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Diff between CRDCH model in PR 112 vs v1.0.1
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| --- ccdhmodel.yaml 2021-09-16 14:57:11.000000000 -0400 | |
| +++ crdch_model.yaml 2021-09-16 14:56:48.000000000 -0400 | |
| @@ -1,84 +1,84 @@ | |
| name: CRDC-H | |
| notes: | |
| - Derived from [CDM_Dictionary_v1 (Active)](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4) | |
| -id: https://example.org/ccdh | |
| -version: v1.0-3-g99ffd30c-dirty | |
| +id: https://example.org/crdch | |
| +version: v0.2-346-g2a758251 | |
| imports: | |
| - linkml:types | |
| license: https://creativecommons.org/publicdomain/zero/1.0/ | |
| prefixes: | |
| linkml: https://w3id.org/linkml/ | |
| - ccdh: https://example.org/ccdh/ | |
| + crdch: https://example.org/crdch/ | |
| NCIT: http://purl.obolibrary.org/obo/NCIT_ | |
| GDC: http://example.org/gdc/ | |
| PDC: http://example.org/pdc/ | |
| ICDC: http://example.org/icdc/ | |
| HTAN: http://example.org/htan/ | |
| -default_prefix: ccdh | |
| +default_prefix: crdch | |
| types: | |
| - ccdh_string: | |
| - name: ccdh_string | |
| + crdch_string: | |
| + name: crdch_string | |
| description: A sequence of Unicode characters. There are no limits on the number | |
| of characters in the string. | |
| notes: | |
| - - Derived from [ccdh_string in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| + - Derived from [crdch_string in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| typeof: string | |
| - ccdh_integer: | |
| - name: ccdh_integer | |
| + crdch_integer: | |
| + name: crdch_integer | |
| description: An integer number. This data type is based on the decimal type, | |
| but the fractional component is not allowed. There are no restrictions on the | |
| size of the integer. | |
| notes: | |
| - - Derived from [ccdh_integer in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| + - Derived from [crdch_integer in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| typeof: integer | |
| - ccdh_decimal: | |
| - name: ccdh_decimal | |
| + crdch_decimal: | |
| + name: crdch_decimal | |
| description: A rational number that has a decimal representation. This data type | |
| does not restrict the size or precision of the number. | |
| notes: | |
| - - Derived from [ccdh_decimal in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| + - Derived from [crdch_decimal in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| typeof: decimal | |
| - ccdh_boolean: | |
| - name: ccdh_boolean | |
| + crdch_boolean: | |
| + name: crdch_boolean | |
| description: "Value representing either \u201Ctrue\u201D or \u201Cfalse\u201D\ | |
| . Permissible values (case-sensitive) = \u201Ctrue\u201D, \u201Cfalse\u201D\ | |
| , \u201C1\u201D, \u201C0\u201D." | |
| notes: | |
| - - Derived from [ccdh_boolean in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| + - Derived from [crdch_boolean in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| typeof: boolean | |
| - ccdh_dateTime: | |
| - name: ccdh_dateTime | |
| + crdch_dateTime: | |
| + name: crdch_dateTime | |
| description: A date and time string specified using a specialized concatenation | |
| of the date and time data types, in the general format YYYY-MM-DDThh:mm:ss+zz:zz. | |
| notes: | |
| - - Derived from [ccdh_dateTime in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| + - Derived from [crdch_dateTime in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| typeof: datetime | |
| - ccdh_curie: | |
| - name: ccdh_curie | |
| + crdch_curie: | |
| + name: crdch_curie | |
| description: "A compact URI (CURIE), which is a bipartite identifier of the form\ | |
| \ prefix:reference, in which the prefix is a convenient abbreviation of a URI.\ | |
| \ It is expressed in the format \u201Cprefix:reference\u201D. When a mapping\ | |
| \ of prefix to base URI is provided (external to this data type), a CURIE may\ | |
| \ be mapped to a URI." | |
| notes: | |
| - - Derived from [ccdh_curie in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| + - Derived from [crdch_curie in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| typeof: uriorcurie | |
| - ccdh_code: | |
| - name: ccdh_code | |
| + crdch_code: | |
| + name: crdch_code | |
| description: '' | |
| notes: | |
| - - Derived from [ccdh_code in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| + - Derived from [crdch_code in sheet Primitives](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=497370447) | |
| typeof: string | |
| enums: | |
| - enum_CCDH_AlcoholExposureObservation_category: | |
| - name: enum_CCDH_AlcoholExposureObservation_category | |
| + enum_CRDCH_AlcoholExposureObservation_category: | |
| + name: enum_CRDCH_AlcoholExposureObservation_category | |
| description: Autogenerated Enumeration for CRDC-H AlcoholExposureObservation category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.AlcoholExposureObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.AlcoholExposureObservation.category | |
| - code_set_version: '2021-06-08T21:46:34.657367+00:00' | |
| - enum_CCDH_AlcoholExposureObservation_observation_type: | |
| - name: enum_CCDH_AlcoholExposureObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:33.878100+00:00' | |
| + enum_CRDCH_AlcoholExposureObservation_observation_type: | |
| + name: enum_CRDCH_AlcoholExposureObservation_observation_type | |
| description: Types of observations about a Subject's exposure to alcohol. | |
| notes: | |
| - Derived from [AlcoholExposureObservation.observation_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| @@ -99,49 +99,27 @@ | |
| text: alcohol_intensity | |
| description: Category to describe the patient's current level of alcohol use | |
| as self-reported by the patient. | |
| - enum_CCDH_AlcoholExposureObservation_method_type: | |
| - name: enum_CCDH_AlcoholExposureObservation_method_type | |
| + enum_CRDCH_AlcoholExposureObservation_method_type: | |
| + name: enum_CRDCH_AlcoholExposureObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H AlcoholExposureObservation method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.AlcoholExposureObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.AlcoholExposureObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:34.994186+00:00' | |
| - enum_CCDH_AlcoholExposureObservation_valueCodeableConcept: | |
| - name: enum_CCDH_AlcoholExposureObservation_valueCodeableConcept | |
| - description: Autogenerated Enumeration for CRDC-H AlcoholExposureObservation valueCodeableConcept | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.AlcoholExposureObservation.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.AlcoholExposureObservation.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:35.145050+00:00' | |
| - permissible_values: | |
| - Unknown: | |
| - text: Unknown | |
| - Heavy Drinker: | |
| - text: Heavy Drinker | |
| - Drinker: | |
| - text: Drinker | |
| - Occasional Drinker: | |
| - text: Occasional Drinker | |
| - description: Occasional Drinker | |
