fd0c533 --- /dev/null +++ b/gdcdictionary/schemas/cancer_diag.yaml @@ -0,0 +1,2171 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "cancer_diag" +title: Cancer Diagnoses +type: object +namespace: https://rerf.datacommons.org/ +category: medical_history +program: '*' +project: '*' +description: History of subject's cancer diagnoses +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - state + - created_datetime + - updated_datetime + +links: + - name: subjects + backref: cancer_diags + label: describing + target_type: subject + multiplicity: many_to_one + required: true + +required: + - submitter_id + - type + - subjects + - sysid + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +properties: + + $ref: "_definitions.yaml#/ubiquitous_properties" + + diag_dt: + description: Date of diagnosis + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + updt: + description: Last update of cancer diagnosis record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + sysid: + description: Globally unique identifier for subject + type: integer + + file_no: + description: Case number (or file number) for the subject + type: integer + + seq_no: + description: Sequence number for multiple occurrence of cancer + type: integer + + res: + description: 1=in city, 2=in prefecture, 3=outside prefecture, 9=unknown + enum: + - 1 - in city + - 2 - in prefecture + - 3 - outside prefecture + - 9 - unknown + + city: + description: City where patient was living at the time of diagnosis 1=Hiro, 2=Naga + enum: + - 1 - Hiroshima + - 2 - Nagasaki + + machi: + description: Similar to zip code + enum: + - "1" + - "2" + - "3" + - 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"8601" + - "8602" + - "8603" + - "8604" + - "8605" + - "8606" + - "8800" + - "9000" + - "9991" + - "9992" + - "9993" + + motiv: + description: Reason for subject's visit to the hospital + enum: + - 1 - Group examination + - 2 - Health examination + - 3 - Subjective symptom + - 4 - Others + - 9 - Unknown + + behavior: + description: Behavior of the cancer (1 = malignant) + enum: + - 0 - Benign + - 1 - Uncertain whether benign or malignant + - 2 - Carcinoma in-situ, Intraepithelial, Non-infiltrative, non-invasive + - 3 - Malignant + - 6 - Malignant, metastatic site. Secondary site + - 9 - Malignant, uncertain + + onc_rev: + description: ICDO version + enum: + - 1 - ICD-O 1st + - 2 - ICD-O 2nd + - 3 - ICD-O 3rd + + dco: + description: Death-certificate-only diagnosis + type: integer + + icdot: + description: ICDO topography code + type: string + + icdom: + description: ICDO morphology code + type: string + + icd_grp: + description: Code to gather specific ICDOT/ICDOM values into a simple diagnosis + code + enum: + - 10 - Tuberculosis + - 99 - Other Infect/Parasit Dis + - 140 - Lip + - 141 - Tongue + - 142 - Salivary Glands (Major) + - 143 - Mouth + - 146 - Pharynx + - 150 - Esophagus + - 151 - Stomach + - 152 - Small intestine + - 153 - Colon + - 154 - Rectum + - 155 - Liver (primary) + - 155 - Liver (NOS) + - 156 - Gallbladder etc. + - 157 - Pancreas + - 159 - Other Digestive + - 159 - Other Digestive + - 160 - Nasal cavity etc. + - 161 - Larynx + - 162 - Lung + - 169 - Other respiratory + - 170 - Bone + - 171 - Connective Tissue + - 172 - Melanoma of the Skin + - 173 - Non-melanoma skin + - 174 - Breast (Male and Female) + - 179 - Uterus NOS + - 180 - Cervix Uteri + - 182 - Corpus Uteri + - 183 - Ovary etc. + - 183 - Ovary etc. + - 184 - Other Female genital + - 185 - Prostate + - 187 - Other male genital + - 188 - Urinary bladder + - 189 - Kidney + - 189 - Renal Pelvis & Ureter + - 189 - Other Urinary + - 191 - Brain + - 192 - Meninges + - 192 - Other nervous system + - 193 - Thyroid + - 194 - Other primary + - 199 - Secondary & unspecified + - 200 - Non - Hodgkin's lymphoma + - 201 - Hodgkin's lymphoma + - 203 - Multiple myeloma + - 204 - Acute lymphoid leukemia + - 204 - Chronic lymphoid leukemia + - 204 - Other/unspec lymphoid leukemia + - 205 - Acute myeloid leukemia + - 205 - Chronic myeloid leukemia + - 205 - Other/unspec myeloid leukemia + - 208 - Acute NOS + - 208 - Chronic NOS + - 208 - Adult T-cell leukemia + - 208 - Other/unspec leukemia + - 210 - Salivary Gland (Major) + - 211 - Stomach + - 211 - Colon + - 218 - Myoma Uteri + - 225 - Brain + - 225 - Meninges + - 225 - Other nervous system + - 226 - Thyroid + - 229 - Other benign neoplasm + - 240 - Thyroid + - 250 - Diabetes + - 250 - Other Endocrine + - 260 - Nutritional and metabolic + - 280 - Blood and Blood-Forming organs + - 290 - Mental disorders + - 320 - Nerv syst & sense organs + - 390 - Rheumatic heart disease + - 402 - Hypertensive heart disease + - 404 - Other Hypertensive disease + - 410 - Coronary heart disease + - 429 - Other heart disease + - 430 - Stroke + - 459 - Other Circulatory disease + - 480 - Pneumonia & influenza + - 490 - Emphysema & bronchitis + - 519 - Other respiratory disease + - 531 - Ulcer + - 570 - Other liver disease + - 571 - Cirrhosis + - 579 - Other digestive disease + - 580 - Urinary disease + - 600 - Genital disease + - 780 - Ill-defined conditions incl. senility + - 799 - Other non-external causes + - 800 - Accident + - 850 - Injury and poisoning (**) + - 950 - Suicide + - 960 - Homicide & other external + - 999 - unknown + + diag_dt_year: + description: Year of diagnosis + type: integer + + diag_dt_month: + description: Month of diagnosis + type: integer + + diag_dt_day: + description: Day of diagnosis + type: integer + + subjects: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/cancer_incidence.yaml b/gdcdictionary/schemas/cancer_incidence.yaml deleted file mode 100644 index 055e26a..0000000 --- a/gdcdictionary/schemas/cancer_incidence.yaml +++ /dev/null @@ -1,130 +0,0 @@ -$schema: "http://json-schema.org/draft-04/schema#" - -id: "cancer_incidence" -title: Cancer Incidence -type: object -nodeTerms: null -namespace: https://rerf.datacommons.org/ -category: medical_history -program: '*' -project: '*' -description: Cancer incidence table. -additionalProperties: false -submittable: true -validators: null - -systemProperties: - - id - - project_id - - state - - created_datetime - - updated_datetime - -links: - - name: subjects - backref: cancer_incidences - label: describing - target_type: subject - multiplicity: many_to_one - required: true - -required: - - submitter_id - - type - - subjects - -uniqueKeys: - - [id] - - [project_id, submitter_id] - -properties: - - $ref: "_definitions.yaml#/ubiquitous_properties" - - atm: - description: atm. From RERF 'summ_dx_fix' table. - type: integer - - autopsy: - description: autopsy. From RERF 'summ_dx_fix' table. - type: integer - - behavior: - description: behavior. From RERF 'summ_dx_fix' table. - type: integer - - dco: - description: dco. From RERF 'summ_dx_fix' table. - type: integer - - early: - description: early. From RERF 'summ_dx_fix' table. - type: integer - - fileno: - description: fileno. From RERF 'summ_dx_fix' table. - type: integer - - icd_conf: - description: icd_conf. From RERF 'summ_dx_fix' table. - type: integer - - icd_grp: - description: icd_grp. From RERF 'summ_dx_fix' table. - type: integer - - icd_sgrp: - description: icd_sgrp. From RERF 'summ_dx_fix' table. - type: integer - - icdom: - description: icdom. From RERF 'summ_dx_fix' table. - type: integer - - icdot: - description: icdot. From RERF 'summ_dx_fix' table. - type: string - - latent: - description: latent. From RERF 'summ_dx_fix' table. - type: integer - - leftright: - description: leftright. From RERF 'summ_dx_fix' table. - type: integer - - loc: - description: loc. From RERF 'summ_dx_fix' table. - type: string - - machi: - description: Location. From RERF 'summ_dx_fix' table. - type: integer - - motiv: - description: motiv. From RERF 'summ_dx_fix' table. - type: integer - - multiple: - description: multiple. From RERF 'summ_dx_fix' table. - type: integer - - onc_rev: - description: onc_rev. From RERF 'summ_dx_fix' table. - type: integer - - res: - description: res. From RERF 'summ_dx_fix' table. - type: integer - - s_death: - description: s_death. From RERF 'summ_dx_fix' table. - type: integer - - seqno: - description: Identifies the order of cancer diagnosis dates. From RERF 'summ_dx_fix' - table. - type: integer - - subjects: - $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/death.yaml b/gdcdictionary/schemas/death.yaml deleted file mode 100644 index b6f0830..0000000 --- a/gdcdictionary/schemas/death.yaml +++ /dev/null @@ -1,77 +0,0 @@ -$schema: "http://json-schema.org/draft-04/schema#" - -id: "death" -title: Death -type: object -nodeTerms: null -namespace: https://rerf.datacommons.org/ -category: clinical -program: '*' -project: '*' -description: Data related to a person's death. -additionalProperties: false -submittable: true -validators: null - -systemProperties: - - id - - project_id - - state - - created_datetime - - updated_datetime - -links: - - name: subjects - backref: deaths - label: describing - target_type: subject - multiplicity: one_to_one - required: true - -required: - - submitter_id - - type - - subjects - -uniqueKeys: - - [id] - - [project_id, submitter_id] - -properties: - - $ref: "_definitions.yaml#/ubiquitous_properties" - - death_cause: - description: The cause of death. From RERF 'icd_grp_fk' table. - type: string - - death_df: - description: death_df. From RERF 'deaths' table. - type: integer - - death_dt: - description: Death date. From RERF 'deaths' table. - type: string - - death_icd: - description: The ICD code for the cause of death. From RERF 'death_icd' table. - type: string - - death_icd_grp: - description: A grouping for the cause of death based on ICD codes. From RERF 'death_icd' table. - type: integer - - death_icd_rev: - description: The revision number of the ICD code used. From RERF 'death_icd' table. - type: integer - - death_icd_sgrp: - description: A sub-grouping for the cause of death. From RERF 'death_icd' table. - type: integer - - death_res: - description: death_res. From RERF 'death_icd' table. - type: integer - - subjects: - $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/diagnostic_test.yaml b/gdcdictionary/schemas/diagnostic_test.yaml deleted file mode 100644 index c2c2fd6..0000000 --- a/gdcdictionary/schemas/diagnostic_test.yaml +++ /dev/null @@ -1,494 +0,0 @@ -$schema: "http://json-schema.org/draft-04/schema#" - -id: "diagnostic_test" -title: Diagnostic Test -type: object -nodeTerms: null -namespace: https://rerf.datacommons.org/ -category: clinical -program: '*' -project: '*' -description: The result of a standard clinical test that is performed for diagnostic - or health monitoring purposes, including biopsies and other small surgical procedures, - biomarker assays, and imaging tests. -additionalProperties: false -submittable: true -validators: null - -systemProperties: - - id - - project_id - - state - - created_datetime - - updated_datetime - -links: - - name: subjects - backref: diagnostic_tests - label: describes - target_type: subject - multiplicity: many_to_one - required: true - -required: - - submitter_id - - type - - subjects - - days_to_test - - test_type - -uniqueKeys: - - [id] - - [project_id, submitter_id] - -properties: - - $ref: "_definitions.yaml#/ubiquitous_properties" - - analyte_name: - description: The name of analyte or biomarker tested in the case that the test - is a quantitative assay. - type: string - - assay_kit_name: - description: The name of the kit used for the test or assay; please also indicate - the kit vendor and version in 'assay_kit_vendor' and 'assay_kit_version'. - type: string - - assay_kit_vendor: - description: The name of the vendor or manufacturer of the kit used for the test; - please also indicate the kit name and version in 'assay_kit_name' and 'assay_kit_version'. - type: string - - assay_kit_version: - description: The version of the kit used for the test; please also indicate the - kit name and vendor in 'assay_kit_name' and 'assay_kit_vendor'. - type: string - - days_to_test: - description: Number of days between the date used for index and the date the patient - was diagnosed with a comorbidity. - type: integer - - equipment_manufacturer: - description: The name of the manufacturer of the equipment used for the test; - please also indicate the model number in 'equipment_model'. - type: string - - equipment_model: - description: The equipment name and model number used for the test; please also - indicate the manufacturer name in 'equipment_manufacturer'. - type: string - - test_anatomic_site: - description: Indicate the anatomic site of the biopsy, image or other diagnostic - test - enum: - - Abdomen - - Abdominal Wall - - Acetabulum - - Adenoid - - Adipose - - Adrenal - - Alveolar Ridge - - Amniotic Fluid - - Ampulla of Vater - - Anal Sphincter - - Ankle - - Anorectum - - Antecubital Fossa - - Antrum - - Anus - - Aorta - - Aortic Body - - Appendix - - Aqueous Fluid - - Arm - - Artery - - Ascending Colon - - Ascending Colon Hepatic Flexure - - Auditory Canal - - Autonomic Nervous System - - Axilla - - Back - - Bile Duct - - Bladder - - Blood - - Blood Vessel - - Bone - - Bone Marrow - - Bowel - - Brain - - Brain Stem - - Breast - - Broad Ligament - - Bronchiole - - Bronchus - - Brow - - Buccal Cavity - - Buccal Mucosa - - Buttock - - Calf - - Capillary - - Cardia - - Carina - - Carotid Artery - - Carotid Body - - Cartilage - - Cecum - - Cell-Line - - Central Nervous System - - Cerebellum - - Cerebral Cortex - - Cerebrospinal Fluid - - Cerebrum - - Cervical Spine - - Cervix - - Chest - - Chest Wall - - Chin - - Clavicle - - Clitoris - - Colon - - Colon (Mucosa Only) - - Common Duct - - Conjunctiva - - Connective Tissue - - Dermal - - Descending Colon - - Diaphragm - - Duodenum - - Ear - - Ear Canal - - Ear, Pinna (External) - - Effusion - - Elbow - - Endocrine Gland - - Epididymis - - Epidural Space - - Esophagogastric Junction - - Esophagus - - Esophagus (Mucosa Only) - - Eye - - Fallopian Tube - - Femoral Artery - - Femoral Vein - - Femur - - Fibroblasts - - Fibula - - Finger - - Floor of Mouth - - Fluid - - Foot - - Forearm - - Forehead - - Foreskin - - Frontal Cortex - - Frontal Lobe - - Fundus of Stomach - - Gallbladder - - Ganglia - - Gastroesophageal Junction - - Gastrointestinal Tract - - Groin - - Gum - - Hand - - Hard Palate - - Head (Face Or Neck) NOS - - Head and Neck - - Heart - - Hepatic - - Hepatic Duct - - Hepatic Vein - - Hip - - Hippocampus - - Humerus - - Hypopharynx - - Ileum - - Ilium - - Index Finger - - Ischium - - Islet Cells - - Jaw - - Jejunum - - Joint - - Kidney - - Knee - - Lacrimal Gland - - Large Bowel - - Laryngopharynx - - Larynx - - Leg - - Leptomeninges - - Ligament - - Lip - - Liver - - Lumbar Spine - - Lung - - Lymph Node - - Lymph Node(s) Axilla - - Lymph Node(s) Cervical - - Lymph Node(s) Distant - - Lymph Node(s) Epitrochlear - - Lymph Node(s) Femoral - - Lymph Node(s) Hilar - - Lymph Node(s) Iliac-Common - - Lymph Node(s) Iliac-External - - Lymph Node(s) Inguinal - - Lymph Node(s) Internal Mammary - - Lymph Node(s) Mammary - - Lymph Node(s) Mesenteric - - Lymph Node(s) Occipital - - Lymph Node(s) Paraaortic - - Lymph Node(s) Parotid - - Lymph Node(s) Pelvic - - Lymph Node(s) Popliteal - - Lymph Node(s) Regional - - Lymph Node(s) Retroperitoneal - - Lymph Node(s) Scalene - - Lymph Node(s) Splenic - - Lymph Node(s) Subclavicular - - Lymph Node(s) Submandibular - - Lymph Node(s) Supraclavicular - - Lymph Nodes(s) Mediastinal - - Mandible - - Maxilla - - Mediastinal Soft Tissue - - Mediastinum - - Mesentery - - Mesothelium - - Middle Finger - - Mitochondria - - Muscle - - Nails - - Nasal Cavity - - Nasal Soft Tissue - - Nasopharynx - - Neck - - Nerve - - Nerve(s) Cranial - - Occipital Cortex - - Ocular Orbits - - Omentum - - Oral Cavity - - Oral Cavity (Mucosa Only) - - Oropharynx - - Other - - Ovary - - Palate - - Pancreas - - Paraspinal Ganglion - - Parathyroid - - Parotid Gland - - Patella - - Pelvis - - Penis - - Pericardium - - Periorbital Soft Tissue - - Peritoneal Cavity - - Peritoneum - - Pharynx - - Pineal - - Pineal Gland - - Pituitary Gland - - Placenta - - Pleura - - Popliteal Fossa - - Prostate - - Pylorus - - Rectosigmoid Junction - - Rectum - - Retina - - Retro-Orbital Region - - Retroperitoneum - - Rib - - Ring Finger - - Round Ligament - - Sacrum - - Salivary Gland - - Scalp - - Scapula - - Sciatic Nerve - - Scrotum - - Seminal Vesicle - - Shoulder - - Sigmoid Colon - - Sinus - - Sinus(es), Maxillary - - Skeletal Muscle - - Skin - - Skull - - Small Bowel - - Small Bowel (Mucosa Only) - - Small Finger - - Soft Tissue - - Spinal Column - - Spinal Cord - - Spleen - - Splenic Flexure - - Sternum - - Stomach - - Stomach (Mucosa Only) - - Subcutaneous Tissue - - Synovium - - Temporal Cortex - - Tendon - - Testis - - Thigh - - Thoracic Spine - - Thorax - - Throat - - Thumb - - Thymus - - Thyroid - - Tibia - - Tongue - - Tonsil - - Tonsil (Pharyngeal) - - Trachea Major Bronchi - - Transverse Colon - - Trunk - - Umbilical Cord - - Unknown - - Ureter - - Urethra - - Urinary Tract - - Uterus - - Uvula - - Vagina - - Vas Deferens - - Vein - - Venous - - Vertebra - - Vulva - - White Blood Cells - - Wrist - - test_result: - description: The categorical result of the laboratory test. - enum: - - 1 plus - - 2 plus - - 3 plus - - Abnormal - - Anisocytosis - - Clinically Significant Abnormal - - Elliptocytosis - - Equivocal - - Hypochromic - - Macrocytic - - Microcytic - - Negative - - "No" - - Normal - - Normocytic - - Not Identified w/in stability - - Not Reported - - Poikilocytosis - - Polychromatophilia - - Positive - - Too High - - Too Low - - Trace - - Unknown - - "Yes" - - test_sample_composition: - description: Indicate the composition or type of biological sample used for the - test (e.g., blood, urine, solid tissue, saliva, etc.) - enum: - - Bone Marrow Components - - Bone Marrow Components NOS - - Buccal Cells - - Buffy Coat - - Cell - - Cerebrospinal Fluid (CSF) - - Circulating Tumor Cell (CTC) - - Control Analyte - - Derived Cell Line - - EBV Immortalized - - Fibroblasts from Bone Marrow Normal - - Granulocytes - - Human Original Cells - - Lymphocytes - - Mononuclear Cells from Bone Marrow Normal - - Not Applicable - - Oral Swab - - Other (specify) - - Peripheral Blood Components NOS - - Peripheral Blood Nucleated Cells - - Peripheral Whole Blood - - Plasma - - Pleural Effusion - - Saliva - - Serum - - Solid Normal Tissue - - Solid Tumor Tissue - - Sputum - - Unknown - - Urine - - Whole Blood - - Whole Bone Marrow - - test_sample_composition_other: - type: string - - test_type: - description: The general type or category of the laboratory test - enum: - - Abnormal Laboratory Test - - Biopsy - - Blood Chemistry Test - - Coagulation Panel - - Complete Blood Count - - Cultures - - Imaging - - Lipid Panel - - Liver Panel - - Prothrombin Time - - Serum Test - - Urinalysis - - test_units: - description: The units corresponding to a test_value for a test_analyte_type - enum: - - Array Signal (log2) - - Average Ct - - Cell Count - - Coefficient of Variance (PCT) - - Copy Number per 25ng RNA - - Cycle threshold (Ct) - - Normalized Ion Intensity by Endogenous Arginine and Autoscaled - - Not Applicable - - Optical Density - - Other (specify) - - SD - - Standard Deviation Ct - - U/mL - - Units of Activity - - cells/microliter - - copies/microliter - - counts - - katal - - mM - - mg/dL - - mg/mL - - micrograms/mL - - micromoles/g/h - - nM - - ng/mL - - pg/mL - - uIU/mL - - test_units_other: - description: The units corresponding to a 'test_value' for an 'analyte_name' if - 'Other (specify)' was chosen for 'test_units - type: string - - test_value: - description: The numerical value representing the diagnostic test measurement - of the 'analyte_name'; also indicate the 'test_units'. - type: number - - subjects: - $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/dose.yaml b/gdcdictionary/schemas/dose.yaml index 89e6f11..6b6b6ed 100644 --- a/gdcdictionary/schemas/dose.yaml +++ b/gdcdictionary/schemas/dose.yaml @@ -1,14 +1,13 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "dose" -title: Dose +title: Organ Dose type: object -nodeTerms: null namespace: https://rerf.datacommons.org/ category: clinical program: '*' project: '*' -description: Radiation dose data. +description: Estimates of organ-level radiation dosage additionalProperties: false submittable: true validators: null @@ -32,6 +31,7 @@ required: - submitter_id - type - subjects + - sysid uniqueKeys: - [id] @@ -41,93 +41,44 @@ properties: $ref: "_definitions.yaml#/ubiquitous_properties" - a02g: - description: a02g. From RERF 'ds02_dose' table. - type: number - - a02n: - description: a02n. From RERF 'ds02_dose' table. - type: number - - abscissa: - description: abscissa. From RERF 'dose_masterlist' table. - type: integer - - calgroup02: - description: calgroup02. From RERF 'dose_masterlist' table. + sysid: + description: Globally unique identifier for subject type: integer - dose_organ: - description: dose_organ. From RERF 'dosetype_fk' table. - type: string - dosetype: - description: dosetype. From RERF 'ds02_dose' table. - type: integer - - ds02cal: - description: ds02cal. From RERF 'dose_masterlist' table. - type: integer - - ds02cat: - description: ds02cat. From RERF 'dose_masterlist' table. - type: integer - - ds86cal: - description: ds86cal. From RERF 'dose_masterlist' table. + description: Type of dose (organ) type: integer - expcity: - description: The city of exposure. From RERF 'dose_masterlist' table. - type: integer - - expstatus02: - description: expstatus02. From RERF 'dose_masterlist' table. - type: integer - - expstatus86: - description: expstatus86. From RERF 'dose_masterlist' table. - type: integer - - gdist: - description: Ground distance (meters). From RERF 'dose_masterlist' table. - type: integer - - ordinate: - description: ordinate. From RERF 'dose_masterlist' table. - type: integer - - organ_cancer: - description: organ_cancer. From RERF 'dosetype_fk' table. - type: string - - prish: - description: prish. From RERF 'dose_masterlist' table. - type: integer - - sdist: - description: sdist. From RERF 'dose_masterlist' table. - type: integer - - sealevel02: - description: sealevel02. From RERF 'dose_masterlist' table. + a02g: + description: Gamma dose type: number - sealevel86: - description: sealevel86. From RERF 'dose_masterlist' table. - type: integer - - shloc: - description: shloc. From RERF 'dose_masterlist' table. - type: integer - - survangle: - description: survangle. From RERF 'dose_masterlist' table. - type: integer + a02n: + description: Neutron dose + type: number - t65cal: - description: t65cal. From RERF 'dose_masterlist' table. - type: integer + discript: + description: Organ name + enum: + - 1 - skeleton + - 2 - marrow + - 3 - urinary + - 4 - brain + - 5 - breast + - 6 - eye lense + - 7 - colon + - 8 - liver + - 9 - lungs + - 10 - ovary + - 11 - pancreas + - 12 - stomach + - 13 - testes + - 14 - thyroid + - 15 - uterus + - 16 - fia_kerma + - 17 - skin + - 18 - distal_fia + - 19 - sh_kerma subjects: $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/exam.yaml b/gdcdictionary/schemas/exam.yaml new file mode 100644 index 0000000..b08b3de --- /dev/null +++ b/gdcdictionary/schemas/exam.yaml @@ -0,0 +1,81 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "exam" +title: AHS Exam Index +type: object +namespace: https://rerf.datacommons.org/ +category: administrative +program: '*' +project: '*' +description: Adult Health Study clinical follow-up visits +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - state + - created_datetime + - updated_datetime + +links: + - name: subjects + backref: exams + label: performed_on + target_type: subject + multiplicity: many_to_one + required: true + +required: + - submitter_id + - type + - subjects + - sysid + - smp_id + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +properties: + + $ref: "_definitions.yaml#/ubiquitous_properties" + + smp_dt: + description: Date of visit + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + updt: + description: Last update of AHS exam index record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + sysid: + description: Globally unique identifier for subject + type: integer + + smp_id: + description: Unique visit ID + type: integer + + primary_id: + description: Matches smp_id on a primary visit (subject might be asked to attend + a follow-up) + type: integer + + smp_dt_year: + description: Year of visit + type: integer + + smp_dt_month: + description: Month of visit + type: integer + + smp_dt_day: + description: Day of visit + type: integer + + subjects: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/exam_diag.yaml b/gdcdictionary/schemas/exam_diag.yaml new file mode 100644 index 0000000..c09fb52 --- /dev/null +++ b/gdcdictionary/schemas/exam_diag.yaml @@ -0,0 +1,66 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "exam_diag" +title: AHS Exam Diagnoses +type: object +namespace: https://rerf.datacommons.org/ +category: medical_history +program: '*' +project: '*' +description: Adult Health Study clinical diagnoses at visits +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - state + - created_datetime + - updated_datetime + +links: + - name: ahs_exam_indexes + backref: exam_diags + label: derived_from + target_type: exam + multiplicity: many_to_one + required: true + +required: + - submitter_id + - type + - ahs_exam_indexes + - smp_id + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +properties: + + $ref: "_definitions.yaml#/ubiquitous_properties" + + updt: + description: Last update of subject's diagnosis + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + smp_id: + description: Visit ID + type: integer + + icd_rev: + description: ICD version + enum: + - "7" + - "8" + - "9" + - "10" + + icd: + description: ICD code for diagnosis + type: string + + ahs_exam_indexes: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/exam_meas.yaml b/gdcdictionary/schemas/exam_meas.yaml new file mode 100644 index 0000000..699db1d --- /dev/null +++ b/gdcdictionary/schemas/exam_meas.yaml @@ -0,0 +1,74 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "exam_meas" +title: AHS Exam Measures +type: object +namespace: https://rerf.datacommons.org/ +category: medical_history +program: '*' +project: '*' +description: Adult Health Study diagnostic measures at visits +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - state + - created_datetime + - updated_datetime + +links: + - name: ahs_exam_indexes + backref: exam_meas + label: derived_from + target_type: exam + multiplicity: many_to_one + required: true + +required: + - submitter_id + - type + - ahs_exam_indexes + - smp_id + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +properties: + + $ref: "_definitions.yaml#/ubiquitous_properties" + + updt: + description: Last update of measure record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + smp_id: + description: Visit ID + type: integer + + item_no: + description: Identifier for measure + type: integer + + amount: + description: Measure amount + type: number + + unit: + description: Unit of measure + type: string + + explain_s: + description: Short explanation + type: string + + explain_l: + description: Long explanation + type: string + + ahs_exam_indexes: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/followup.yaml b/gdcdictionary/schemas/f1.yaml similarity index 54% rename from gdcdictionary/schemas/followup.yaml rename to gdcdictionary/schemas/f1.yaml index 3a9dbe1..2dcb84d 100644 --- a/gdcdictionary/schemas/followup.yaml +++ b/gdcdictionary/schemas/f1.yaml @@ -1,14 +1,13 @@ $schema: "http://json-schema.org/draft-04/schema#" -id: "followup" -title: Follow-up +id: "f1" +title: F1 Program type: object -nodeTerms: null namespace: https://rerf.datacommons.org/ -category: clinical +category: administrative program: '*' project: '*' -description: Mortality follow-up data. +description: Programs within the F1 cohort additionalProperties: false submittable: true validators: null @@ -22,8 +21,8 @@ systemProperties: links: - name: subjects - backref: followups - label: describing + backref: f1s + label: member_of target_type: subject multiplicity: many_to_one required: true @@ -32,6 +31,7 @@ required: - submitter_id - type - subjects + - sysid