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Merge pull request #4 from uc-cdis/sample_demographic_changes
fixed sample node and added demographic node
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| $schema: "http://json-schema.org/draft-04/schema#" | ||
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| id: "demographic" | ||
| title: Demographic | ||
| type: object | ||
| namespace: https://prometheus.data-commons.org/ | ||
| category: clinical | ||
| program: '*' | ||
| project: '*' | ||
| description: > | ||
| Data for the characterization of the patient by means of segementing the population (e.g., | ||
| characterization by age, sex, or race). | ||
| additionalProperties: false | ||
| submittable: true | ||
| validators: null | ||
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| systemProperties: | ||
| - id | ||
| - project_id | ||
| - state | ||
| - created_datetime | ||
| - updated_datetime | ||
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| links: | ||
| - name: subjects | ||
| backref: demographics | ||
| label: describes | ||
| target_type: subject | ||
| multiplicity: one_to_one | ||
| required: true | ||
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| required: | ||
| - type | ||
| - submitter_id | ||
| - subjects | ||
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| uniqueKeys: | ||
| #unclear if want submitter ID for clinical | ||
| - [id] | ||
| - [project_id, submitter_id] | ||
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| properties: | ||
| $ref: "_definitions.yaml#/ubiquitous_properties" | ||
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| # HARMONIZED VARIABLES ACROSS GTEX AND TOPMED PROJECTS | ||
| age_at_index: | ||
| description: > | ||
| The subject's age (in years) on the reference or anchor date used during date obfuscation (HARMONIZED). If age is greater than 89 years, see 'age_at_index_gt89'. | ||
| type: number | ||
| maximum: 89 | ||
| minimum: 0 | ||
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| age_at_index_gt89: | ||
| description: > | ||
| Indicate whether the subject's age (in years) on the reference or anchor date used during date obfuscation (HARMONIZED) is greater than 89 years. | ||
| enum: | ||
| - "Yes" | ||
| - "No" | ||
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| annotated_sex: | ||
| term: | ||
| $ref: "_terms.yaml#/gender" | ||
| enum: | ||
| - female | ||
| - male | ||
| - unknown | ||
| - unspecified | ||
| - not reported | ||
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| race: | ||
| term: | ||
| $ref: "_terms.yaml#/race" | ||
| description: > | ||
| Harmonized race category of participant. Acceptable values: white,american indian or alaska native,black or african american,asian,native hawaiian or other pacific islander,hispanic,multiple,other,Unknown,not reported,not allowed to collect (HARMONIZED) | ||
| type: array | ||
| items: | ||
| enum: | ||
| - "white" | ||
| - "american indian or alaska native" | ||
| - "black or african american" | ||
| - "asian" | ||
| - "native hawaiian or other pacific islander" | ||
| - "hispanic" | ||
| - "multiple" | ||
| - "other" | ||
| - "Unknown" | ||
| - "not reported" | ||
| - "not allowed to collect" | ||
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| ethnicity: | ||
| term: | ||
| $ref: "_terms.yaml#/ethnicity" | ||
| enum: | ||
| - "hispanic or latino" | ||
| - "inconsistent/contradictory" | ||
| - "not hispanic or latino" | ||
| - "Unknown" | ||
| - "not reported" | ||
| - "not allowed to collect" | ||
|
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| weight: | ||
| term: | ||
| $ref: "_terms.yaml#/weight" | ||
| type: number | ||
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| bmi_baseline: | ||
| term: | ||
| $ref: "_terms.yaml#/bmi" | ||
| type: number | ||
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| height_baseline: | ||
| term: | ||
| $ref: "_terms.yaml#/height" | ||
| type: number | ||
|
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| age_at_height_baseline: | ||
| description: > | ||
| age at measurement of height_baseline (years) (HARMONIZED) | ||
| type: number | ||
|
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| unit_height_baseline: | ||
| description: > | ||
| harmonization unit for height_baseline (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
|
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| unit_race: | ||
| description: > | ||
| harmonization unit for race (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
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| unit_ethnicity: | ||
| description: > | ||
| harmonization unit for ethnicity (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
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| hispanic_subgroup: | ||
| description: > | ||