| - Not Reported: | |
| - text: Not Reported | |
| - Lifelong Non-Drinker: | |
| - text: Lifelong Non-Drinker | |
| - Non-Drinker: | |
| - text: Non-Drinker | |
| - 'No': | |
| - text: 'No' | |
| - description: 'No' | |
| - 'Yes': | |
| - text: 'Yes' | |
| - description: 'Yes' | |
| - enum_CCDH_BodySite_site: | |
| - name: enum_CCDH_BodySite_site | |
| + code_set_version: '2021-09-16T18:44:34.406479+00:00' | |
| + enum_CRDCH_AlcoholExposureObservation_value_enum: | |
| + name: enum_CRDCH_AlcoholExposureObservation_value_enum | |
| + description: Autogenerated Enumeration for CRDC-H AlcoholExposureObservation value_enum | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.AlcoholExposureObservation.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.AlcoholExposureObservation.value_enum | |
| + code_set_version: '2021-09-16T18:44:34.514806+00:00' | |
| + enum_CRDCH_BodySite_site: | |
| + name: enum_CRDCH_BodySite_site | |
| description: Autogenerated Enumeration for CRDC-H BodySite site | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.BodySite.site"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.BodySite.site | |
| - code_set_version: '2021-06-08T21:46:35.307181+00:00' | |
| + code_set_version: '2021-09-16T18:44:34.625170+00:00' | |
| permissible_values: | |
| Eye and adnexa: | |
| text: Eye and adnexa | |
| @@ -1626,13 +1604,13 @@ | |
| text: Paranasal Sinuses | |
| Submandibular Gland: | |
| text: Submandibular Gland | |
| - enum_CCDH_BodySite_qualifier: | |
| - name: enum_CCDH_BodySite_qualifier | |
| + enum_CRDCH_BodySite_qualifier: | |
| + name: enum_CRDCH_BodySite_qualifier | |
| description: Autogenerated Enumeration for CRDC-H BodySite qualifier | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.BodySite.qualifier"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.BodySite.qualifier | |
| - code_set_version: '2021-06-08T21:46:35.970279+00:00' | |
| + code_set_version: '2021-09-16T18:44:35.538945+00:00' | |
| permissible_values: | |
| Bilateral: | |
| text: Bilateral | |
| @@ -1647,22 +1625,22 @@ | |
| description: Right | |
| Not Reported: | |
| text: Not Reported | |
| - enum_CCDH_BiologicProduct_product_type: | |
| - name: enum_CCDH_BiologicProduct_product_type | |
| + enum_CRDCH_BiologicProduct_product_type: | |
| + name: enum_CRDCH_BiologicProduct_product_type | |
| description: Autogenerated Enumeration for CRDC-H BiologicProduct product_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.BiologicProduct.product_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.BiologicProduct.product_type | |
| - code_set_version: '2021-06-08T21:46:36.125883+00:00' | |
| - enum_CCDH_CancerGradeObservation_category: | |
| - name: enum_CCDH_CancerGradeObservation_category | |
| + code_set_version: '2021-09-16T18:44:35.652466+00:00' | |
| + enum_CRDCH_CancerGradeObservation_category: | |
| + name: enum_CRDCH_CancerGradeObservation_category | |
| description: Autogenerated Enumeration for CRDC-H CancerGradeObservation category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.CancerGradeObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservation.category | |
| - code_set_version: '2021-06-08T21:46:36.275105+00:00' | |
| - enum_CCDH_CancerGradeObservation_observation_type: | |
| - name: enum_CCDH_CancerGradeObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:35.761495+00:00' | |
| + enum_CRDCH_CancerGradeObservation_observation_type: | |
| + name: enum_CRDCH_CancerGradeObservation_observation_type | |
| description: '' | |
| notes: | |
| - Derived from [CancerGradeObservation.observation_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| @@ -1709,106 +1687,29 @@ | |
| text: tumor_grade | |
| description: Text value to express the degree of abnormality of cancer cells, | |
| a measure of differentiation and aggressiveness. | |
| - enum_CCDH_CancerGradeObservation_method_type: | |
| - name: enum_CCDH_CancerGradeObservation_method_type | |
| + enum_CRDCH_CancerGradeObservation_method_type: | |
| + name: enum_CRDCH_CancerGradeObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H CancerGradeObservation method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.CancerGradeObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:36.568736+00:00' | |
| - enum_CCDH_CancerGradeObservation_valueCodeableConcept: | |
| - name: enum_CCDH_CancerGradeObservation_valueCodeableConcept | |
| - description: Autogenerated Enumeration for CRDC-H CancerGradeObservation valueCodeableConcept | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.CancerGradeObservation.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservation.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:36.725365+00:00' | |
| - permissible_values: | |
| - Pattern 1: | |
| - text: Pattern 1 | |
| - Pattern 4: | |
| - text: Pattern 4 | |
| - Pattern 5: | |
| - text: Pattern 5 | |
| - Pattern 3: | |
| - text: Pattern 3 | |
| - Pattern 2: | |
| - text: Pattern 2 | |
| - Not Reported: | |
| - text: Not Reported | |
| - Unknown: | |
| - text: Unknown | |
| - Low Grade (G1): | |
| - text: Low Grade (G1) | |
| - description: Enneking Low Surgical Grade | |
| - High Grade (G2): | |
| - text: High Grade (G2) | |
| - description: Enneking High Surgical Grade | |
| - Low Grade: | |
| - text: Low Grade | |
| - description: Low Grade | |
| - GX: | |
| - text: GX | |
| - description: Grade Cannot be Assessed | |
| - G1: | |
| - text: G1 | |
| - description: Well Differentiated | |
| - High Grade: | |
| - text: High Grade | |
| - description: High Grade | |
| - G2: | |
| - text: G2 | |
| - description: Moderately Differentiated | |
| - G3: | |
| - text: G3 | |
| - description: Poorly Differentiated | |
| - G4: | |
| - text: G4 | |
| - description: Undifferentiated Histology | |
| - Intermediate Grade: | |
| - text: Intermediate Grade | |
| - description: Intermediate Grade | |
| - GB: | |
| - text: GB | |
| - description: Borderline Histologic Grade | |
| - not reported: | |
| - text: not reported | |
| - High Grade Dysplasia: | |
| - text: High Grade Dysplasia | |
| - Indefinite for Dysplasia: | |
| - text: Indefinite for Dysplasia | |
| - Low Grade Dysplasia: | |
| - text: Low Grade Dysplasia | |
| - Negative/ No Dysplasia: | |
| - text: Negative/ No Dysplasia | |
| - Group 1: | |
| - text: Group 1 | |
| - Group 3: | |
| - text: Group 3 | |
| - Group 5: | |
| - text: Group 5 | |
| - Group 4: | |
| - text: Group 4 | |
| - Group 2: | |
| - text: Group 2 | |
| - Differentiating: | |
| - text: Differentiating | |
| - description: Differentiating Neuroblastoma | |
| - Undifferentiated: | |
| - text: Undifferentiated | |
| - description: Undifferentiated Neuroblastoma | |
| - Poorly Differentiated: | |
| - text: Poorly Differentiated | |
| - description: Poorly Differentiated Neuroblastoma | |
| - enum_CCDH_CancerGradeObservationSet_category: | |
| - name: enum_CCDH_CancerGradeObservationSet_category | |
| + code_set_version: '2021-09-16T18:44:35.974664+00:00' | |