uniqueKeys: - [id] @@ -41,14 +41,26 @@ properties: $ref: "_definitions.yaml#/ubiquitous_properties" - fup: - description: Indicates vital status at last follow-up ("1" or "3" is alive; "2" - indicates dead; "3" is lost to follow-up). From RERF 'mort_fup' table. + updt: + description: Last update of F1 program record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + sysid: + description: Globally unique identifier for subject type: integer - last_dt: - description: Last contact date (DDmonYYYY). From RERF 'mort_fup' table. - type: string + prog: + description: Program code + enum: + - A - AHS sample (ME-200-2) + - B - BGS + - C - Cyto + - G - GE3 + - I - IQ sample + - M - Mortality sample + - P - PLC + - Y - mail subjects: $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/inutero.yaml b/gdcdictionary/schemas/inutero.yaml new file mode 100644 index 0000000..3e3ee33 --- /dev/null +++ b/gdcdictionary/schemas/inutero.yaml @@ -0,0 +1,66 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "inutero" +title: Inutero Program +type: object +namespace: https://rerf.datacommons.org/ +category: administrative +program: '*' +project: '*' +description: Programs within the Inutero cohort +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - state + - created_datetime + - updated_datetime + +links: + - name: subjects + backref: inuteros + label: member_of + target_type: subject + multiplicity: many_to_one + required: true + +required: + - submitter_id + - type + - subjects + - sysid + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +properties: + + $ref: "_definitions.yaml#/ubiquitous_properties" + + updt: + description: Last update of inutero program record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" + + sysid: + description: Globally unique identifier for subject + type: integer + + prog: + description: Program code + enum: + - A - AHS sample (ME-200-2) + - B - BGS + - C - Cyto + - G - GE3 + - I - IQ sample + - M - Mortality sample + - P - PLC + - Y - mail + + subjects: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/sample.yaml b/gdcdictionary/schemas/sample.yaml index e160c21..94bfb5c 100644 --- a/gdcdictionary/schemas/sample.yaml +++ b/gdcdictionary/schemas/sample.yaml @@ -3,9 +3,8 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "sample" title: Sample type: object -nodeTerms: null namespace: https://rerf.datacommons.org/ -category: biospecimen +category: clinical program: '*' project: '*' description: Any material sample taken from a biological entity for testing, diagnostic, @@ -28,7 +27,7 @@ systemProperties: links: - name: subjects backref: samples - label: derived_from + label: taken_from target_type: subject multiplicity: many_to_one required: true @@ -37,6 +36,7 @@ required: - submitter_id - type - subjects + - sysid uniqueKeys: - [id] @@ -46,6 +46,157 @@ properties: $ref: "_definitions.yaml#/ubiquitous_properties" + tissue_type: + term: + $ref: "_terms.yaml#/tissue_type" + enum: + - Abnormal + - Normal + - Not Reported + - Peritumoral + - Tumor + - Unknown + + preservation_method: + term: + $ref: "_terms.yaml#/preservation_method" + enum: + - Cryopreserved + - FFPE + - Fresh + - Frozen + - Not Applicable + - Not Reported + - OCT + - Snap Frozen + - Unknown + + method_of_sample_procurement: + term: + $ref: "_terms.yaml#/method_of_sample_procurement" + enum: + - Abdomino-perineal Resection of Rectum + - Anterior Resection of Rectum + - Aspirate + - Autopsy + - Biopsy + - Blood Draw + - Bone Marrow Aspirate + - Core Biopsy + - Cystectomy + - Endo Rectal Tumor Resection + - Endoscopic Biopsy + - Endoscopic Mucosal Resection (EMR) + - Enucleation + - Excisional Biopsy + - Fine Needle Aspiration + - Full Hysterectomy + - Gross Total Resection + - Hand Assisted Laparoscopic Radical Nephrectomy + - Hysterectomy NOS + - Incisional Biopsy + - Indeterminant + - Laparoscopic Biopsy + - Laparoscopic Partial Nephrectomy + - Laparoscopic Radical Nephrectomy + - Laparoscopic Radical Prostatectomy with Robotics + - Laparoscopic Radical Prostatectomy without Robotics + - Left Hemicolectomy + - Lobectomy + - Local Resection (Exoresection, wall resection) + - Lumpectomy + - Modified Radical Mastectomy + - Needle Biopsy + - Not Reported + - Open Craniotomy + - Open Partial Nephrectomy + - Open Radical Nephrectomy + - Open Radical Prostatectomy + - Orchiectomy + - Other + - Other Surgical Resection + - Pan-Procto Colectomy + - Pancreatectomy + - Paracentesis + - Pneumonectomy + - Right Hemicolectomy + - Sigmoid Colectomy + - Simple Mastectomy + - Subtotal Resection + - Surgical Resection + - Thoracoscopic Biopsy + - Total Colectomy + - Total Mastectomy + - Transplant + - Transurethral resection (TURBT) + - Transverse Colectomy + - Tumor Resection + - Unknown + - Wedge Resection + - Whipple Procedure + + initial_weight: + term: + $ref: "_terms.yaml#/initial_weight" + type: number + + freezing_method: + term: + $ref: "_terms.yaml#/freezing_method" + type: string + + days_to_collection: + term: + $ref: "_terms.yaml#/days_to_collection" + type: integer + + composition: + term: + $ref: "_terms.yaml#/composition" + enum: + - 2D Classical Conditionally Reprogrammed Cells + - 2D Modified Conditionally Reprogrammed Cells + - 3D Air-Liquid Interface Organoid + - 3D Neurosphere + - 3D Organoid + - Adherent Cell Line + - Bone Marrow Components + - Bone Marrow Components NOS + - Buccal Cells + - Buffy Coat + - Cell + - Control Analyte + - Derived Cell Line + - EBV Immortalized + - Fibroblasts from Bone Marrow Normal + - Granulocytes + - Human Original Cells + - Liquid Suspension Cell Line + - Lymphocytes + - Mononuclear Cells from Bone Marrow Normal + - Not Reported + - Peripheral Blood Components NOS + - Peripheral Whole Blood + - Plasma + - Pleural Effusion + - Saliva + - Serum + - Solid Tissue + - Sorted Cells + - Sputum + - Unknown + - Whole Bone Marrow + + biospecimen_laterality: + term: + $ref: "_terms.yaml#/biospecimen_laterality" + enum: + - Bilateral + - Left + - Not Reported + - Right + - Unknown + biospecimen_anatomic_site: term: $ref: "_terms.yaml#/biospecimen_anatomic_site" @@ -334,156 +485,5 @@ properties: - White Blood Cells - Wrist - biospecimen_laterality: - term: - $ref: "_terms.yaml#/biospecimen_laterality" - enum: - - Bilateral - - Left - - Not Reported - - Right - - Unknown - - composition: - term: - $ref: "_terms.yaml#/composition" - enum: - - 2D Classical Conditionally Reprogrammed Cells - - 2D Modified Conditionally Reprogrammed Cells - - 3D Air-Liquid Interface Organoid - - 3D Neurosphere - - 3D Organoid - - Adherent Cell Line - - Bone Marrow Components - - Bone Marrow Components NOS - - Buccal Cells - - Buffy Coat - - Cell - - Control Analyte - - Derived Cell Line - - EBV Immortalized - - Fibroblasts from Bone Marrow Normal - - Granulocytes - - Human Original Cells - - Liquid Suspension Cell Line - - Lymphocytes - - Mononuclear Cells from Bone Marrow Normal - - Not Reported - - Peripheral Blood Components NOS - - Peripheral Whole Blood - - Plasma - - Pleural Effusion - - Saliva - - Serum - - Solid Tissue - - Sorted Cells - - Sputum - - Unknown - - Whole Bone Marrow - - days_to_collection: - term: - $ref: "_terms.yaml#/days_to_collection" - type: integer - - freezing_method: - term: - $ref: "_terms.yaml#/freezing_method" - type: string - - initial_weight: - term: - $ref: "_terms.yaml#/initial_weight" - type: number - - method_of_sample_procurement: - term: - $ref: "_terms.yaml#/method_of_sample_procurement" - enum: - - Abdomino-perineal Resection of Rectum - - Anterior Resection of Rectum - - Aspirate - - Autopsy - - Biopsy - - Blood Draw - - Bone Marrow Aspirate - - Core Biopsy - - Cystectomy - - Endo Rectal Tumor Resection - - Endoscopic Biopsy - - Endoscopic Mucosal Resection (EMR) - - Enucleation - - Excisional Biopsy - - Fine Needle Aspiration - - Full Hysterectomy - - Gross Total Resection - - Hand Assisted Laparoscopic Radical Nephrectomy - - Hysterectomy NOS - - Incisional Biopsy - - Indeterminant - - Laparoscopic Biopsy - - Laparoscopic Partial Nephrectomy - - Laparoscopic Radical Nephrectomy - - Laparoscopic Radical Prostatectomy with Robotics - - Laparoscopic Radical Prostatectomy without Robotics - - Left Hemicolectomy - - Lobectomy - - Local Resection (Exoresection, wall resection) - - Lumpectomy - - Modified Radical Mastectomy - - Needle Biopsy - - Not Reported - - Open Craniotomy - - Open Partial Nephrectomy - - Open Radical Nephrectomy - - Open Radical Prostatectomy - - Orchiectomy - - Other - - Other Surgical Resection - - Pan-Procto Colectomy - - Pancreatectomy - - Paracentesis - - Pneumonectomy - - Right Hemicolectomy - - Sigmoid Colectomy - - Simple Mastectomy - - Subtotal Resection - - Surgical Resection - - Thoracoscopic Biopsy - - Total Colectomy - - Total Mastectomy - - Transplant - - Transurethral resection (TURBT) - - Transverse Colectomy - - Tumor Resection - - Unknown - - Wedge Resection - - Whipple Procedure - - preservation_method: - term: - $ref: "_terms.yaml#/preservation_method" - enum: - - Cryopreserved - - FFPE - - Fresh - - Frozen - - Not Applicable - - Not Reported - - OCT - - Snap Frozen - - Unknown - - tissue_type: - term: - $ref: "_terms.yaml#/tissue_type" - enum: - - Abnormal - - Normal - - Not Reported - - Peritumoral - - Tumor - - Unknown - subjects: $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/study.yaml b/gdcdictionary/schemas/study.yaml index e15ee0d..9481879 100644 --- a/gdcdictionary/schemas/study.yaml +++ b/gdcdictionary/schemas/study.yaml @@ -3,7 +3,6 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "study" title: Study type: object -nodeTerms: null namespace: https://rerf.datacommons.org/ category: administrative program: '*' @@ -41,44 +40,6 @@ uniqueKeys: properties: - associated_study: - description: The submitter_id for any study with which this study is associated, - paired, or matched. - type: string - - created_datetime: - $ref: "_definitions.yaml#/datetime" - - data_description: - description: Brief description of the data being provided for this study. Free - text - type: string - - id: - description: The UUID for the study. - $ref: "_definitions.yaml#/UUID" - - project_id: - $ref: "_definitions.yaml#/project_id" - - state: - $ref: "_definitions.yaml#/state" - - study_description: - description: A brief description of the study being performed. Free text - type: string - - study_design: - description: Summary of the goals the study is designed to discover. General description - of the study's place in relation to a clinical application. - enum: - - Analytical - - Clinical - - Clinical Assay - - Clinical Utility - - Pre-Analytical - - Research/Early Development - study_objective: description: The general objective of the study. What the study hopes to discover or determine through testing. @@ -92,12 +53,37 @@ properties: - Specificity/Sensitivity - Stability + study_design: + description: Summary of the goals the study is designed to discover. General description + of the study's place in relation to a clinical application. + enum: + - Analytical + - Clinical + - Clinical Assay + - Clinical Utility + - Pre-Analytical + - Research/Early Development + study_setup: description: A high level description of the setup used to achieve the study objectives. enum: - Detection/Enumeration/Isolation - Genetic Analysis + associated_study: + description: The submitter_id for any study with which this study is associated, + paired, or matched. + type: string + + data_description: + description: Brief description of the data being provided for this study. Free + text + type: string + + study_description: + description: A brief description of the study being performed. Free text + type: string + submitter_id: description: A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the @@ -107,6 +93,20 @@ properties: type: type: string + created_datetime: + $ref: "_definitions.yaml#/datetime" + + id: + $ref: "_definitions.yaml#/UUID" + description: The UUID for the study. + + project_id: + $ref: "_definitions.yaml#/project_id" + description: The dash separated combination of the program code and project name. + + state: + $ref: "_definitions.yaml#/state" + updated_datetime: $ref: "_definitions.yaml#/datetime" diff --git a/gdcdictionary/schemas/subject.yaml b/gdcdictionary/schemas/subject.yaml index f75f063..6ba2c16 100644 --- a/gdcdictionary/schemas/subject.yaml +++ b/gdcdictionary/schemas/subject.yaml @@ -3,7 +3,6 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "subject" title: Subject type: object -nodeTerms: null namespace: https://rerf.datacommons.org/ category: administrative program: '*' @@ -33,6 +32,7 @@ required: - submitter_id - type - studies + - sysid uniqueKeys: - [id] @@ -42,204 +42,487 @@ properties: $ref: "_definitions.yaml#/ubiquitous_properties" - abscissa: - description: abscissa. From RERF 'dose_masterlist' table. - type: integer + lss: + description: Is the subject in the LSS cohort? + type: boolean - age_in: - description: Age at entry date (entry_dt). From RERF 'base_mortality' table. - type: number + inutero: + description: Is the subject in the Inutero cohort? + type: boolean - age_out: - description: Age at last follow-up, age at death, or age at end of study. From - RERF 'base_mortality' table. - type: number + f1: + description: Is the subject in the F1 cohort? + type: boolean ahs: - description: Indication of whether a person was in the Adult Health Study (AHS) - cohort (0- not AHS, 1- AHS (original), 2- AHS (addition)). From RERF 'lss_master' - table. - type: integer - - bdy: - description: Birth day. From RERF 'births' table. - type: integer + description: Is the subject in the AHS cohort? + type: boolean - birth_dt: - description: Birth date (DDmonYYYY, e.g., 21dec1912). From RERF 'births' table. + updt: + description: Last updated date type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - bmo: - description: Birth month. From RERF 'births' table. - type: integer + lss_entry_dt: + description: Subject's date of entry into the LSS cohort + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - byr: - description: Birth year. From RERF 'births' table. - type: integer + lss_updt: + description: Last update of subject's LSS record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - calgroup02: - description: calgroup02. From RERF 'dose_masterlist' table. - type: integer + inutero_entry_dt: + description: Date when the subject became a member of the Inutero cohort + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - cancerdeath: - description: Indicator for a death of interest. From RERF 'base_mortality' table. - type: integer + inutero_updt: + description: Last update of subject's Inutero record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - city: - description: The city in which a person was exposed to radiation (1- Hiroshima, - 2- Nagasaki). From RERF 'id' table. - type: integer + f1_entry_dt: + description: Date when the subject became a member of the F1 cohort + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - col_dose: - description: Radiation dose received by colon. From RERF 'base_mortality' table. - type: number + f1_updt: + description: Last update of subject's F1 record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - death_cause: - description: The cause of death. From RERF 'icd_grp_fk' table. + ahs_updt: + description: Last update of subject's AHS record type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - death_df: - description: death_df. From RERF 'deaths' table. - type: integer + mfup_last_contact: + description: Mortality follow-up date of last contact + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" death_dt: - description: Death date. From RERF 'deaths' table. + description: Date of death of the subject type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - death_icd: - description: The ICD code for the cause of death. From RERF 'death_icd' table. + death_updt: + description: Last update of the subject's death record type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - death_icd_grp: - description: A grouping for the cause of death. From RERF 'death_icd' table. - type: integer + death_icd_updt: + description: Last update of subject's death ICD record + type: string + pattern: "^[0-9]{1,2}\\/[0-9]{1,2}\\/[0-9]{4}$" - death_icd_rev: - description: The revision number of the ICD code used. From RERF 'death_icd' table. - type: integer + mfup_last_status: + description: Mortality follow-up last known status of the subject (1 - alive, + 2 - dead, 3 - lost, etc) + enum: + - 1 - Alive + - 2 - Dead + - 3 - foreign nationality + - 6 - cessation of follow-up + - 7 - unknown permanent domicile + - 8 - exclusion from study subjects + - 9 - Follow-up halted due to excessive subject age + + dose_expcity: + description: Subject's city of exposure 1 - Hiro, 2 - Naga + enum: + - 1 - Hiroshima + - 2 - Nagasaki - death_icd_sgrp: - description: A grouping for the cause of death. From RERF 'death_icd' table. - type: integer + dose_expstatus86: + description: Exposure status based on 1986 algorithm + enum: + - 1 - In city ATB + - 2 - NIC late entry or entrance unknown + - 3 - NIC early entry + - 4 - NIC presumed (F1 orginal mortality sample's parent) + - 5 - NIC from GE3 + - 8 - No Information + - 9 - Unknown + + dose_expstatus02: + description: Exposure status based on 2002 algorithm + enum: + - 1 - In city, No distal terrain + - 2 - In city, Distal terrain (Hijiyama and Konpirasan) + - 3 - NIC late entry or extrance unknown + - 4 - NIC early entry + - 5 - NIC presumed (F1 original mortality sample parent) + - 6 - NIC from GE3 + - 9 - Unknown + + dose_prish: + description: Subject's primary shield + enum: + - 1 - Open, with flush burns + - 10 - Other shielding + - 11 - No shielding information + - 12 - NIC + - 2 - Japanese-house (inside and outside) + - 3 - Tenement house (row-house) + - 4 - Japanese house and Terrain + - 5 - Tenement and Terrain + - 6 - Globe terrain + - 7 - Modelled factory + - 8 - Unmodelled factory + - 9 - Concrete building + + death_src: + description: Source of the information of subject's death (ex. Death certificate, + etc.) + enum: + - 60 - 1960 census + - AH - Adult Health Study + - BR - Birth record + - CN - Contact Card + - CR - Cross Index + - DE - Death Certification + - FU - Fuhyo + - G3 - Genetic study (GE-3) + - JS - Residence registry inquiry (regional cancer registry) + - KO - Koseki + - MC - Master File Code + - MF - Master File record + - MO - Mortality + - MQ - Master Sample Questionnaire + - OT - Other + - SK - Death certificate (regional cancer registry) + - TE - Hibakusha Techo + - TI - Tissue Registry Data Base + - TR - Tumor Registry Data Base + - YU - Mail Survey + + dose_source: + description: What is the source of the exposure information? Ex. Questionnaire + enum: + - CD300 - CD300 + - F1MO - F1 Mortality Original Parents without DS86 + - GE3 - GE3 + - LSS - LSS + - M - Acute Effects known + - MSQ - PLC + - T65D - T65D - death_res: - description: death_res. From RERF 'death_icd' table. + sysid: + description: Globally unique identifier for subject type: integer - dose_organ: - description: dose_organ. From RERF 'dosetype_fk' table. - type: string + city: + description: 1 = Hiro, 2 = Naga + enum: + - 1 - Hiroshima + - 2 - Nagasaki - ds02cal: - description: ds02cal. From RERF 'dose_masterlist' table. - type: integer + sex: + description: 1 = male + enum: + - 1 - Male + - 2 - Female + - 3 - Other + - 4 - Unknown - ds02cat: - description: ds02cat. From RERF 'dose_masterlist' table. - type: integer + lss_sample_class: + description: Subject's recruitment class into LSS cohort? + enum: + - 1 - Original LSS + - 2 - Reserved (less than 2.5km) + - 3 - Nagasaki Distal Additions + - 4 - NIC - early + - 5 - NIC - late + + lss_census: + description: Census info used for recruitment into LSS cohort? + enum: + - 1 - national census 1950 + - 2 - ABCC 1st sample census + - 3 - ABCC 2nd sample census + - 4 - NIC 1953 census (Hiroshima) + - 5 - Setai-Daicho (Nagasaki) - ds86cal: - description: ds86cal. From RERF 'dose_masterlist' table. + mother_sysid: + description: The globally unique identifier for the subject's mother type: integer - entry_dt: - description: Entry date (DDmonYYYY, e.g., 21dec1912). From RERF 'lss_master' table. - type: string - - expcity: - description: The city of exposure. From RERF 'dose_masterlist' table. + father_sysid: + description: The globally unique identifier for the subject's father type: integer - expstatus02: - description: expstatus02. From RERF 'dose_masterlist' table. - type: integer + f1_sample: + description: Subject's recruitment class into F1 cohort? + enum: + - 1 - F1 mortality original + - 2 - F1 mortality extension + - 3 - F1 BGS original + - 4 - F1 BGS extension + - 5 - F1 GE3 only + + f1_ind: + description: Must = 1 + enum: + - 0 - Not included in F1 cohort + - 1 - Included in F1 cohort - expstatus86: - description: expstatus86. From RERF 'dose_masterlist' table. - type: integer + ahs_subgroup: + description: Subgroup to which the subject belongs. + enum: + - 1 - original(ME-200) + - 2 - extension(ME-200-1) + - 3 - PE-86(ME-200-2) + - 4 - young extension(ME-200-3) - fup: - description: Indicates vital status at last follow-up ("1" or "3" is alive; "2" - indicates dead). From RERF 'mort_fup' table. - type: integer + ahs_exp_category: + description: Exposure category? + enum: + - 1 - proximal (< 2000m), some symptom + - 2 - proximal (< 2000m), no symptom + - 3 - distal (Hiroshima; 3000-3499m, Nagasaki; 3000-3999m) + - 4 - Unexposed - gdist: - description: Ground distance (meters). From RERF 'dose_masterlist' table. - type: integer + death_icd_rev: + description: ICD version + enum: + - "7" + - "8" + - "9" + - "10" + + death_icd_grp: + description: RERF-specific ICD grouping code + enum: + - 10 - Tuberculosis + - 99 - Other Infect/Parasit Dis + - 140 - Lip + - 141 - Tongue + - 142 - Salivary Glands (Major) + - 143 - Mouth + - 146 - Pharynx + - 150 - Esophagus + - 151 - Stomach + - 152 - Small intestine + - 153 - Colon + - 154 - Rectum + - 155 - Liver (primary) + - 155 - Liver (NOS) + - 156 - Gallbladder etc. + - 157 - Pancreas + - 159 - Other Digestive + - 159 - Other Digestive + - 160 - Nasal cavity etc. + - 161 - Larynx + - 162 - Lung + - 169 - Other respiratory + - 170 - Bone + - 171 - Connective Tissue + - 172 - Melanoma of the Skin + - 173 - Non-melanoma skin + - 174 - Breast (Male and Female) + - 179 - Uterus NOS + - 180 - Cervix Uteri + - 182 - Corpus Uteri + - 183 - Ovary etc. + - 183 - Ovary etc. + - 184 - Other Female genital + - 185 - Prostate + - 187 - Other male genital + - 188 - Urinary bladder + - 189 - Kidney + - 189 - Renal Pelvis & Ureter + - 189 - Other Urinary + - 191 - Brain + - 192 - Meninges + - 192 - Other nervous system + - 193 - Thyroid + - 194 - Other primary + - 199 - Secondary & unspecified + - 200 - Non - Hodgkin's lymphoma + - 201 - Hodgkin's lymphoma + - 203 - Multiple myeloma + - 204 - Acute lymphoid leukemia + - 204 - Chronic lymphoid leukemia + - 204 - Other/unspec lymphoid leukemia + - 205 - Acute myeloid leukemia + - 205 - Chronic myeloid leukemia + - 205 - Other/unspec myeloid leukemia + - 208 - Acute NOS + - 208 - Chronic NOS + - 208 - Adult T-cell leukemia + - 208 - Other/unspec leukemia + - 210 - Salivary Gland (Major) + - 211 - Stomach + - 211 - Colon + - 218 - Myoma Uteri + - 225 - Brain + - 225 - Meninges + - 225 - Other nervous system + - 226 - Thyroid + - 229 - Other benign neoplasm + - 240 - Thyroid + - 250 - Diabetes + - 250 - Other Endocrine + - 260 - Nutritional and metabolic + - 280 - Blood and Blood-Forming organs + - 290 - Mental disorders + - 320 - Nerv syst & sense organs + - 390 - Rheumatic heart disease + - 402 - Hypertensive heart disease + - 404 - Other Hypertensive disease + - 410 - Coronary heart disease + - 429 - Other heart disease + - 430 - Stroke + - 459 - Other Circulatory disease + - 480 - Pneumonia & influenza + - 490 - Emphysema & bronchitis + - 519 - Other respiratory disease + - 531 - Ulcer + - 570 - Other liver disease + - 571 - Cirrhosis + - 579 - Other digestive disease + - 580 - Urinary disease + - 600 - Genital disease + - 780 - Ill-defined conditions incl. senility + - 799 - Other non-external causes + - 800 - Accident + - 850 - Injury and poisoning (**) + - 950 - Suicide + - 960 - Homicide & other external + - 999 - unknown + + dose_abscissa: + description: X coordinate of subject's position on exposure + type: integer + + dose_ordinate: + description: Y coordinate of subject's position on exposure + type: integer + + dose_gdist: + description: Subject's ground distance from explosion + type: integer + + dose_shloc: + description: Shield location + enum: + - 1 - Inside + - 2 - Outside + - 3 - NIC + - 4 - Unknown - index_date: - description: The reference or anchor date used during date obfuscation, where - a single date is obscurred by creating one or more date ranges in relation to - this date. + dose_ds02cal: + description: Calculated location? enum: - - Diagnosis - - First Patient Visit - - Infection - - Study Enrollment + - Unexposed (NIC) + - Dose Known (FIA known SKR known) + - No selected for DS86 Calculation, ground distance > 3000m + - Dose Uncalculated (FIA known SKR uncalculated) + - Dose Unknown (FIA unknown, SKR unknown) + + dose_ds02cat: + description: Calculation algorithm + enum: + - 0 - InOpen + - 1 - 9P House + - 2 - 9P School + - 3 - Factory + - 4 - 9P Factory + - 5 - Globe + - 6 - Globe Terrain + - 7 - Other House + - 8 - 9P Other + - 9 - Concrete building + - 10 - Other Outside + - 11 - Other Inside + - 12 - NIC + - 13 - No Shielding Information + + dose_calgroup02: + description: Calculation information + type: integer + + kerma_fiau02g: + description: Overall dose (gamma radiation) + type: number + + kerma_fiau02n: + description: Overall dose (neutron radiation) + type: number - last_dt: - description: Last contact date (DDmonYYYY). From RERF 'mort_fup' table. + kerma_trunc02: + description: Truncation factor + type: number + + kerma_adjust02: + description: Adjustment factor + type: number + + death_icd: + description: ICD code type: string - machi: - description: Location. From RERF 'summ_dx_fix' table. + lss_entry_dt_year: + description: Subject's year of entry into the LSS cohort type: integer - nic: - description: Not in City. From RERF 'base_mortality' table. + lss_entry_dt_month: + description: Subject's month of entry into the LSS cohort type: integer - ordinate: - description: ordinate. From RERF 'dose_masterlist' table. + lss_entry_dt_day: + description: Subject's day of entry into the LSS cohort type: integer - prish: - description: prish. From RERF 'dose_masterlist' table. + inutero_entry_dt_year: + description: Year when the subject became a member of the Inutero cohort type: integer - res: - description: res. From RERF 'summ_dx_fix' table. + inutero_entry_dt_month: + description: Month when the subject became a member of the Inutero cohort type: integer - s_death: - description: s_death. From RERF 'summ_dx_fix' table. + inutero_entry_dt_day: + description: Day when the subject became a member of the Inutero cohort type: integer - sc: - description: sc (1, 2, 3, 4, 5). From RERF 'lss_master' table. + f1_entry_dt_year: + description: Year when the subject became a member of the F1 cohort type: integer - sdist: - description: sdist. From RERF 'dose_masterlist' table. + f1_entry_dt_month: + description: Month when the subject became a member of the F1 cohort type: integer - sealevel02: - description: sealevel02. From RERF 'dose_masterlist' table. - type: number + f1_entry_dt_day: + description: Day when the subject became a member of the F1 cohort + type: integer - sealevel86: - description: sealevel86. From RERF 'dose_masterlist' table. + mfup_last_contact_year: + description: Mortality follow-up year of last contact type: integer - sex: - description: The sex of a person (1- Male, 2- Female). From RERF 'id' table. + mfup_last_contact_month: + description: Mortality follow-up month of last contact type: integer - shloc: - description: shloc. From RERF 'dose_masterlist' table. + mfup_last_contact_day: + description: Mortality follow-up day of last contact type: integer - survangle: - description: survangle. From RERF 'dose_masterlist' table. + death_dt_year: + description: Year of death of the subject type: integer - sysid: - description: A unique identifier for an individual person in a study. From RERF - 'id' table. + death_dt_month: + description: Month of death of the subject type: integer - t65cal: - description: t65cal. From RERF 'dose_masterlist' table. + death_dt_day: + description: Day of death of the subject type: integer studies: diff --git a/gdcdictionary/tsvs/enums_rerf-v1.tsv b/gdcdictionary/tsvs/enums_rerf-v1.tsv new file mode 100644 index 0000000..e708f44 --- /dev/null +++ b/gdcdictionary/tsvs/enums_rerf-v1.tsv @@ -0,0 +1,2757 @@ + +study study_design Analytical +study study_design Clinical +study study_design Clinical Assay +study study_design Clinical Utility +study study_design Pre-Analytical +study study_design Research/Early Development +study study_objective Accuracy +study study_objective Clinical Detection +study study_objective Interference +study study_objective Limit of Detection +study study_objective Precision (Repeatability) +study study_objective Precision (Reproducibility) +study study_objective Specificity/Sensitivity +study study_objective Stability +study study_setup Detection/Enumeration/Isolation +study study_setup Genetic Analysis +subject death_src 60 - 1960 census +subject death_src AH - Adult Health Study +subject death_src BR - Birth record +subject death_src CN - Contact Card +subject death_src CR - Cross Index +subject death_src DE - Death Certification +subject death_src FU - Fuhyo +subject death_src G3 - Genetic study (GE-3) +subject death_src JS - Residence registry inquiry (regional cancer registry) +subject death_src KO - Koseki +subject death_src MC - Master File Code +subject death_src MF - Master File record +subject death_src MO - Mortality +subject death_src MQ - Master Sample Questionnaire +subject death_src OT - Other +subject death_src SK - Death certificate (regional cancer registry) +subject death_src TE - Hibakusha Techo +subject death_src TI - Tissue Registry Data Base +subject death_src TR - Tumor Registry Data Base +subject death_src YU - Mail Survey +subject dose_expcity 1 - Hiroshima +subject dose_expcity 2 - Nagasaki +subject dose_expstatus02 1 - In city, No distal terrain +subject dose_expstatus02 2 - In city, Distal terrain (Hijiyama and Konpirasan) +subject dose_expstatus02 3 - NIC late entry or extrance unknown +subject dose_expstatus02 4 - NIC early entry +subject dose_expstatus02 5 - NIC presumed (F1 original mortality sample parent) +subject dose_expstatus02 6 - NIC from GE3 +subject dose_expstatus02 9 - Unknown +subject dose_expstatus86 1 - In city ATB +subject dose_expstatus86 2 - NIC late entry or entrance unknown +subject dose_expstatus86 3 - NIC early entry +subject dose_expstatus86 4 - NIC presumed (F1 orginal mortality sample's parent) +subject dose_expstatus86 5 - NIC from GE3 +subject dose_expstatus86 8 - No Information +subject dose_expstatus86 9 - Unknown +subject dose_prish 1 - Open, with flush burns +subject dose_prish 10 - Other shielding +subject dose_prish 11 - No shielding information +subject dose_prish 12 - NIC +subject dose_prish 2 - Japanese-house (inside and outside) +subject dose_prish 3 - Tenement house (row-house) +subject dose_prish 4 - Japanese house and Terrain +subject dose_prish 5 - Tenement and Terrain +subject dose_prish 6 - Globe terrain +subject dose_prish 7 - Modelled factory +subject dose_prish 8 - Unmodelled factory +subject dose_prish 9 - Concrete building +subject dose_source CD300 - CD300 +subject dose_source F1MO - F1 Mortality Original Parents without DS86 +subject dose_source GE3 - GE3 +subject dose_source LSS - LSS +subject dose_source M - Acute Effects known +subject dose_source MSQ - PLC +subject dose_source T65D - T65D +subject mfup_last_status 1 - Alive +subject mfup_last_status 2 - Dead +subject mfup_last_status 3 - foreign nationality +subject mfup_last_status 6 - cessation of follow-up +subject mfup_last_status 7 - unknown permanent domicile +subject mfup_last_status 8 - exclusion from study subjects +subject mfup_last_status 9 - Follow-up halted due to excessive subject age +sample tissue_type Abnormal +sample tissue_type Normal +sample tissue_type Not Reported +sample tissue_type Peritumoral +sample tissue_type Tumor +sample tissue_type Unknown +sample preservation_method Cryopreserved +sample preservation_method FFPE +sample preservation_method Fresh +sample preservation_method Frozen +sample preservation_method Not Applicable +sample preservation_method Not Reported +sample preservation_method OCT +sample preservation_method Snap Frozen +sample preservation_method Unknown +sample method_of_sample_procurement Abdomino-perineal Resection of Rectum +sample method_of_sample_procurement Anterior Resection of Rectum +sample method_of_sample_procurement Aspirate +sample method_of_sample_procurement Autopsy +sample method_of_sample_procurement Biopsy +sample method_of_sample_procurement Blood Draw +sample method_of_sample_procurement Bone Marrow Aspirate +sample method_of_sample_procurement Core Biopsy +sample method_of_sample_procurement Cystectomy +sample method_of_sample_procurement Endo Rectal Tumor Resection +sample composition 2D Classical Conditionally Reprogrammed Cells +sample composition 2D Modified Conditionally Reprogrammed Cells +sample composition 3D Air-Liquid Interface Organoid +sample composition 3D Neurosphere +sample composition 3D Organoid +sample composition Adherent Cell Line +sample biospecimen_laterality Bilateral +sample biospecimen_laterality Left +sample biospecimen_laterality Not Reported +sample biospecimen_laterality Right +sample biospecimen_laterality Unknown +sample biospecimen_anatomic_site Abdomen +sample biospecimen_anatomic_site Abdominal Wall +sample biospecimen_anatomic_site Acetabulum +sample biospecimen_anatomic_site Adenoid +sample biospecimen_anatomic_site Adipose +sample biospecimen_anatomic_site Adrenal +sample biospecimen_anatomic_site Alveolar Ridge +sample biospecimen_anatomic_site Amniotic Fluid +sample biospecimen_anatomic_site Ampulla Of Vater +sample biospecimen_anatomic_site Anal Sphincter +sample biospecimen_anatomic_site Ankle +sample biospecimen_anatomic_site Anorectum +sample biospecimen_anatomic_site Antecubital Fossa +sample biospecimen_anatomic_site Antrum +sample biospecimen_anatomic_site Anus +sample biospecimen_anatomic_site Aorta +sample biospecimen_anatomic_site Aortic Body +sample biospecimen_anatomic_site Appendix +sample biospecimen_anatomic_site Aqueous Fluid +sample biospecimen_anatomic_site Arm +sample biospecimen_anatomic_site Artery +sample biospecimen_anatomic_site Ascending Colon +sample biospecimen_anatomic_site Ascending Colon Hepatic Flexure +sample biospecimen_anatomic_site Auditory Canal +sample biospecimen_anatomic_site Autonomic Nervous System +sample biospecimen_anatomic_site Axilla +sample biospecimen_anatomic_site Back +sample biospecimen_anatomic_site Bile Duct +sample biospecimen_anatomic_site Bladder +sample biospecimen_anatomic_site Blood +sample biospecimen_anatomic_site Blood Vessel +sample biospecimen_anatomic_site Bone +sample biospecimen_anatomic_site Bone Marrow +sample biospecimen_anatomic_site Bowel +sample biospecimen_anatomic_site Brain +sample biospecimen_anatomic_site Brain Stem +sample biospecimen_anatomic_site Breast +sample biospecimen_anatomic_site Broad Ligament +sample biospecimen_anatomic_site Bronchiole +sample biospecimen_anatomic_site Bronchus +sample biospecimen_anatomic_site Brow +sample biospecimen_anatomic_site Buccal Cavity +sample biospecimen_anatomic_site Buccal Mucosa +sample biospecimen_anatomic_site Buttock +sample biospecimen_anatomic_site Calf +sample biospecimen_anatomic_site Capillary +sample biospecimen_anatomic_site Cardia +sample biospecimen_anatomic_site Carina +sample biospecimen_anatomic_site Carotid Artery +sample biospecimen_anatomic_site Carotid Body +sample biospecimen_anatomic_site Cartilage +sample biospecimen_anatomic_site Cecum +sample biospecimen_anatomic_site Cell-Line +sample biospecimen_anatomic_site Central Nervous System +sample biospecimen_anatomic_site Cerebellum +sample biospecimen_anatomic_site Cerebral Cortex +sample biospecimen_anatomic_site Cerebrospinal Fluid +sample biospecimen_anatomic_site Cerebrum +sample biospecimen_anatomic_site Cervical Spine +sample biospecimen_anatomic_site Cervix +sample biospecimen_anatomic_site Chest +sample biospecimen_anatomic_site Chest Wall +sample biospecimen_anatomic_site Chin +sample biospecimen_anatomic_site Clavicle +sample biospecimen_anatomic_site Clitoris +sample biospecimen_anatomic_site Colon +sample biospecimen_anatomic_site Colon - Mucosa Only +sample biospecimen_anatomic_site Common Duct +sample biospecimen_anatomic_site Conjunctiva +sample biospecimen_anatomic_site Connective Tissue +sample biospecimen_anatomic_site Dermal +sample biospecimen_anatomic_site Descending Colon +sample biospecimen_anatomic_site Diaphragm +sample biospecimen_anatomic_site Duodenum +sample biospecimen_anatomic_site Ear +sample biospecimen_anatomic_site Ear Canal +sample biospecimen_anatomic_site Ear, Pinna (External) +sample biospecimen_anatomic_site Effusion +sample biospecimen_anatomic_site Elbow +sample biospecimen_anatomic_site Endocrine Gland +sample biospecimen_anatomic_site Epididymis +sample biospecimen_anatomic_site Epidural Space +sample biospecimen_anatomic_site Esophageal, Distal +sample biospecimen_anatomic_site Esophageal, Mid +sample biospecimen_anatomic_site Esophageal, Proximal +sample biospecimen_anatomic_site Esophagogastric Junction +sample biospecimen_anatomic_site Esophagus +sample biospecimen_anatomic_site Esophagus - Mucosa Only +sample biospecimen_anatomic_site Eye +sample biospecimen_anatomic_site Fallopian Tube +sample biospecimen_anatomic_site Femoral Artery +sample biospecimen_anatomic_site Femoral Vein +sample biospecimen_anatomic_site Femur +sample biospecimen_anatomic_site Fibroblasts +sample biospecimen_anatomic_site Fibula +sample biospecimen_anatomic_site Finger +sample biospecimen_anatomic_site Floor Of Mouth +sample biospecimen_anatomic_site Fluid +sample biospecimen_anatomic_site Foot +sample biospecimen_anatomic_site Forearm +sample biospecimen_anatomic_site Forehead +sample biospecimen_anatomic_site Foreskin +sample biospecimen_anatomic_site Frontal Cortex +sample biospecimen_anatomic_site Frontal Lobe +sample biospecimen_anatomic_site Fundus Of Stomach +sample biospecimen_anatomic_site Gallbladder +sample biospecimen_anatomic_site Ganglia +sample biospecimen_anatomic_site Gastroesophageal Junction +sample biospecimen_anatomic_site Gastrointestinal Tract +sample biospecimen_anatomic_site Groin +sample biospecimen_anatomic_site Gum +sample biospecimen_anatomic_site Hand +sample biospecimen_anatomic_site Hard Palate +sample biospecimen_anatomic_site Head - Face Or Neck, Nos +sample biospecimen_anatomic_site Head and Neck +sample biospecimen_anatomic_site Heart +sample biospecimen_anatomic_site Hepatic +sample biospecimen_anatomic_site Hepatic Duct +sample biospecimen_anatomic_site Hepatic Flexure +sample biospecimen_anatomic_site Hepatic Vein +sample biospecimen_anatomic_site Hip +sample biospecimen_anatomic_site Hippocampus +sample biospecimen_anatomic_site Humerus +sample biospecimen_anatomic_site Hypopharynx +sample biospecimen_anatomic_site Ileum +sample biospecimen_anatomic_site Ilium +sample biospecimen_anatomic_site Index Finger +sample biospecimen_anatomic_site Ischium +sample biospecimen_anatomic_site Islet Cells +sample biospecimen_anatomic_site Jaw +sample biospecimen_anatomic_site Jejunum +sample biospecimen_anatomic_site Joint +sample biospecimen_anatomic_site Kidney +sample biospecimen_anatomic_site Knee +sample biospecimen_anatomic_site Lacrimal Gland +sample biospecimen_anatomic_site Large Bowel +sample biospecimen_anatomic_site Laryngopharynx +sample biospecimen_anatomic_site Larynx +sample biospecimen_anatomic_site Leg +sample biospecimen_anatomic_site Leptomeninges +sample biospecimen_anatomic_site Ligament +sample biospecimen_anatomic_site Lip +sample biospecimen_anatomic_site Liver +sample biospecimen_anatomic_site Lumbar Spine +sample biospecimen_anatomic_site Lung +sample biospecimen_anatomic_site Lymph Node +sample biospecimen_anatomic_site Lymph Node(s) Axilla +sample biospecimen_anatomic_site Lymph Node(s) Cervical +sample biospecimen_anatomic_site Lymph Node(s) Distant +sample biospecimen_anatomic_site Lymph Node(s) Epitrochlear +sample biospecimen_anatomic_site Lymph Node(s) Femoral +sample biospecimen_anatomic_site Lymph Node(s) Hilar +sample biospecimen_anatomic_site Lymph Node(s) Iliac-Common +sample biospecimen_anatomic_site Lymph Node(s) Iliac-External +sample biospecimen_anatomic_site Lymph Node(s) Inguinal +sample biospecimen_anatomic_site Lymph Node(s) Internal Mammary +sample biospecimen_anatomic_site Lymph Node(s) Mammary +sample biospecimen_anatomic_site Lymph Node(s) Mesenteric +sample biospecimen_anatomic_site Lymph Node(s) Occipital +sample biospecimen_anatomic_site Lymph Node(s) Paraaortic +sample biospecimen_anatomic_site Lymph Node(s) Parotid +sample biospecimen_anatomic_site Lymph Node(s) Pelvic +sample biospecimen_anatomic_site Lymph Node(s) Popliteal +sample biospecimen_anatomic_site Lymph Node(s) Regional +sample biospecimen_anatomic_site Lymph Node(s) Retroperitoneal +sample biospecimen_anatomic_site Lymph Node(s) Scalene +sample biospecimen_anatomic_site Lymph Node(s) Splenic +sample biospecimen_anatomic_site Lymph Node(s) Subclavicular +sample biospecimen_anatomic_site Lymph Node(s) Submandibular +sample biospecimen_anatomic_site Lymph Node(s) Supraclavicular +sample biospecimen_anatomic_site Lymph Nodes(s) Mediastinal +sample biospecimen_anatomic_site Mandible +sample biospecimen_anatomic_site Maxilla +sample biospecimen_anatomic_site Mediastinal Soft Tissue +sample biospecimen_anatomic_site Mediastinum +sample biospecimen_anatomic_site Mesentery +sample biospecimen_anatomic_site Mesothelium +sample biospecimen_anatomic_site Middle Finger +sample biospecimen_anatomic_site Mitochondria +sample biospecimen_anatomic_site Muscle +sample biospecimen_anatomic_site