| classification of Hispanic/Latino background for Hispanic/Latino subjects where country or region of origin information is available (HARMONIZED) | ||
| enum: | ||
| - "CentralAmerican" | ||
| - "CostaRican" | ||
| - "Cuban" | ||
| - "Dominican" | ||
| - "Mexican" | ||
| - "PuertoRican" | ||
| - "SouthAmerican" | ||
| - "Multiple" | ||
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| unit_hispanic_subgroup: | ||
| description: > | ||
| harmonization unit for hispanic_subgroup (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
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| age_at_bmi_baseline: | ||
| description: > | ||
| age at measurement of bmi (years) (HARMONIZED) | ||
| type: number | ||
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| age_at_weight_baseline: | ||
| description: > | ||
| age at measurement of weight_baseline (years) (HARMONIZED) | ||
| type: number | ||
|
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| subcohort: | ||
| description: > | ||
| A distinct subgroup within a study, generally indicating subjects who share similar characteristics due to study design. Subjects may belong to only one subcohort. (HARMONIZED) | ||
| enum: | ||
| - "Amish_HAPI" | ||
| - "Amish_Longevity" | ||
| - "Amish_Wellness" | ||
| - "ARIC_NoSubcohortStructure" | ||
| - "CARDIA_NoSubcohortStructure" | ||
| - "CFS_NoSubcohortStructure" | ||
| - "CHS_AfricanAmerican" | ||
| - "CHS_Original" | ||
| - "COPDGene_NoSubcohortStructure" | ||
| - "CRA_NoSubcohortStructure" | ||
| - "FHS_Gen3" | ||
| - "FHS_NewOffspringSpouse" | ||
| - "FHS_Offspring" | ||
| - "FHS_Omni1" | ||
| - "FHS_Omni2" | ||
| - "FHS_Original" | ||
| - "GENOA_AfricanAmerican" | ||
| - "GENOA_EuropeanAmerican" | ||
| - "GOLDN_NoSubcohortStructure" | ||
| - "HCHS_SOL_NoSubcohortStructure" | ||
| - "HVH_NoSubcohortStructure" | ||
| - "JHS_NoSubcohortStructure" | ||
| - "Mayo_VTE_GENEVA" | ||
| - "MESA_AirNR" | ||
| - "MESA_Classic" | ||
| - "MESA_Family" | ||
| - "SAS_NoSubcohortStructure" | ||
| - "WHI_ClinicalTrial" | ||
| - "WHI_ObservationalStudy" | ||
|
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| unit_annotated_sex: | ||
| description: > | ||
| harmonization unit for annotated_sex (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
|
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| unit_bmi_baseline: | ||
| description: > | ||
| harmonization unit for bmi_baseline (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
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| unit_subcohort: | ||
| description: > | ||
| harmonization unit for subcohort (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
|
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| unit_weight_baseline: | ||
| description: > | ||
| harmonization unit for weight_baseline (A "harmonization unit" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) | ||
| type: string | ||
|
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| weight_baseline: | ||
| description: > | ||
| Body weight at baseline. (kg) (HARMONIZED) | ||
| type: number | ||
|
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| population: | ||
| description: > | ||
| CHB Han Chinese in Beijing, China EAS; JPT Japanese in Tokyo, Japan EAS; CHS Southern Han Chinese EAS; CDX Chinese Dai in Xishuangbanna, China EAS; KHV Kinh in Ho Chi Minh City, Vietnam EAS; CEU Utah Residents (CEPH) with Northern and Western European Ancestry EUR; TSI Toscani in Italia EUR; FIN Finnish in Finland EUR; GBR British in England and Scotland EUR; IBS Iberian Population in Spain EUR; YRI Yoruba in Ibadan, Nigeria AFR; LWK Luhya in Webuye, Kenya AFR; GWD Gambian in Western Divisions in the Gambia AFR; MSL Mende in Sierra Leone AFR; ESN Esan in Nigeria AFR; ASW Americans of African Ancestry in SW USA AFR; ACB African Caribbeans in Barbados AFR; MXL Mexican Ancestry from Los Angeles USA AMR; PUR Puerto Ricans from Puerto Rico AMR; CLM Colombians from Medellin, Colombia AMR; PEL Peruvians from Lima, Peru AMR; GIH Gujarati Indian from Houston, Texas SAS; PJL Punjabi from Lahore, Pakistan SAS; BEB Bengali from Bangladesh SAS; STU Sri Lankan Tamil from the UK SAS; ITU Indian Telugu from the UK | ||
| enum: | ||
| - "CHB" | ||
| - "JPT" | ||
| - "CHS" | ||
| - "CDX" | ||
| - "KHV" | ||
| - "CEU" | ||
| - "TSI" | ||
| - "FIN" | ||
| - "GBR" | ||
| - "IBS" | ||
| - "YRI" | ||
| - "LWK" | ||
| - "GWD" | ||
| - "MSL" | ||
| - "ESN" | ||
| - "ASW" | ||
| - "ACB" | ||
| - "MXL" | ||
| - "PUR" | ||
| - "CLM" | ||
| - "PEL" | ||
| - "GIH" | ||
| - "PJL" | ||
| - "BEB" | ||
| - "STU" | ||
| - "ITU" | ||
| - "other" | ||
| - "Unknown" | ||
| - "not reported" | ||
| - "not allowed to collect" | ||
|
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| subjects: | ||
| $ref: "_definitions.yaml#/to_one" |
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