| + enum_CRDCH_CancerGradeObservation_value_enum: | |
| + name: enum_CRDCH_CancerGradeObservation_value_enum | |
| + description: Autogenerated Enumeration for CRDC-H CancerGradeObservation value_enum | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.CancerGradeObservation.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservation.value_enum | |
| + code_set_version: '2021-09-16T18:44:36.083906+00:00' | |
| + enum_CRDCH_CancerGradeObservationSet_category: | |
| + name: enum_CRDCH_CancerGradeObservationSet_category | |
| description: Autogenerated Enumeration for CRDC-H CancerGradeObservationSet category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.CancerGradeObservationSet.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerGradeObservationSet.category | |
| - code_set_version: '2021-06-08T21:46:36.909181+00:00' | |
| - enum_CCDH_CancerGradeObservationSet_method_type: | |
| - name: enum_CCDH_CancerGradeObservationSet_method_type | |
| + code_set_version: '2021-09-16T18:44:36.191138+00:00' | |
| + enum_CRDCH_CancerGradeObservationSet_method_type: | |
| + name: enum_CRDCH_CancerGradeObservationSet_method_type | |
| description: A morphologic classification system of malignant tumors, usually | |
| relating to disease progression and clinical outcome. It is based upon the presence | |
| or absence of several morphologic parameters, including tumor cell necrosis, | |
| @@ -1830,15 +1731,15 @@ | |
| Unspecified grading system: | |
| text: Unspecified grading system | |
| description: '' | |
| - enum_CCDH_CancerStageObservation_category: | |
| - name: enum_CCDH_CancerStageObservation_category | |
| + enum_CRDCH_CancerStageObservation_category: | |
| + name: enum_CRDCH_CancerStageObservation_category | |
| description: Autogenerated Enumeration for CRDC-H CancerStageObservation category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.CancerStageObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservation.category | |
| - code_set_version: '2021-06-08T21:46:37.208984+00:00' | |
| - enum_CCDH_CancerStageObservation_observation_type: | |
| - name: enum_CCDH_CancerStageObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:36.400019+00:00' | |
| + enum_CRDCH_CancerStageObservation_observation_type: | |
| + name: enum_CRDCH_CancerStageObservation_observation_type | |
| description: Types of observations or components of a cancer staging assessment. | |
| notes: | |
| - Derived from [CancerStageObservation.observation_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| @@ -1895,462 +1796,29 @@ | |
| text: Ann Arbor Substage Modifier | |
| description: The substage classification modifiers amend each stage based | |
| on distinct features. | |
| - enum_CCDH_CancerStageObservation_method_type: | |
| - name: enum_CCDH_CancerStageObservation_method_type | |
| + enum_CRDCH_CancerStageObservation_method_type: | |
| + name: enum_CRDCH_CancerStageObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H CancerStageObservation method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.CancerStageObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:37.506605+00:00' | |
| - enum_CCDH_CancerStageObservation_valueCodeableConcept: | |
| - name: enum_CCDH_CancerStageObservation_valueCodeableConcept | |
| - description: Autogenerated Enumeration for CRDC-H CancerStageObservation valueCodeableConcept | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.CancerStageObservation.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservation.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:37.645523+00:00' | |
| - permissible_values: | |
| - N2: | |
| - text: N2 | |
| - description: N2 Stage Finding | |
| - N3: | |
| - text: N3 | |
| - description: N3 Stage Finding | |
| - N0 (i-): | |
| - text: N0 (i-) | |
| - description: N0 (i-) Stage Finding | |
| - N3b: | |
| - text: N3b | |
| - description: N3b Stage Finding | |
| - NX: | |
| - text: NX | |
| - description: NX Stage Finding | |
| - N1bIII: | |
| - text: N1bIII | |
| - description: N1bIII Stage Finding | |
| - N1bII: | |
| - text: N1bII | |
| - description: N1bII Stage Finding | |
| - N0 (mol+): | |
| - text: N0 (mol+) | |
| - description: N0 (mol+) Stage Finding | |
| - N1c: | |
| - text: N1c | |
| - description: N1c Stage Finding | |
| - N1b: | |
| - text: N1b | |
| - description: N1b Stage Finding | |
| - N1bIV: | |
| - text: N1bIV | |
| - description: N1bIV Stage Finding | |
| - N1: | |
| - text: N1 | |
| - description: N1 Stage Finding | |
| - N4: | |
| - text: N4 | |
| - description: N4 Stage Finding | |
| - N2b: | |
| - text: N2b | |
| - description: N2b Stage Finding | |
| - N0 (mol-): | |
| - text: N0 (mol-) | |
| - description: N0 (mol-) Stage Finding | |
| - N0: | |
| - text: N0 | |
| - description: N0 Stage Finding | |
| - N3a: | |
| - text: N3a | |
| - description: N3a Stage Finding | |
| - N1a: | |
| - text: N1a | |
| - description: N1a Stage Finding | |
| - N2c: | |
| - text: N2c | |
| - description: N2c Stage Finding | |
| - N0 (i+): | |
| - text: N0 (i+) | |
| - description: N0 (i+) Stage Finding | |
| - N2a: | |
| - text: N2a | |
| - description: N2a Stage Finding | |
| - N1mi: | |
| - text: N1mi | |
| - description: N1mi Stage Finding | |
| - Unknown: | |
| - text: Unknown | |
| - description: Unknown | |
| - Not Reported: | |
| - text: Not Reported | |
| - description: Not Reported | |
| - N1bI: | |
| - text: N1bI | |
| - description: N1bI Stage Finding | |
| - N3c: | |
| - text: N3c | |
| - description: N3c Stage Finding | |
| - 'Yes': | |
| - text: 'Yes' | |
| - description: 'Yes' | |
| - 'No': | |
| - text: 'No' | |
| - description: 'No' | |
| - Not Allowed To Collect: | |
| - text: Not Allowed To Collect | |
| - Stage IVB: | |
| - text: Stage IVB | |
| - description: FIGO Stage IVB | |
| - Stage II: | |
| - text: Stage II | |
| - description: SIOP/COG/NWTSG Stage II | |
| - Stage IIA: | |
| - text: Stage IIA | |
| - description: Enneking Stage IIA | |
| - Stage 0: | |
| - text: Stage 0 | |
| - description: FIGO Stage 0 | |
| - Stage IIID: | |
| - text: Stage IIID | |
| - Stage IV: | |
| - text: Stage IV | |
| - description: SIOP/COG/NWTSG Stage IV | |
| - Stage IIIA: | |
| - text: Stage IIIA | |
| - description: FIGO Stage IIIA | |
| - Stage III: | |
| - text: Stage III | |
| - description: SIOP/COG/NWTSG Stage III | |
| - Stage IVC: | |
| - text: Stage IVC | |
| - description: Stage IVC | |
| - Stage Tis: | |
| - text: Stage Tis | |
| - description: Tis Stage Finding | |
| - Stage IVA: | |
| - text: Stage IVA | |
| - description: FIGO Stage IVA | |
| - Stage IS: | |
| - text: Stage IS | |
| - description: Stage Is | |
| - Stage IA2: | |
| - text: Stage IA2 | |
| - description: FIGO Stage IA2 | |
| - Stage IB: | |
| - text: Stage IB | |
| - description: Enneking Stage IB | |
| - Stage 0a: | |
| - text: Stage 0a | |
| - description: Stage 0a | |
| - Stage IIIB: | |
| - text: Stage IIIB | |
| - description: FIGO Stage IIIB | |
| - Stage IIC: | |
| - text: Stage IIC | |
| - Stage IC: | |
| - text: Stage IC | |