Nails +sample biospecimen_anatomic_site Nasal Cavity +sample biospecimen_anatomic_site Nasal Soft Tissue +sample biospecimen_anatomic_site Nasopharynx +sample biospecimen_anatomic_site Neck +sample biospecimen_anatomic_site Nerve +sample biospecimen_anatomic_site Nerve(s) Cranial +sample biospecimen_anatomic_site Occipital Cortex +sample biospecimen_anatomic_site Ocular Orbits +sample biospecimen_anatomic_site Omentum +sample biospecimen_anatomic_site Oral Cavity +sample biospecimen_anatomic_site Oral Cavity - Mucosa Only +sample biospecimen_anatomic_site Oropharynx +sample biospecimen_anatomic_site Other +sample biospecimen_anatomic_site Ovary +sample biospecimen_anatomic_site Palate +sample biospecimen_anatomic_site Pancreas +sample biospecimen_anatomic_site Paraspinal Ganglion +sample biospecimen_anatomic_site Parathyroid +sample biospecimen_anatomic_site Parotid Gland +sample biospecimen_anatomic_site Patella +sample biospecimen_anatomic_site Pelvis +sample biospecimen_anatomic_site Penis +sample biospecimen_anatomic_site Pericardium +sample biospecimen_anatomic_site Periorbital Soft Tissue +sample biospecimen_anatomic_site Peritoneal Cavity +sample biospecimen_anatomic_site Peritoneum +sample biospecimen_anatomic_site Pharynx +sample biospecimen_anatomic_site Pineal +sample biospecimen_anatomic_site Pineal Gland +sample biospecimen_anatomic_site Pituitary Gland +sample biospecimen_anatomic_site Placenta +sample biospecimen_anatomic_site Pleura +sample biospecimen_anatomic_site Popliteal Fossa +sample biospecimen_anatomic_site Prostate +sample biospecimen_anatomic_site Pylorus +sample biospecimen_anatomic_site Rectosigmoid Junction +sample biospecimen_anatomic_site Rectum +sample biospecimen_anatomic_site Retina +sample biospecimen_anatomic_site Retro-Orbital Region +sample biospecimen_anatomic_site Retroperitoneum +sample biospecimen_anatomic_site Rib +sample biospecimen_anatomic_site Ring Finger +sample biospecimen_anatomic_site Round Ligament +sample biospecimen_anatomic_site Sacrum +sample biospecimen_anatomic_site Salivary Gland +sample biospecimen_anatomic_site Scalp +sample biospecimen_anatomic_site Scapula +sample biospecimen_anatomic_site Sciatic Nerve +sample biospecimen_anatomic_site Scrotum +sample biospecimen_anatomic_site Seminal Vesicle +sample biospecimen_anatomic_site Shoulder +sample biospecimen_anatomic_site Sigmoid Colon +sample biospecimen_anatomic_site Sinus +sample biospecimen_anatomic_site Sinus(es), Maxillary +sample biospecimen_anatomic_site Skeletal Muscle +sample biospecimen_anatomic_site Skin +sample biospecimen_anatomic_site Skull +sample biospecimen_anatomic_site Small Bowel +sample biospecimen_anatomic_site Small Bowel - Mucosa Only +sample biospecimen_anatomic_site Small Finger +sample biospecimen_anatomic_site Soft Tissue +sample biospecimen_anatomic_site Spinal Column +sample biospecimen_anatomic_site Spinal Cord +sample biospecimen_anatomic_site Spleen +sample biospecimen_anatomic_site Splenic Flexure +sample biospecimen_anatomic_site Sternum +sample biospecimen_anatomic_site Stomach +sample biospecimen_anatomic_site Stomach - Mucosa Only +sample biospecimen_anatomic_site Subcutaneous Tissue +sample biospecimen_anatomic_site Synovium +sample biospecimen_anatomic_site Temporal Cortex +sample biospecimen_anatomic_site Tendon +sample biospecimen_anatomic_site Testis +sample biospecimen_anatomic_site Thigh +sample biospecimen_anatomic_site Thoracic Spine +sample biospecimen_anatomic_site Thorax +sample biospecimen_anatomic_site Throat +sample biospecimen_anatomic_site Thumb +sample biospecimen_anatomic_site Thymus +sample biospecimen_anatomic_site Thyroid +sample biospecimen_anatomic_site Tibia +sample biospecimen_anatomic_site Tongue +sample biospecimen_anatomic_site Tonsil +sample biospecimen_anatomic_site Tonsil (Pharyngeal) +sample biospecimen_anatomic_site Trachea +sample biospecimen_anatomic_site Transverse Colon +sample biospecimen_anatomic_site Trunk +sample biospecimen_anatomic_site Umbilical Cord +sample biospecimen_anatomic_site Unknown +sample biospecimen_anatomic_site Ureter +sample biospecimen_anatomic_site Urethra +sample biospecimen_anatomic_site Urinary Tract +sample biospecimen_anatomic_site Uterus +sample biospecimen_anatomic_site Uvula +sample biospecimen_anatomic_site Vagina +sample biospecimen_anatomic_site Vas Deferens +sample biospecimen_anatomic_site Vein +sample biospecimen_anatomic_site Venous +sample biospecimen_anatomic_site Vertebra +sample biospecimen_anatomic_site Vulva +sample biospecimen_anatomic_site White Blood Cells +sample biospecimen_anatomic_site Wrist +sample composition Bone Marrow Components +sample composition Bone Marrow Components NOS +sample composition Buccal Cells +sample composition Buffy Coat +sample composition Cell +sample composition Control Analyte +sample composition Derived Cell Line +sample composition EBV Immortalized +sample composition Fibroblasts from Bone Marrow Normal +sample composition Granulocytes +sample composition Human Original Cells +sample composition Liquid Suspension Cell Line +sample composition Lymphocytes +sample composition Mononuclear Cells from Bone Marrow Normal +sample composition Not Reported +sample composition Peripheral Blood Components NOS +sample composition Peripheral Whole Blood +sample composition Plasma +sample composition Pleural Effusion +sample composition Saliva +sample composition Serum +sample composition Solid Tissue +sample composition Sorted Cells +sample composition Sputum +sample composition Unknown +sample composition Whole Bone Marrow +sample method_of_sample_procurement Endoscopic Biopsy +sample method_of_sample_procurement Endoscopic Mucosal Resection (EMR) +sample method_of_sample_procurement Enucleation +sample method_of_sample_procurement Excisional Biopsy +sample method_of_sample_procurement Fine Needle Aspiration +sample method_of_sample_procurement Full Hysterectomy +sample method_of_sample_procurement Gross Total Resection +sample method_of_sample_procurement Hand Assisted Laparoscopic Radical Nephrectomy +sample method_of_sample_procurement Hysterectomy NOS +sample method_of_sample_procurement Incisional Biopsy +sample method_of_sample_procurement Indeterminant +sample method_of_sample_procurement Laparoscopic Biopsy +sample method_of_sample_procurement Laparoscopic Partial Nephrectomy +sample method_of_sample_procurement Laparoscopic Radical Nephrectomy +sample method_of_sample_procurement Laparoscopic Radical Prostatectomy with Robotics +sample method_of_sample_procurement Laparoscopic Radical Prostatectomy without Robotics +sample method_of_sample_procurement Left Hemicolectomy +sample method_of_sample_procurement Lobectomy +sample method_of_sample_procurement Local Resection (Exoresection, wall resection) +sample method_of_sample_procurement Lumpectomy +sample method_of_sample_procurement Modified Radical Mastectomy +sample method_of_sample_procurement Needle Biopsy +sample method_of_sample_procurement Not Reported +sample method_of_sample_procurement Open Craniotomy +sample method_of_sample_procurement Open Partial Nephrectomy +sample method_of_sample_procurement Open Radical Nephrectomy +sample method_of_sample_procurement Open Radical Prostatectomy +sample method_of_sample_procurement Orchiectomy +sample method_of_sample_procurement Other +sample method_of_sample_procurement Other Surgical Resection +sample method_of_sample_procurement Pan-Procto Colectomy +sample method_of_sample_procurement Pancreatectomy +sample method_of_sample_procurement Paracentesis +sample method_of_sample_procurement Pneumonectomy +sample method_of_sample_procurement Right Hemicolectomy +sample method_of_sample_procurement Sigmoid Colectomy +sample method_of_sample_procurement Simple Mastectomy +sample method_of_sample_procurement Subtotal Resection +sample method_of_sample_procurement Surgical Resection +sample method_of_sample_procurement Thoracoscopic Biopsy +sample method_of_sample_procurement Total Colectomy +sample method_of_sample_procurement Total Mastectomy +sample method_of_sample_procurement Transplant +sample method_of_sample_procurement Transurethral resection (TURBT) +sample method_of_sample_procurement Transverse Colectomy +sample method_of_sample_procurement Tumor Resection +sample method_of_sample_procurement Unknown +sample method_of_sample_procurement Wedge Resection +sample method_of_sample_procurement Whipple Procedure +aliquot aliquot_container Not Applicable +aliquot aliquot_container Other +aliquot aliquot_container Slide +aliquot aliquot_container Vial +aliquot analyte_type Cell Count +aliquot analyte_type DNA +aliquot analyte_type Morphology +aliquot analyte_type Peptide +aliquot analyte_type Protein +aliquot analyte_type RNA +aliquot preservation_method Cryopreserved +aliquot preservation_method FFPE +aliquot preservation_method Fresh +aliquot preservation_method Frozen +aliquot preservation_method OCT +aliquot preservation_method Snap Frozen +aliquot preservation_method Unknown +subject lss_sample_class 1 - Original LSS +subject lss_sample_class 2 - Reserved (less than 2.5km) +subject lss_sample_class 3 - Nagasaki Distal Additions +subject lss_sample_class 4 - NIC - early +subject lss_sample_class 5 - NIC - late +subject lss_census 1 - national census 1950 +subject lss_census 2 - ABCC 1st sample census +subject lss_census 3 - ABCC 2nd sample census +subject lss_census 4 - NIC 1953 census (Hiroshima) +subject lss_census 5 - Setai-Daicho (Nagasaki) +subject ahs_subgroup 1 - original(ME-200) +subject ahs_subgroup 2 - extension(ME-200-1) +subject ahs_subgroup 3 - PE-86(ME-200-2) +subject ahs_subgroup 4 - young extension(ME-200-3) +subject ahs_exp_category 1 - proximal (< 2000m), some symptom +subject ahs_exp_category 2 - proximal (< 2000m), no symptom +subject ahs_exp_category 3 - distal (Hiroshima; 3000-3499m, Nagasaki; 3000-3999m) +subject ahs_exp_category 4 - Unexposed +subject f1_sample 1 - F1 mortality original +subject f1_sample 2 - F1 mortality extension +subject f1_sample 3 - F1 BGS original +subject f1_sample 4 - F1 BGS extension +subject f1_sample 5 - F1 GE3 only +subject f1_ind 0 - Not included in F1 cohort +subject f1_ind 1 - Included in F1 cohort +inutero prog A - AHS sample (ME-200-2) +inutero prog B - BGS +inutero prog C - Cyto +inutero prog G - GE3 +inutero prog I - IQ sample +inutero prog M - Mortality sample +inutero prog P - PLC +inutero prog Y - mail +f1 prog A - AHS sample (ME-200-2) +f1 prog B - BGS +f1 prog C - Cyto +f1 prog G - GE3 +f1 prog I - IQ sample +f1 prog M - Mortality sample +f1 prog P - PLC +f1 prog Y - mail +exam_diag icd_rev 7 +exam_diag icd_rev 8 +exam_diag icd_rev 9 +exam_diag icd_rev 10 +subject death_icd_rev 7 +subject death_icd_rev 8 +subject death_icd_rev 9 +subject death_icd_rev 10 +subject death_icd_grp 10 - Tuberculosis +subject death_icd_grp 99 - Other Infect/Parasit Dis +subject death_icd_grp 140 - Lip +subject death_icd_grp 141 - Tongue +subject death_icd_grp 142 - Salivary Glands (Major) +subject death_icd_grp 143 - Mouth +subject death_icd_grp 146 - Pharynx +subject death_icd_grp 150 - Esophagus +subject death_icd_grp 151 - Stomach +subject death_icd_grp 152 - Small intestine +subject death_icd_grp 153 - Colon +subject death_icd_grp 154 - Rectum +subject death_icd_grp 155 - Liver (primary) +subject death_icd_grp 155 - Liver (NOS) +subject death_icd_grp 156 - Gallbladder etc. +subject death_icd_grp 157 - Pancreas +subject death_icd_grp 159 - Other Digestive +subject death_icd_grp 159 - Other Digestive +subject death_icd_grp 160 - Nasal cavity etc. +subject death_icd_grp 161 - Larynx +subject death_icd_grp 162 - Lung +subject death_icd_grp 169 - Other respiratory +subject death_icd_grp 170 - Bone +subject death_icd_grp 171 - Connective Tissue +subject death_icd_grp 172 - Melanoma of the Skin +subject death_icd_grp 173 - Non-melanoma skin +subject death_icd_grp 174 - Breast (Male and Female) +subject death_icd_grp 179 - Uterus NOS +subject death_icd_grp 180 - Cervix Uteri +subject death_icd_grp 182 - Corpus Uteri +subject death_icd_grp 183 - Ovary etc. +subject death_icd_grp 183 - Ovary etc. +subject death_icd_grp 184 - Other Female genital +subject death_icd_grp 185 - Prostate +subject death_icd_grp 187 - Other male genital +subject death_icd_grp 188 - Urinary bladder +subject death_icd_grp 189 - Kidney +subject death_icd_grp 189 - Renal Pelvis & Ureter +subject death_icd_grp 189 - Other Urinary +subject death_icd_grp 191 - Brain +subject death_icd_grp 192 - Meninges +subject death_icd_grp 192 - Other nervous system +subject death_icd_grp 193 - Thyroid +subject death_icd_grp 194 - Other primary +subject death_icd_grp 199 - Secondary & unspecified +subject death_icd_grp 200 - Non - Hodgkin's lymphoma +subject death_icd_grp 201 - Hodgkin's lymphoma +subject death_icd_grp 203 - Multiple myeloma +subject death_icd_grp 204 - Acute lymphoid leukemia +subject death_icd_grp 204 - Chronic lymphoid leukemia +subject death_icd_grp 204 - Other/unspec lymphoid leukemia +subject death_icd_grp 205 - Acute myeloid leukemia +subject death_icd_grp 205 - Chronic myeloid leukemia +subject death_icd_grp 205 - Other/unspec myeloid leukemia +subject death_icd_grp 208 - Acute NOS +subject death_icd_grp 208 - Chronic NOS +subject death_icd_grp 208 - Adult T-cell leukemia +subject death_icd_grp 208 - Other/unspec leukemia +subject death_icd_grp 210 - Salivary Gland (Major) +subject death_icd_grp 211 - Stomach +subject death_icd_grp 211 - Colon +subject death_icd_grp 218 - Myoma Uteri +subject death_icd_grp 225 - Brain +subject death_icd_grp 225 - Meninges +subject death_icd_grp 225 - Other nervous system +subject death_icd_grp 226 - Thyroid +subject death_icd_grp 229 - Other benign neoplasm +subject death_icd_grp 240 - Thyroid +subject death_icd_grp 250 - Diabetes +subject death_icd_grp 250 - Other Endocrine +subject death_icd_grp 260 - Nutritional and metabolic +subject death_icd_grp 280 - Blood and Blood-Forming organs +subject death_icd_grp 290 - Mental disorders +subject death_icd_grp 320 - Nerv syst & sense organs +subject death_icd_grp 390 - Rheumatic heart disease +subject death_icd_grp 402 - Hypertensive heart disease +subject death_icd_grp 404 - Other Hypertensive disease +subject death_icd_grp 410 - Coronary heart disease +subject death_icd_grp 429 - Other heart disease +subject death_icd_grp 430 - Stroke +subject death_icd_grp 459 - Other Circulatory disease +subject death_icd_grp 480 - Pneumonia & influenza +subject death_icd_grp 490 - Emphysema & bronchitis +subject death_icd_grp 519 - Other respiratory disease +subject death_icd_grp 531 - Ulcer +subject death_icd_grp 570 - Other liver disease +subject death_icd_grp 571 - Cirrhosis +subject death_icd_grp 579 - Other digestive disease +subject death_icd_grp 580 - Urinary disease +subject death_icd_grp 600 - Genital disease +subject death_icd_grp 780 - Ill-defined conditions incl. senility +subject death_icd_grp 799 - Other non-external causes +subject death_icd_grp 800 - Accident +subject death_icd_grp 850 - Injury and poisoning (**) +subject death_icd_grp 950 - Suicide +subject death_icd_grp 960 - Homicide & other external +subject death_icd_grp 999 - unknown +subject dose_shloc 1 - Inside +subject dose_shloc 2 - Outside +subject dose_shloc 3 - NIC +subject dose_shloc 4 - Unknown +subject dose_ds02cal Unexposed (NIC) +subject dose_ds02cal Dose Known (FIA known SKR known) +subject dose_ds02cal No selected for DS86 Calculation, ground distance > 3000m +subject dose_ds02cal Dose Uncalculated (FIA known SKR uncalculated) +subject dose_ds02cal Dose Unknown (FIA unknown, SKR unknown) +subject dose_ds02cat 0 - InOpen +subject dose_ds02cat 1 - 9P House +subject dose_ds02cat 2 - 9P School +subject dose_ds02cat 3 - Factory +subject dose_ds02cat 4 - 9P Factory +subject dose_ds02cat 5 - Globe +subject dose_ds02cat 6 - Globe Terrain +subject dose_ds02cat 7 - Other House +subject dose_ds02cat 8 - 9P Other +subject dose_ds02cat 9 - Concrete building +subject dose_ds02cat 10 - Other Outside +subject dose_ds02cat 11 - Other Inside +subject dose_ds02cat 12 - NIC +subject dose_ds02cat 13 - No Shielding Information +dose discript 1 - skeleton +dose discript 2 - marrow +dose discript 3 - urinary +dose discript 4 - brain +dose discript 5 - breast +dose discript 6 - eye lense +dose discript 7 - colon +dose discript 8 - liver +dose discript 9 - lungs +dose discript 10 - ovary +dose discript 11 - pancreas +dose discript 12 - stomach +dose discript 13 - testes +dose discript 14 - thyroid +dose discript 15 - uterus +dose discript 16 - fia_kerma +dose discript 17 - skin +dose discript 18 - distal_fia +dose discript 19 - sh_kerma +cancer_diag res 1 - in city +cancer_diag res 2 - in prefecture +cancer_diag res 3 - outside prefecture +cancer_diag res 9 - unknown +cancer_diag city 1 - Hiroshima +cancer_diag city 2 - Nagasaki +cancer_diag motiv 1 - Group examination +cancer_diag motiv 2 - Health examination +cancer_diag motiv 3 - Subjective symptom +cancer_diag motiv 4 - Others +cancer_diag motiv 9 - Unknown +cancer_diag behavior 0 - Benign +cancer_diag behavior 1 - Uncertain whether benign or malignant +cancer_diag behavior 2 - Carcinoma in-situ, Intraepithelial, Non-infiltrative, non-invasive +cancer_diag behavior 3 - Malignant +cancer_diag behavior 6 - Malignant, metastatic site. Secondary site +cancer_diag behavior 9 - Malignant, uncertain +cancer_diag onc_rev 1 - ICD-O 1st +cancer_diag onc_rev 2 - ICD-O 2nd +cancer_diag onc_rev 3 - ICD-O 3rd +cancer_diag icd_grp 10 - Tuberculosis +cancer_diag icd_grp 99 - Other Infect/Parasit Dis +cancer_diag icd_grp 140 - Lip +cancer_diag icd_grp 141 - Tongue +cancer_diag icd_grp 142 - Salivary Glands (Major) +cancer_diag icd_grp 143 - Mouth +cancer_diag icd_grp 146 - Pharynx +cancer_diag icd_grp 150 - Esophagus +cancer_diag icd_grp 151 - Stomach +cancer_diag icd_grp 152 - Small intestine +cancer_diag icd_grp 153 - Colon +cancer_diag icd_grp 154 - Rectum +cancer_diag icd_grp 155 - Liver (primary) +cancer_diag icd_grp 155 - Liver (NOS) +cancer_diag icd_grp 156 - Gallbladder etc. +cancer_diag icd_grp 157 - Pancreas +cancer_diag icd_grp 159 - Other Digestive +cancer_diag icd_grp 159 - Other Digestive +cancer_diag icd_grp 160 - Nasal cavity etc. +cancer_diag icd_grp 161 - Larynx +cancer_diag icd_grp 162 - Lung +cancer_diag icd_grp 169 - Other respiratory +cancer_diag icd_grp 170 - Bone +cancer_diag icd_grp 171 - Connective Tissue +cancer_diag icd_grp 172 - Melanoma of the Skin +cancer_diag icd_grp 173 - Non-melanoma skin +cancer_diag icd_grp 174 - Breast (Male and Female) +cancer_diag icd_grp 179 - Uterus NOS +cancer_diag icd_grp 180 - Cervix Uteri +cancer_diag icd_grp 182 - Corpus Uteri +cancer_diag icd_grp 183 - Ovary etc. +cancer_diag icd_grp 183 - Ovary etc. +cancer_diag icd_grp 184 - Other Female genital +cancer_diag icd_grp 185 - Prostate +cancer_diag icd_grp 187 - Other male genital +cancer_diag icd_grp 188 - Urinary bladder +cancer_diag icd_grp 189 - Kidney +cancer_diag icd_grp 189 - Renal Pelvis & Ureter +cancer_diag icd_grp 189 - Other Urinary +cancer_diag icd_grp 191 - Brain +cancer_diag icd_grp 192 - Meninges +cancer_diag icd_grp 192 - Other nervous system +cancer_diag icd_grp 193 - Thyroid +cancer_diag icd_grp 194 - Other primary +cancer_diag icd_grp 199 - Secondary & unspecified +cancer_diag icd_grp 200 - Non - Hodgkin's lymphoma +cancer_diag icd_grp 201 - Hodgkin's lymphoma +cancer_diag icd_grp 203 - Multiple myeloma +cancer_diag icd_grp 204 - Acute lymphoid leukemia +cancer_diag icd_grp 204 - Chronic lymphoid leukemia +cancer_diag icd_grp 204 - Other/unspec lymphoid leukemia +cancer_diag icd_grp 205 - Acute myeloid leukemia +cancer_diag icd_grp 205 - Chronic myeloid leukemia +cancer_diag icd_grp 205 - Other/unspec myeloid leukemia +cancer_diag icd_grp 208 - Acute NOS +cancer_diag icd_grp 208 - Chronic NOS +cancer_diag icd_grp 208 - Adult T-cell leukemia +cancer_diag icd_grp 208 - Other/unspec leukemia +cancer_diag icd_grp 210 - Salivary Gland (Major) +cancer_diag icd_grp 211 - Stomach +cancer_diag icd_grp 211 - Colon +cancer_diag icd_grp 218 - Myoma Uteri +cancer_diag icd_grp 225 - Brain +cancer_diag icd_grp 225 - Meninges +cancer_diag icd_grp 225 - Other nervous system +cancer_diag icd_grp 226 - Thyroid +cancer_diag icd_grp 229 - Other benign neoplasm +cancer_diag icd_grp 240 - Thyroid +cancer_diag icd_grp 250 - Diabetes +cancer_diag icd_grp 250 - Other Endocrine +cancer_diag icd_grp 260 - Nutritional and metabolic +cancer_diag icd_grp 280 - Blood and Blood-Forming organs +cancer_diag icd_grp 290 - Mental disorders +cancer_diag icd_grp 320 - Nerv syst & sense organs +cancer_diag icd_grp 390 - Rheumatic heart disease +cancer_diag icd_grp 402 - Hypertensive heart disease +cancer_diag icd_grp 404 - Other Hypertensive disease +cancer_diag icd_grp 410 - Coronary heart disease +cancer_diag icd_grp 429 - Other heart disease +cancer_diag icd_grp 430 - Stroke +cancer_diag icd_grp 459 - Other Circulatory disease +cancer_diag icd_grp 480 - Pneumonia & influenza +cancer_diag icd_grp 490 - Emphysema & bronchitis +cancer_diag icd_grp 519 - Other respiratory disease +cancer_diag icd_grp 531 - Ulcer +cancer_diag icd_grp 570 - Other liver disease +cancer_diag icd_grp 571 - Cirrhosis +cancer_diag icd_grp 579 - Other digestive disease +cancer_diag icd_grp 580 - Urinary disease +cancer_diag icd_grp 600 - Genital disease +cancer_diag icd_grp 780 - Ill-defined conditions incl. senility +cancer_diag icd_grp 799 - Other non-external causes +cancer_diag icd_grp 800 - Accident +cancer_diag icd_grp 850 - Injury and poisoning (**) +cancer_diag icd_grp 950 - Suicide +cancer_diag icd_grp 960 - Homicide & other external +cancer_diag icd_grp 999 - unknown +cancer_diag machi 1 +cancer_diag machi 2 +cancer_diag machi 3 +cancer_diag machi 4 +cancer_diag machi 5 +cancer_diag machi 6 +cancer_diag machi 7 +cancer_diag machi 8 +cancer_diag machi 9 +cancer_diag machi 10 +cancer_diag machi 11 +cancer_diag machi 12 +cancer_diag machi 13 +cancer_diag machi 14 +cancer_diag machi 15 +cancer_diag machi 16 +cancer_diag machi 17 +cancer_diag machi 18 +cancer_diag machi 19 +cancer_diag machi 20 +cancer_diag machi 21 +cancer_diag machi 22 +cancer_diag machi 23 +cancer_diag machi 24 +cancer_diag machi 25 +cancer_diag machi 26 +cancer_diag machi 27 +cancer_diag machi 28 +cancer_diag machi 29 +cancer_diag machi 30 +cancer_diag machi 31 +cancer_diag machi 32 +cancer_diag machi 33 +cancer_diag machi 34 +cancer_diag machi 35 +cancer_diag machi 36 +cancer_diag machi 37 +cancer_diag machi 38 +cancer_diag machi 39 +cancer_diag machi 40 +cancer_diag machi 41 +cancer_diag machi 42 +cancer_diag machi 43 +cancer_diag machi 44 +cancer_diag machi 45 +cancer_diag machi 46 +cancer_diag machi 47 +cancer_diag machi 48 +cancer_diag machi 49 +cancer_diag machi 50 +cancer_diag machi 51 +cancer_diag machi 52 +cancer_diag machi 53 +cancer_diag machi 54 +cancer_diag machi 55 +cancer_diag machi 56 +cancer_diag machi 57 +cancer_diag machi 58 +cancer_diag machi 59 +cancer_diag machi 60 +cancer_diag machi 61 +cancer_diag machi 62 +cancer_diag machi 63 +cancer_diag machi 64 +cancer_diag machi 65 +cancer_diag machi 66 +cancer_diag machi 67 +cancer_diag machi 68 +cancer_diag machi 69 +cancer_diag machi 70 +cancer_diag machi 71 +cancer_diag machi 72 +cancer_diag machi 73 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machi 118 +cancer_diag machi 119 +cancer_diag machi 120 +cancer_diag machi 121 +cancer_diag machi 122 +cancer_diag machi 123 +cancer_diag machi 124 +cancer_diag machi 125 +cancer_diag machi 126 +cancer_diag machi 127 +cancer_diag machi 128 +cancer_diag machi 129 +cancer_diag machi 130 +cancer_diag machi 131 +cancer_diag machi 132 +cancer_diag machi 133 +cancer_diag machi 134 +cancer_diag machi 135 +cancer_diag machi 136 +cancer_diag machi 137 +cancer_diag machi 138 +cancer_diag machi 139 +cancer_diag machi 140 +cancer_diag machi 141 +cancer_diag machi 142 +cancer_diag machi 143 +cancer_diag machi 144 +cancer_diag machi 145 +cancer_diag machi 146 +cancer_diag machi 147 +cancer_diag machi 148 +cancer_diag machi 149 +cancer_diag machi 150 +cancer_diag machi 151 +cancer_diag machi 152 +cancer_diag machi 153 +cancer_diag machi 154 +cancer_diag machi 155 +cancer_diag machi 156 +cancer_diag machi 157 +cancer_diag machi 158 +cancer_diag machi 159 +cancer_diag machi 160 +cancer_diag machi 161 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machi 9993 +birth birth_source 60 - 1960 census +birth birth_source AH - Adult Health Study +birth birth_source BR - Birth record +birth birth_source CN - Contact Card +birth birth_source CR - Cross Index +birth birth_source DE - Death Certification +birth birth_source FU - Fuhyo +birth birth_source G3 - Genetic study (GE-3) +birth birth_source JS - Residence registry inquiry (regional cancer registry) +birth birth_source KO - Koseki +birth birth_source MC - Master File Code +birth birth_source MF - Master File record +birth birth_source MO - Mortality +birth birth_source MQ - Master Sample Questionnaire +birth birth_source OT - Other +birth birth_source SK - Death certificate (regional cancer registry) +birth birth_source TE - Hibakusha Techo +birth birth_source TI - Tissue Registry Data Base +birth birth_source TR - Tumor Registry Data Base +birth birth_source YU - Mail Survey +birth birth_ind 0 - Not use +birth birth_ind 1 - use +subject city 1 - Hiroshima +subject city 2 - Nagasaki +subject sex 1 - Male +subject sex 2 - Female +subject sex 3 - Other +subject sex 4 - Unknown diff --git a/gdcdictionary/tsvs/nodes_rerf.tsv b/gdcdictionary/tsvs/jan2020_nodes_rerf.tsv similarity index 100% rename from gdcdictionary/tsvs/nodes_rerf.tsv rename to gdcdictionary/tsvs/jan2020_nodes_rerf.tsv diff --git a/gdcdictionary/tsvs/variables_rerf.tsv b/gdcdictionary/tsvs/jan2020_variables_rerf.tsv similarity index 100% rename from gdcdictionary/tsvs/variables_rerf.tsv rename to gdcdictionary/tsvs/jan2020_variables_rerf.tsv diff --git a/gdcdictionary/tsvs/nodes_rerf-v1.tsv b/gdcdictionary/tsvs/nodes_rerf-v1.tsv new file mode 100644 index 0000000..0296eb2 --- /dev/null +++ b/gdcdictionary/tsvs/nodes_rerf-v1.tsv @@ -0,0 +1,13 @@ +<$schema> <type> <nodeTerms> <namespace> <category> <program> <project> <description> <additionalProperties> <submittable> <validators> <systemProperties> <required> <uniqueKeys> <link_name> <link_backref> <link_label> <link_target> <link_multiplicity> <link_required> <link_group_exclusive> <link_group_required> <property_ref> +http://json-schema.org/draft-04/schema# study Study object https://rerf.datacommons.org/ administrative * * A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing. FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, study_description, projects id | project_id, submitter_id projects studies performed_for project many_to_one TRUE +http://json-schema.org/draft-04/schema# subject Subject object https://rerf.datacommons.org/ administrative * * The collection of all data related to a specific subject in the context of a specific project. FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, studies, sysid id | project_id, submitter_id studies subjects member_of study many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# birth Births object https://rerf.datacommons.org/ clinical * * Birth data from multiple sources FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, subjects, sysid id | project_id, submitter_id subjects births describing subject many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# dose Organ Dose object https://rerf.datacommons.org/ clinical * * Estimates of organ-level radiation dosage FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, subjects, sysid id | project_id, submitter_id subjects doses describing subject many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# cancer_diag Cancer Diagnoses object https://rerf.datacommons.org/ medical_history * * History of subject's cancer diagnoses FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, subjects, sysid id | project_id, submitter_id subjects cancer_diags describing subject many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# inutero Inutero Program object https://rerf.datacommons.org/ administrative * * Programs within the Inutero cohort FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, subjects, sysid