| - description: FIGO Stage IC | |
| - Stage IB2: | |
| - text: Stage IB2 | |
| - description: FIGO Stage IB2 | |
| - Stage IIIC: | |
| - text: Stage IIIC | |
| - description: FIGO Stage IIIC | |
| - Stage IIA1: | |
| - text: Stage IIA1 | |
| - description: Stage IIA1 Cervical Cancer | |
| - Stage IB1: | |
| - text: Stage IB1 | |
| - description: FIGO Stage IB1 | |
| - Stage IIIC1: | |
| - text: Stage IIIC1 | |
| - description: FIGO Stage IIIC1 | |
| - Stage IA: | |
| - text: Stage IA | |
| - description: Enneking Stage IA | |
| - Stage IA3: | |
| - text: Stage IA3 | |
| - Stage IIA2: | |
| - text: Stage IIA2 | |
| - description: Stage IIA2 Cervical Cancer | |
| - Stage IIB: | |
| - text: Stage IIB | |
| - description: Enneking Stage IIB | |
| - Stage IIIC2: | |
| - text: Stage IIIC2 | |
| - description: FIGO Stage IIIC2 | |
| - Stage I: | |
| - text: Stage I | |
| - description: SIOP/COG/NWTSG Stage I | |
| - Stage X: | |
| - text: Stage X | |
| - description: Stage X | |
| - Stage 0is: | |
| - text: Stage 0is | |
| - description: Stage 0is | |
| - Stage IA1: | |
| - text: Stage IA1 | |
| - description: FIGO Stage IA1 | |
| - Ta: | |
| - text: Ta | |
| - description: Ta Stage Finding | |
| - T3: | |
| - text: T3 | |
| - description: T3 Stage Finding | |
| - T2b: | |
| - text: T2b | |
| - description: T2b Stage Finding | |
| - T2a2: | |
| - text: T2a2 | |
| - description: Stage T2a2 Finding | |
| - T1a: | |
| - text: T1a | |
| - description: T1a Stage Finding | |
| - T3d: | |
| - text: T3d | |
| - description: T3d Stage Finding | |
| - T4: | |
| - text: T4 | |
| - description: T4 Stage Finding | |
| - T4a: | |
| - text: T4a | |
| - description: T4a Stage Finding | |
| - Tis: | |
| - text: Tis | |
| - description: Tis Stage Finding | |
| - T3a: | |
| - text: T3a | |
| - description: T3a Stage Finding | |
| - T2c: | |
| - text: T2c | |
| - description: T2c Stage Finding | |
| - T1b2: | |
| - text: T1b2 | |
| - description: T1b2 Stage Finding | |
| - T0: | |
| - text: T0 | |
| - description: T0 Stage Finding | |
| - T2a: | |
| - text: T2a | |
| - description: T2a Stage Finding | |
| - T1mi: | |
| - text: T1mi | |
| - description: T1mi Stage Finding | |
| - T4b: | |
| - text: T4b | |
| - description: T4b Stage Finding | |
| - T1a1: | |
| - text: T1a1 | |
| - description: Stage T1a1 Finding | |
| - T1b1: | |
| - text: T1b1 | |
| - description: T1b1 Stage Finding | |
| - TX: | |
| - text: TX | |
| - description: TX Stage Finding | |
| - T2d: | |
| - text: T2d | |
| - description: T2d Stage Finding | |
| - T4d: | |
| - text: T4d | |
| - description: T4d Stage Finding | |
| - T2a1: | |
| - text: T2a1 | |
| - description: Stage T2a1 Finding | |
| - Tis (LCIS): | |
| - text: Tis (LCIS) | |
| - description: Tis Stage Finding Lobular Breast Carcinoma In Situ | |
| - T2: | |
| - text: T2 | |
| - description: T2 Stage Finding | |
| - Tis (DCIS): | |
| - text: Tis (DCIS) | |
| - description: Tis Stage Finding Ductal Breast Carcinoma In Situ | |
| - T4e: | |
| - text: T4e | |
| - description: T4e Stage Finding | |
| - T3c: | |
| - text: T3c | |
| - description: T3c Stage Finding | |
| - T1: | |
| - text: T1 | |
| - description: T1 Stage Finding | |
| - T1a2: | |
| - text: T1a2 | |
| - description: Stage T1a2 Finding | |
| - T3b: | |
| - text: T3b | |
| - description: T3b Stage Finding | |
| - T4c: | |
| - text: T4c | |
| - description: T4c Stage Finding | |
| - T1b: | |
| - text: T1b | |
| - description: T1b Stage Finding | |
| - Tis (Paget's): | |
| - text: Tis (Paget's) | |
| - description: Tis Stage Finding Paget Disease of the Breast without Invasive | |
| - Carcinoma | |
| - T1c: | |
| - text: T1c | |
| - description: T1c Stage Finding | |
| - M1d: | |
| - text: M1d | |
| - M1a: | |
| - text: M1a | |
| - description: M1a Stage Finding | |
| - M1: | |
| - text: M1 | |
| - description: M1 Stage Finding | |
| - MX: | |
| - text: MX | |
| - description: MX Stage Finding | |
| - M1c: | |
| - text: M1c | |
| - description: M1c Stage Finding | |
| - cM0 (i+): | |
| - text: cM0 (i+) | |
| - description: cM0 (i+) Stage Finding | |
| - M2: | |
| - text: M2 | |
| - description: M2 Stage Finding | |
| - M0: | |
| - text: M0 | |
| - description: M0 Stage Finding | |
| - M1b: | |
| - text: M1b | |
| - description: M1b Stage Finding | |
| - Stage 4S: | |
| - text: Stage 4S | |
| - description: INSS Stage 4S | |
| - Stage 3: | |
| - text: Stage 3 | |
| - description: INSS Stage 3 | |
| - Stage 4: | |
| - text: Stage 4 | |
| - description: INSS Stage 4 | |
| - Stage 2A: | |
| - text: Stage 2A | |
| - description: INSS Stage 2A | |
| - Stage 1: | |
| - text: Stage 1 | |
| - description: INSS Stage 1 | |
| - Stage 2B: | |
| - text: Stage 2B | |
| - description: INSS Stage 2B | |
| - II: | |
| - text: II | |
| - description: II | |
| - III: | |
| - text: III | |
| - description: III | |
| - I: | |
| - text: I | |
| - description: I | |
| - '4': | |
| - text: '4' | |
| - description: Metastatic disease | |
| - '2': | |
| - text: '2' | |
| - description: Unfavorable site, <= 5 cm, no regional node involvement | |
| - '1': | |
| - text: '1' | |
| - description: Favorable Site | |
| - '3': | |
| - text: '3' | |
| - description: Unfavorable site, >5cm, and/or regional node involvement | |
| - Stage IVb: | |
| - text: Stage IVb | |
| - Stage IVa: | |
| - text: Stage IVa | |
| - Stage IIa: | |
| - text: Stage IIa | |
| - Stage IIb: | |
| - text: Stage IIb | |
| - No Metastasis (M0): | |
| - text: No Metastasis (M0) | |
| - Regional or Distant Metastasis (M1): | |
| - text: Regional or Distant Metastasis (M1) | |
| - Stage II Cervix: | |
| - text: Stage II Cervix | |
| - description: Stage II Cervix | |
| - Stage IB Cervix: | |
| - text: Stage IB Cervix | |
| - description: Stage IB Cervix | |
| - Stage IIC1: | |
| - text: Stage IIC1 | |
| - Stage IIA Cervix: | |
| - text: Stage IIA Cervix | |
| - description: Stage IIA Cervix | |
| - 3rd: | |
| - text: 3rd | |
| - description: Third Edition (published 1988) | |
| - 2nd: | |
| - text: 2nd | |
| - description: Second Edition (published 1983) | |
| - 5th: | |
| - text: 5th | |
| - description: Fifth Edition (published 1997) | |
| - 8th: | |
| - text: 8th | |
| - description: Eighth Edition | |
| - 4th: | |
| - text: 4th | |
| - description: Fourth Edition (published 1992) | |
| - 6th: | |
| - text: 6th | |
| - description: Sixth Edition (published 2002) | |
| - 1st: | |
| - text: 1st | |
| - description: First Edition | |
| - 7th: | |
| - text: 7th | |
| - description: Seventh Edition | |
| - Extracompartmental (T2): | |
| - text: Extracompartmental (T2) | |
| - description: Extracompartmental Tumor | |
| - Intracompartmental (T1): | |
| - text: Intracompartmental (T1) | |
| - description: Intracompartmental Tumor | |
| - Good Prognosis: | |
| - text: Good Prognosis | |
| - Poor Prognosis: | |
| - text: Poor Prognosis | |
| - Intermediate Prognosis: | |
| - text: Intermediate Prognosis | |
| - L1: | |
| - text: L1 | |
| - description: INRG Stage L1 | |
| - Ms: | |
| - text: Ms | |
| - description: INRG Stage MS | |
| - M: | |
| - text: M | |
| - description: INRG Stage M | |
| - L2: | |
| - text: L2 | |
| - description: INRG Stage L2 | |
| - Stage IC2: | |
| - text: Stage IC2 | |
| - Stage IC1: | |
| - text: Stage IC1 | |
| - Stage IIIA1: | |
| - text: Stage IIIA1 | |
| - Stage IIIAii: | |
| - text: Stage IIIAii | |
| - Stage IC3: | |
| - text: Stage IC3 | |
| - Stage IIIAi: | |
| - text: Stage IIIAi | |
| - Stage IIIA2: | |
| - text: Stage IIIA2 | |
| - enum_CCDH_CancerStageObservationSet_category: | |
| - name: enum_CCDH_CancerStageObservationSet_category | |
| + code_set_version: '2021-09-16T18:44:36.612118+00:00' | |
| + enum_CRDCH_CancerStageObservation_value_enum: | |
| + name: enum_CRDCH_CancerStageObservation_value_enum | |
| + description: Autogenerated Enumeration for CRDC-H CancerStageObservation value_enum | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.CancerStageObservation.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservation.value_enum | |
| + code_set_version: '2021-09-16T18:44:36.713798+00:00' | |
| + enum_CRDCH_CancerStageObservationSet_category: | |
| + name: enum_CRDCH_CancerStageObservationSet_category | |
| description: Autogenerated Enumeration for CRDC-H CancerStageObservationSet category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.CancerStageObservationSet.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.CancerStageObservationSet.category | |
| - code_set_version: '2021-06-08T21:46:37.994626+00:00' | |
| - enum_CCDH_CancerStageObservationSet_method_type: | |
| - name: enum_CCDH_CancerStageObservationSet_method_type | |
| + code_set_version: '2021-09-16T18:44:36.818382+00:00' | |
| + enum_CRDCH_CancerStageObservationSet_method_type: | |
| + name: enum_CRDCH_CancerStageObservationSet_method_type | |
| description: Classification systems used for defining the point in the natural | |
| history of a malignant disease a patient is when a diagnosis is made | |
| notes: | |
| @@ -2447,13 +1915,13 @@ | |
| text: Unspecified staging system | |
| description: For use when a data contributor has a cancer staging value, but | |
| no clearly specified staging system under which that value falls. | |
| - enum_CCDH_Diagnosis_condition: | |
| - name: enum_CCDH_Diagnosis_condition | |
| + enum_CRDCH_Diagnosis_condition: | |
| + name: enum_CRDCH_Diagnosis_condition | |
| description: Autogenerated Enumeration for CRDC-H Diagnosis condition | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Diagnosis.condition"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.condition | |
| - code_set_version: '2021-06-08T21:46:38.301321+00:00' | |
| + code_set_version: '2021-09-16T18:44:37.038876+00:00' | |
| permissible_values: | |
| Von Recklinghausen disease: | |
| text: Von Recklinghausen disease | |
| @@ -7774,13 +7242,13 @@ | |
| text: Medulloblastoma, group 4 | |
| Malignant lymphoma, small lymphocytic, diffuse: | |
| text: Malignant lymphoma, small lymphocytic, diffuse | |
| - enum_CCDH_Diagnosis_morphology: | |
| - name: enum_CCDH_Diagnosis_morphology | |
| + enum_CRDCH_Diagnosis_morphology: | |
| + name: enum_CRDCH_Diagnosis_morphology | |
| description: Autogenerated Enumeration for CRDC-H Diagnosis morphology | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Diagnosis.morphology"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.morphology | |
| - code_set_version: '2021-06-08T21:46:40.368732+00:00' | |
| + code_set_version: '2021-09-16T18:44:40.038742+00:00' | |
| permissible_values: | |
| 9261/3: | |
| text: 9261/3 | |
| @@ -10078,13 +9546,13 @@ | |
| text: 8950/6 | |
| 8310/6: | |
| text: 8310/6 | |
| - enum_CCDH_Diagnosis_disease_status: | |
| - name: enum_CCDH_Diagnosis_disease_status | |
| + enum_CRDCH_Diagnosis_disease_status: | |
| + name: enum_CRDCH_Diagnosis_disease_status | |
| description: Autogenerated Enumeration for CRDC-H Diagnosis disease_status | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Diagnosis.disease_status"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.disease_status | |
| - code_set_version: '2021-06-08T21:46:41.301442+00:00' | |
| + code_set_version: '2021-09-16T18:44:41.354701+00:00' | |
| permissible_values: | |
| Initial Diagnosis: | |
| text: Initial Diagnosis | |
| @@ -10098,13 +9566,13 @@ | |
| text: Recurrent Disease | |
| Progressive Disease: | |
| text: Progressive Disease | |
| - enum_CCDH_Diagnosis_method_of_diagnosis: | |
| - name: enum_CCDH_Diagnosis_method_of_diagnosis | |
| + enum_CRDCH_Diagnosis_method_of_diagnosis: | |
| + name: enum_CRDCH_Diagnosis_method_of_diagnosis | |
| description: Autogenerated Enumeration for CRDC-H Diagnosis method_of_diagnosis | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Diagnosis.method_of_diagnosis"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Diagnosis.method_of_diagnosis | |
| - code_set_version: '2021-06-08T21:46:41.452895+00:00' | |
| + code_set_version: '2021-09-16T18:44:41.464275+00:00' | |
| permissible_values: | |
| Surgical Resection: | |
| text: Surgical Resection | |
| @@ -10186,15 +9654,15 @@ | |
| Imaging: | |
| text: Imaging | |
| description: Imaging Technique | |
| - enum_CCDH_DimensionalObservation_category: | |
| - name: enum_CCDH_DimensionalObservation_category | |
| + enum_CRDCH_DimensionalObservation_category: | |
| + name: enum_CRDCH_DimensionalObservation_category | |
| description: Autogenerated Enumeration for CRDC-H DimensionalObservation category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.DimensionalObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservation.category | |
| - code_set_version: '2021-06-08T21:46:41.627216+00:00' | |
| - enum_CCDH_DimensionalObservation_observation_type: | |
| - name: enum_CCDH_DimensionalObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:41.600861+00:00' | |
| + enum_CRDCH_DimensionalObservation_observation_type: | |
| + name: enum_CRDCH_DimensionalObservation_observation_type | |
| description: Types of measurements that describe the physical dimensions of an | |
| entity (e.g. a Specimen) | |
| notes: | |
| @@ -10223,29 +9691,29 @@ | |
| surface_area: | |
| text: surface_area | |
| description: The total surface area of the specimen | |
| - enum_CCDH_DimensionalObservation_method_type: | |
| - name: enum_CCDH_DimensionalObservation_method_type | |
| + enum_CRDCH_DimensionalObservation_method_type: | |
| + name: enum_CRDCH_DimensionalObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H DimensionalObservation method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.DimensionalObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:41.940395+00:00' | |
| - enum_CCDH_DimensionalObservationSet_category: | |
| - name: enum_CCDH_DimensionalObservationSet_category | |
| + code_set_version: '2021-09-16T18:44:41.810052+00:00' | |
| + enum_CRDCH_DimensionalObservationSet_category: | |
| + name: enum_CRDCH_DimensionalObservationSet_category | |