id | project_id, submitter_id subjects inuteros member_of subject many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# f1 F1 Program object https://rerf.datacommons.org/ administrative * * Programs within the F1 cohort FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, subjects, sysid id | project_id, submitter_id subjects f1s member_of subject many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# exam AHS Exam Index object https://rerf.datacommons.org/ administrative * * Adult Health Study clinical follow-up visits FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, subjects, sysid, smp_id id | project_id, submitter_id subjects exams performed_on subject many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# exam_diag AHS Exam Diagnoses object https://rerf.datacommons.org/ medical_history * * Adult Health Study clinical diagnoses at visits FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, ahs_exam_indexes, smp_id id | project_id, submitter_id ahs_exam_indexes exam_diags derived_from exam many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# exam_meas AHS Exam Measures object https://rerf.datacommons.org/ medical_history * * Adult Health Study diagnostic measures at visits FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, ahs_exam_indexes, smp_id id | project_id, submitter_id ahs_exam_indexes exam_meas derived_from exam many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# sample Sample object https://rerf.datacommons.org/ clinical * * Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Samples can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products. FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, subjects, sysid id | project_id, submitter_id subjects samples taken_from subject many_to_one TRUE _definitions.yaml#/ubiquitous_properties +http://json-schema.org/draft-04/schema# aliquot Aliquot object https://rerf.datacommons.org/ clinical * * A portion taken from a sample used for analysis, including analytes extracted from a sample. FALSE TRUE id, project_id, state, created_datetime, updated_datetime submitter_id, type, samples, sysid id | project_id, submitter_id samples aliquots taken_from sample many_to_many TRUE _definitions.yaml#/ubiquitous_properties diff --git a/gdcdictionary/tsvs/variables_rerf-v1.tsv b/gdcdictionary/tsvs/variables_rerf-v1.tsv new file mode 100644 index 0000000..e81b7d7 --- /dev/null +++ b/gdcdictionary/tsvs/variables_rerf-v1.tsv @@ -0,0 +1,156 @@ +<node> <property> <terms> <description> <type> <pattern> <maximum> <minimum> <systemAlias> <format> <default> +subject lss Is the subject in the LSS cohort? boolean +subject inutero Is the subject in the Inutero cohort? boolean +subject f1 Is the subject in the F1 cohort? boolean +subject ahs Is the subject in the AHS cohort? boolean +subject updt Last updated date string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject lss_entry_dt Subject's date of entry into the LSS cohort string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject lss_updt Last update of subject's LSS record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject inutero_entry_dt Date when the subject became a member of the Inutero cohort string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject inutero_updt Last update of subject's Inutero record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject f1_entry_dt Date when the subject became a member of the F1 cohort string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject f1_updt Last update of subject's F1 record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject ahs_updt Last update of subject's AHS record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject mfup_last_contact Mortality follow-up date of last contact string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject death_dt Date of death of the subject string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject death_updt Last update of the subject's death record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject death_icd_updt Last update of subject's death ICD record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +birth birth_dt Date of birth string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +birth birth_updt Last update of subject's birth records string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +cancer_diag diag_dt Date of diagnosis string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +cancer_diag updt Last update of cancer diagnosis record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +inutero updt Last update of inutero program record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +f1 updt Last update of F1 program record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +exam smp_dt Date of visit string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +exam updt Last update of AHS exam index record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +exam_diag updt Last update of subject's diagnosis string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +exam_meas updt Last update of measure record string ^[0-9]{1,2}\/[0-9]{1,2}\/[0-9]{4}$ +subject mfup_last_status Mortality follow-up last known status of the subject (1 - alive, 2 - dead, 3 - lost, etc) enum +subject dose_expcity Subject's city of exposure 1 - Hiro, 2 - Naga enum +subject dose_expstatus86 Exposure status based on 1986 algorithm enum +subject dose_expstatus02 Exposure status based on 2002 algorithm enum +subject dose_prish Subject's primary shield enum +subject death_src Source of the information of subject's death (ex. Death certificate, etc.) enum +study study_objective The general objective of the study. What the study hopes to discover or determine through testing. enum +study study_design Summary of the goals the study is designed to discover. General description of the study's place in relation to a clinical application. enum +subject dose_source What is the source of the exposure information? Ex. Questionnaire enum +study study_setup A high level description of the setup used to achieve the study objectives. enum +subject sysid Globally unique identifier for subject integer +subject city 1 = Hiro, 2 = Naga enum +subject sex 1 = male enum +subject lss_sample_class Subject's recruitment class into LSS cohort? enum +subject lss_census Census info used for recruitment into LSS cohort? enum +subject mother_sysid The globally unique identifier for the subject's mother integer +subject father_sysid The globally unique identifier for the subject's father integer +subject f1_sample Subject's recruitment class into F1 cohort? enum +subject f1_ind Must = 1 enum +subject ahs_subgroup Subgroup to which the subject belongs. enum +subject ahs_exp_category Exposure category? enum +subject death_icd_rev ICD version enum +subject death_icd_grp RERF-specific ICD grouping code enum +subject dose_abscissa X coordinate of subject's position on exposure integer +subject dose_ordinate Y coordinate of subject's position on exposure integer +subject dose_gdist Subject's ground distance from explosion integer +subject dose_shloc Shield location enum +subject dose_ds02cal Calculated location? enum +subject dose_ds02cat Calculation algorithm enum +subject dose_calgroup02 Calculation information integer +birth sysid Globally unique identifier for subject integer +birth birth_ind Indicator of quality of birth data (1 - best information) enum +dose sysid Globally unique identifier for subject integer +dose dosetype Type of dose (organ) integer +cancer_diag sysid Globally unique identifier for subject integer +cancer_diag file_no Case number (or file number) for the subject integer +cancer_diag seq_no Sequence number for multiple occurrence of cancer integer +cancer_diag res 1=in city, 2=in prefecture, 3=outside prefecture, 9=unknown enum +cancer_diag city City where patient was living at the time of diagnosis 1=Hiro, 2=Naga enum +cancer_diag machi Similar to zip code enum +cancer_diag motiv Reason for subject's visit to the hospital enum +cancer_diag behavior Behavior of the cancer (1 = malignant) enum +cancer_diag onc_rev ICDO version enum +cancer_diag dco Death-certificate-only diagnosis integer +inutero sysid Globally unique identifier for subject integer +f1 sysid Globally unique identifier for subject integer +exam sysid Globally unique identifier for subject integer +exam smp_id Unique visit ID integer +exam primary_id Matches smp_id on a primary visit (subject might be asked to attend a follow-up) integer +exam_diag smp_id Visit ID integer +exam_diag icd_rev ICD version enum +exam_meas smp_id Visit ID integer +exam_meas item_no Identifier for measure integer +subject kerma_fiau02g Overall dose (gamma radiation) number +subject kerma_fiau02n Overall dose (neutron radiation) number +subject kerma_trunc02 Truncation factor number +subject kerma_adjust02 Adjustment factor number +dose a02g Gamma dose number +dose a02n Neutron dose number +exam_meas amount Measure amount number +study associated_study The submitter_id for any study with which this study is associated, paired, or matched. string +study data_description Brief description of the data being provided for this study. Free text string +study study_description A brief description of the study being performed. Free text string +study submitter_id A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node. string +study type string +subject death_icd ICD code string +birth birth_source Source of the information of subject's birth (ex. Birth certificate, etc.) enum +dose discript Organ name enum +cancer_diag icdot ICDO topography code string +cancer_diag icdom ICDO morphology code string +cancer_diag icd_grp Code to gather specific ICDOT/ICDOM values into a simple diagnosis code enum +inutero prog Program code enum +f1 prog Program code enum +exam_diag icd ICD code for diagnosis string +exam_meas unit Unit of measure string +exam_meas explain_s Short explanation string +exam_meas explain_l Long explanation string +study created_datetime _definitions.yaml#/datetime +study id _definitions.yaml#/UUID The UUID for the study. +study project_id _definitions.yaml#/project_id The dash separated combination of the program code and project name. +study state _definitions.yaml#/state +study updated_datetime _definitions.yaml#/datetime +sample tissue_type _terms.yaml#/tissue_type enum +sample preservation_method _terms.yaml#/preservation_method enum +sample method_of_sample_procurement _terms.yaml#/method_of_sample_procurement enum +sample initial_weight _terms.yaml#/initial_weight number +sample freezing_method _terms.yaml#/freezing_method string +sample days_to_collection _terms.yaml#/days_to_collection integer +sample composition _terms.yaml#/composition enum +sample biospecimen_laterality _terms.yaml#/biospecimen_laterality enum +sample biospecimen_anatomic_site _terms.yaml#/biospecimen_anatomic_site enum +aliquot aliquot_container The device in which the final aliquot is held. Slides or vials. enum +aliquot aliquot_quantity _terms.yaml#/aliquot_quantity number +aliquot aliquot_volume _terms.yaml#/aliquot_volume number +aliquot analyte_a260_a280_ratio The ratio of absorbance at 260 and 280 nm for nucleic acid analytes. number +aliquot analyte_concentration Concentration of the analyte in the aliquot. number +aliquot analyte_isolation_method The name or general description of the method used to isolate the analyte. string +aliquot analyte_type Any aspect of an aliquot used in an analysis or assay to characterize the sample. These aspects range from molecules, such as DNA and RNA, that can be extracted from the aliquot to general descriptions of the aliquot's components, such as cell count and morphology. enum +aliquot days_to_aliquot The amount of time, in days, between the date used for index and the time the aliquot was separated from the whole sample. integer +aliquot hours_to_analyte The amount of time, in hours, that it took between the sample being fractionated and the analyte being extracted. number +aliquot hours_to_preservation The amount of time, in hours, that it took between the sample being fractionated and the aliquot being frozen or otherwise preserved. number +aliquot preservation_method The method used to preserve the aliquot. enum +aliquot source_center _terms.yaml#/source_center string +aliquot storage_temperature The temperature, in centigrade, at which the aliquot was preserved and/or stored. number +exam smp_dt_year Year of visit integer +exam smp_dt_month Month of visit integer +exam smp_dt_day Day of visit integer +birth birth_dt_year Year of birth integer +birth birth_dt_month Month of birth integer +birth birth_dt_day Day of birth integer +cancer_diag diag_dt_year Year of diagnosis integer +cancer_diag diag_dt_month Month of diagnosis integer +cancer_diag diag_dt_day Day of diagnosis integer +subject lss_entry_dt_year Subject's year of entry into the LSS cohort integer +subject lss_entry_dt_month Subject's month of entry into the LSS cohort integer +subject lss_entry_dt_day Subject's day of entry into the LSS cohort integer +subject inutero_entry_dt_year Year when the subject became a member of the Inutero cohort integer +subject inutero_entry_dt_month Month when the subject became a member of the Inutero cohort integer +subject inutero_entry_dt_day Day when the subject became a member of the Inutero cohort integer +subject f1_entry_dt_year Year when the subject became a member of the F1 cohort integer +subject f1_entry_dt_month Month when the subject became a member of the F1 cohort integer +subject f1_entry_dt_day Day when the subject became a member of the F1 cohort integer +subject mfup_last_contact_year Mortality follow-up year of last contact integer +subject mfup_last_contact_month Mortality follow-up month of last contact integer +subject mfup_last_contact_day Mortality follow-up day of last contact integer +subject death_dt_year Year of death of the subject integer +subject death_dt_month Month of death of the subject integer +subject death_dt_day Day of death of the subject integer +aliquot sysid Unique subject identifier integer