| description: Autogenerated Enumeration for CRDC-H DimensionalObservationSet category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.DimensionalObservationSet.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservationSet.category | |
| - code_set_version: '2021-06-08T21:46:42.100430+00:00' | |
| - enum_CCDH_DimensionalObservationSet_method_type: | |
| - name: enum_CCDH_DimensionalObservationSet_method_type | |
| + code_set_version: '2021-09-16T18:44:41.916576+00:00' | |
| + enum_CRDCH_DimensionalObservationSet_method_type: | |
| + name: enum_CRDCH_DimensionalObservationSet_method_type | |
| description: Autogenerated Enumeration for CRDC-H DimensionalObservationSet method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.DimensionalObservationSet.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.DimensionalObservationSet.method_type | |
| - code_set_version: '2021-06-08T21:46:42.250179+00:00' | |
| - enum_CCDH_Document_document_type: | |
| - name: enum_CCDH_Document_document_type | |
| + code_set_version: '2021-09-16T18:44:42.025041+00:00' | |
| + enum_CRDCH_Document_document_type: | |
| + name: enum_CRDCH_Document_document_type | |
| description: The high-level type of the report (e.g. 'pathology report') | |
| notes: | |
| - Derived from [Document.document_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| @@ -10257,16 +9725,16 @@ | |
| text: protocol | |
| description: A protocol by which the sample was obtained or generated (e.g. | |
| a protocol listed in protocols.io) | |
| - enum_CCDH_EnvironmentalExposureObservation_category: | |
| - name: enum_CCDH_EnvironmentalExposureObservation_category | |
| + enum_CRDCH_EnvironmentalExposureObservation_category: | |
| + name: enum_CRDCH_EnvironmentalExposureObservation_category | |
| description: Autogenerated Enumeration for CRDC-H EnvironmentalExposureObservation | |
| category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.EnvironmentalExposureObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.EnvironmentalExposureObservation.category | |
| - code_set_version: '2021-06-08T21:46:42.559897+00:00' | |
| - enum_CCDH_EnvironmentalExposureObservation_observation_type: | |
| - name: enum_CCDH_EnvironmentalExposureObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:42.244983+00:00' | |
| + enum_CRDCH_EnvironmentalExposureObservation_observation_type: | |
| + name: enum_CRDCH_EnvironmentalExposureObservation_observation_type | |
| description: Types of observations about a Subject's environmental exposures. | |
| notes: | |
| - Derived from [EnvironmentalExposureObservation.observation_type in sheet O_CCDH | |
| @@ -10294,193 +9762,101 @@ | |
| text: type_of_smoke_exposure | |
| description: The text term used to describe the patient's specific type of | |
| smoke exposure. | |
| - enum_CCDH_EnvironmentalExposureObservation_method_type: | |
| - name: enum_CCDH_EnvironmentalExposureObservation_method_type | |
| + enum_CRDCH_EnvironmentalExposureObservation_method_type: | |
| + name: enum_CRDCH_EnvironmentalExposureObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H EnvironmentalExposureObservation | |
| method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.EnvironmentalExposureObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.EnvironmentalExposureObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:42.852526+00:00' | |
| - enum_CCDH_EnvironmentalExposureObservation_valueCodeableConcept: | |
| - name: enum_CCDH_EnvironmentalExposureObservation_valueCodeableConcept | |
| + code_set_version: '2021-09-16T18:44:42.462530+00:00' | |
| + enum_CRDCH_EnvironmentalExposureObservation_value_enum: | |
| + name: enum_CRDCH_EnvironmentalExposureObservation_value_enum | |
| description: Autogenerated Enumeration for CRDC-H EnvironmentalExposureObservation | |
| - valueCodeableConcept | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.EnvironmentalExposureObservation.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.EnvironmentalExposureObservation.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:43.004683+00:00' | |
| - permissible_values: | |
| - Work-related smoke, plumbing: | |
| - text: Work-related smoke, plumbing | |
| - Grilling smoke: | |
| - text: Grilling smoke | |
| - Indoor stove or fireplace smoke, wood burning: | |
| - text: Indoor stove or fireplace smoke, wood burning | |
| - Accidental building fire smoke: | |
| - text: Accidental building fire smoke | |
| - Smoke exposure, NOS: | |
| - text: Smoke exposure, NOS | |
| - Accidental forest fire smoke: | |
| - text: Accidental forest fire smoke | |
| - Cooking-related smoke, NOS: | |
| - text: Cooking-related smoke, NOS | |
| - Work-related smoke, military: | |
| - text: Work-related smoke, military | |
| - Fire smoke, NOS: | |
| - text: Fire smoke, NOS | |
| - Wood burning smoke, NOS: | |
| - text: Wood burning smoke, NOS | |
| - Work-related smoke, generators: | |
| - text: Work-related smoke, generators | |
| - Marijuana smoke: | |
| - text: Marijuana smoke | |
| - Electronic cigarette smoke, NOS: | |
| - text: Electronic cigarette smoke, NOS | |
| - Work-related smoke, fire fighting: | |
| - text: Work-related smoke, fire fighting | |
| - Burning tree smoke: | |
| - text: Burning tree smoke | |
| - Factory smokestack smoke: | |
| - text: Factory smokestack smoke | |
| - Work-related smoke, plastics factory: | |
| - text: Work-related smoke, plastics factory | |
| - Field burning smoke: | |
| - text: Field burning smoke | |
| - Accidental vehicle fire smoke: | |
| - text: Accidental vehicle fire smoke | |
| - Work-related smoke, foundry: | |
| - text: Work-related smoke, foundry | |
| - Gas burning smoke, propane: | |
| - text: Gas burning smoke, propane | |
| - Furnace or boiler smoke: | |
| - text: Furnace or boiler smoke | |
| - Waste burning smoke: | |
| - text: Waste burning smoke | |
| - No Smoke Exposure: | |
| - text: No Smoke Exposure | |
| - Coal smoke, NOS: | |
| - text: Coal smoke, NOS | |
| - Volcanic smoke: | |
| - text: Volcanic smoke | |
| - Oil burning smoke, Kerosene: | |
| - text: Oil burning smoke, Kerosene | |
| - Accidental fire smoke, grass: | |
| - text: Accidental fire smoke, grass | |
| - Electrical fire smoke: | |
| - text: Electrical fire smoke | |
| - Work-related smoke, paint baking: | |
| - text: Work-related smoke, paint baking | |
| - Unknown: | |
| - text: Unknown | |
| - description: Unknown | |
| - Tobacco smoke, cigarettes: | |
| - text: Tobacco smoke, cigarettes | |
| - Accidental fire smoke, NOS: | |
| - text: Accidental fire smoke, NOS | |
| - Recreational fire smoke: | |
| - text: Recreational fire smoke | |
| - Grease fire smoke: | |
| - text: Grease fire smoke | |
| - Hashish smoke: | |
| - text: Hashish smoke | |
| - Smokehouse smoke: | |
| - text: Smokehouse smoke | |
| - Indoor stove or fireplace smoke, coal burning: | |
| - text: Indoor stove or fireplace smoke, coal burning | |
| - Work-related smoke, soldering/welding: | |
| - text: Work-related smoke, soldering/welding | |
| - Tobacco smoke, cigar: | |
| - text: Tobacco smoke, cigar | |
| - Work-related smoke, artificial smoke machines: | |
| - text: Work-related smoke, artificial smoke machines | |
| - Aircraft smoke: | |
| - text: Aircraft smoke | |
| - Environmental tobacco smoke: | |
| - text: Environmental tobacco smoke | |
| - Tobacco smoke, pipe: | |
| - text: Tobacco smoke, pipe | |
| - Indoor stove or fireplace smoke, NOS: | |
| - text: Indoor stove or fireplace smoke, NOS | |
| - Wood burning smoke, factory: | |
| - text: Wood burning smoke, factory | |
| - Oil burning smoke, NOS: | |
| - text: Oil burning smoke, NOS | |
| - Work-related smoke, NOS: | |
| - text: Work-related smoke, NOS | |
| - Machine smoke: | |
| - text: Machine smoke | |
| - Not Reported: | |
| - text: Not Reported | |
| - 'No': | |
| - text: 'No' | |
| - 'Yes': | |
| - text: 'Yes' | |
| - Tobacco smoke, NOS: | |
| - text: Tobacco smoke, NOS | |
| - enum_CCDH_ExecutionTimeObservation_category: | |
| - name: enum_CCDH_ExecutionTimeObservation_category | |
| - description: Autogenerated Enumeration for CRDC-H ExecutionTimeObservation category | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.ExecutionTimeObservation.category"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionTimeObservation.category | |
| - code_set_version: '2021-06-08T21:46:43.196994+00:00' | |
| - enum_CCDH_ExecutionTimeObservation_observation_type: | |
| - name: enum_CCDH_ExecutionTimeObservation_observation_type | |
| - description: Autogenerated Enumeration for CRDC-H ExecutionTimeObservation observation_type | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.ExecutionTimeObservation.observation_type"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionTimeObservation.observation_type | |
| - code_set_version: '2021-06-08T21:46:43.356223+00:00' | |
| - enum_CCDH_ExecutionTimeObservation_method_type: | |
| - name: enum_CCDH_ExecutionTimeObservation_method_type | |
| - description: Autogenerated Enumeration for CRDC-H ExecutionTimeObservation method_type | |
| + value_enum | |
| comments: | |
| - - 'Name according to TCCM: "CRDC-H.ExecutionTimeObservation.method_type"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionTimeObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:43.501758+00:00' | |
| - enum_CCDH_ExecutionConditionObservation_category: | |
| - name: enum_CCDH_ExecutionConditionObservation_category | |
| + - 'Name according to TCCM: "CRDC-H.EnvironmentalExposureObservation.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.EnvironmentalExposureObservation.value_enum | |
| + code_set_version: '2021-09-16T18:44:42.563993+00:00' | |
| + enum_CRDCH_ExecutionConditionObservation_category: | |
| + name: enum_CRDCH_ExecutionConditionObservation_category | |
| description: Autogenerated Enumeration for CRDC-H ExecutionConditionObservation | |
| category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.category | |
| - code_set_version: '2021-06-08T21:46:43.653697+00:00' | |
| - enum_CCDH_ExecutionConditionObservation_observation_type: | |
| - name: enum_CCDH_ExecutionConditionObservation_observation_type | |
| - description: Autogenerated Enumeration for CRDC-H ExecutionConditionObservation | |
| - observation_type | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.observation_type"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.observation_type | |
| - code_set_version: '2021-06-08T21:46:43.802685+00:00' | |
| - enum_CCDH_ExecutionConditionObservation_method_type: | |
| - name: enum_CCDH_ExecutionConditionObservation_method_type | |
| + code_set_version: '2021-09-16T18:44:42.669055+00:00' | |
| + enum_CRDCH_ExecutionConditionObservation_observation_type: | |
| + name: enum_CRDCH_ExecutionConditionObservation_observation_type | |
| + description: Types of observations about the environmental conditions under which | |
| + specific aspects of an activity were performed. | |
| + notes: | |
| + - Derived from [ExecutionConditionObservation.observation_type in sheet O_CCDH | |
| + Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| + permissible_values: | |
| + ischemic_temperature: | |
| + text: ischemic_temperature | |
| + description: A term describing the temperature of a specimen when it experienced | |
| + ischemia. | |
| + enum_CRDCH_ExecutionConditionObservation_method_type: | |
| + name: enum_CRDCH_ExecutionConditionObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H ExecutionConditionObservation | |
| method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:43.946324+00:00' | |
| - enum_CCDH_ExecutionConditionObservation_valueCodeableConcept: | |
| - name: enum_CCDH_ExecutionConditionObservation_valueCodeableConcept | |
| + code_set_version: '2021-09-16T18:44:42.875902+00:00' | |
| + enum_CRDCH_ExecutionConditionObservation_value_enum: | |
| + name: enum_CRDCH_ExecutionConditionObservation_value_enum | |
| description: Autogenerated Enumeration for CRDC-H ExecutionConditionObservation | |
| - valueCodeableConcept | |
| + value_enum | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.value_enum | |
| + code_set_version: '2021-09-16T18:44:42.985912+00:00' | |
| + enum_CRDCH_ExecutionTimeObservation_category: | |
| + name: enum_CRDCH_ExecutionTimeObservation_category | |
| + description: Autogenerated Enumeration for CRDC-H ExecutionTimeObservation category | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.ExecutionTimeObservation.category"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionTimeObservation.category | |
| + code_set_version: '2021-09-16T18:44:43.094334+00:00' | |
| + enum_CRDCH_ExecutionTimeObservation_observation_type: | |
| + name: enum_CRDCH_ExecutionTimeObservation_observation_type | |
| + description: An observation about the duration of specific aspects / parts of | |
| + an activity. | |
| + notes: | |
| + - Derived from [ExecutionTimeObservation.observation_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| + permissible_values: | |
| + time_between_excision_and_freezing: | |
| + text: time_between_excision_and_freezing | |
| + description: The elapsed time between the excision and freezing of the specimen | |
| + from its subject/source. | |
| + time_between_clamping_and_freezing: | |
| + text: time_between_clamping_and_freezing | |
| + description: The elapsed time between the clamping of blood supply and freezing | |
| + of the specimen from its subject/source. | |
| + ischemic_time: | |
| + text: ischemic_time | |
| + description: Duration of time, in seconds, between when the specimen stopped | |
| + receiving oxygen and when it was preserved or processed. | |
| + enum_CRDCH_ExecutionTimeObservation_method_type: | |
| + name: enum_CRDCH_ExecutionTimeObservation_method_type | |
| + description: Autogenerated Enumeration for CRDC-H ExecutionTimeObservation method_type | |
| comments: | |
| - - 'Name according to TCCM: "CRDC-H.ExecutionConditionObservation.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionConditionObservation.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:44.091888+00:00' | |
| - enum_CCDH_HistologicalCompositionObservation_category: | |
| - name: enum_CCDH_HistologicalCompositionObservation_category | |
| + - 'Name according to TCCM: "CRDC-H.ExecutionTimeObservation.method_type"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ExecutionTimeObservation.method_type | |
| + code_set_version: '2021-09-16T18:44:43.312162+00:00' | |
| + enum_CRDCH_HistologicalCompositionObservation_category: | |
| + name: enum_CRDCH_HistologicalCompositionObservation_category | |
| description: Autogenerated Enumeration for CRDC-H HistologicalCompositionObservation | |
| category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservation.category | |
| - code_set_version: '2021-06-08T21:46:44.248760+00:00' | |
| - enum_CCDH_HistologicalCompositionObservation_observation_type: | |
| - name: enum_CCDH_HistologicalCompositionObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:43.424044+00:00' | |
| + enum_CRDCH_HistologicalCompositionObservation_observation_type: | |
| + name: enum_CRDCH_HistologicalCompositionObservation_observation_type | |
| description: Types of measurements that describe microscopic characteristics of | |
| a specimen - typically related to its cellular and tissue composition. | |
| notes: | |
| @@ -10566,108 +9942,103 @@ | |
| text: analysis_area_percentage_pigmented_tumor | |
| description: The area of a sample on a slide that is represented by pigmented | |
| tumor tissue, which will be analyzed. | |
| - enum_CCDH_HistologicalCompositionObservation_method_type: | |
| - name: enum_CCDH_HistologicalCompositionObservation_method_type | |
| + enum_CRDCH_HistologicalCompositionObservation_method_type: | |
| + name: enum_CRDCH_HistologicalCompositionObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H HistologicalCompositionObservation | |
| method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:44.554661+00:00' | |
| - enum_CCDH_HistologicalCompositionObservationSet_category: | |
| - name: enum_CCDH_HistologicalCompositionObservationSet_category | |
| + code_set_version: '2021-09-16T18:44:43.649574+00:00' | |
| + enum_CRDCH_HistologicalCompositionObservationSet_category: | |
| + name: enum_CRDCH_HistologicalCompositionObservationSet_category | |
| description: Autogenerated Enumeration for CRDC-H HistologicalCompositionObservationSet | |
| category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservationSet.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservationSet.category | |
| - code_set_version: '2021-06-08T21:46:44.698914+00:00' | |
| - enum_CCDH_HistologicalCompositionObservationSet_method_type: | |
| - name: enum_CCDH_HistologicalCompositionObservationSet_method_type | |
| + code_set_version: '2021-09-16T18:44:43.757090+00:00' | |
| + enum_CRDCH_HistologicalCompositionObservationSet_method_type: | |
| + name: enum_CRDCH_HistologicalCompositionObservationSet_method_type | |
| description: Autogenerated Enumeration for CRDC-H HistologicalCompositionObservationSet | |
| method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.HistologicalCompositionObservationSet.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.HistologicalCompositionObservationSet.method_type | |
| - code_set_version: '2021-06-08T21:46:44.844591+00:00' | |
| - enum_CCDH_Identifier_type: | |
| - name: enum_CCDH_Identifier_type | |
| + code_set_version: '2021-09-16T18:44:43.860926+00:00' | |
| + enum_CRDCH_Identifier_type: | |
| + name: enum_CRDCH_Identifier_type | |
| description: Autogenerated Enumeration for CRDC-H Identifier type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Identifier.type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Identifier.type | |
| - code_set_version: '2021-06-08T21:46:44.993350+00:00' | |
| - enum_CCDH_Observation_category: | |
| - name: enum_CCDH_Observation_category | |
| + code_set_version: '2021-09-16T18:44:43.973647+00:00' | |
| + enum_CRDCH_Observation_category: | |
| + name: enum_CRDCH_Observation_category | |
| description: Autogenerated Enumeration for CRDC-H Observation category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Observation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.category | |
| - code_set_version: '2021-06-08T21:46:45.143553+00:00' | |
| - enum_CCDH_Observation_observation_type: | |
| - name: enum_CCDH_Observation_observation_type | |
| + code_set_version: '2021-09-16T18:44:44.079897+00:00' | |
| + enum_CRDCH_Observation_observation_type: | |
| + name: enum_CRDCH_Observation_observation_type | |
| description: Autogenerated Enumeration for CRDC-H Observation observation_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Observation.observation_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.observation_type | |
| - code_set_version: '2021-06-08T21:46:45.290945+00:00' | |
| - enum_CCDH_Observation_method_type: | |
| - name: enum_CCDH_Observation_method_type | |
| + code_set_version: '2021-09-16T18:44:44.188133+00:00' | |
| + enum_CRDCH_Observation_method_type: | |
| + name: enum_CRDCH_Observation_method_type | |
| description: Autogenerated Enumeration for CRDC-H Observation method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Observation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.method_type | |
| - code_set_version: '2021-06-08T21:46:45.438145+00:00' | |
| - enum_CCDH_Observation_valueCodeableConcept: | |
| - name: enum_CCDH_Observation_valueCodeableConcept | |
| - description: Autogenerated Enumeration for CRDC-H Observation valueCodeableConcept | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.Observation.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:45.590905+00:00' | |
| - enum_CCDH_ObservationSet_category: | |
| - name: enum_CCDH_ObservationSet_category | |
| + code_set_version: '2021-09-16T18:44:44.301142+00:00' | |
| + enum_CRDCH_Observation_value_enum: | |
| + name: enum_CRDCH_Observation_value_enum | |
| + description: Autogenerated Enumeration for CRDC-H Observation value_enum | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.Observation.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Observation.value_enum | |
| + code_set_version: '2021-09-16T18:44:44.413787+00:00' | |
| + enum_CRDCH_ObservationSet_category: | |
| + name: enum_CRDCH_ObservationSet_category | |
| description: Autogenerated Enumeration for CRDC-H ObservationSet category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.ObservationSet.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ObservationSet.category | |
| - code_set_version: '2021-06-08T21:46:45.742459+00:00' | |
| - enum_CCDH_ObservationSet_method_type: | |
| - name: enum_CCDH_ObservationSet_method_type | |
| + code_set_version: '2021-09-16T18:44:44.522816+00:00' | |
| + enum_CRDCH_ObservationSet_method_type: | |
| + name: enum_CRDCH_ObservationSet_method_type | |
| description: Autogenerated Enumeration for CRDC-H ObservationSet method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.ObservationSet.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ObservationSet.method_type | |
| - code_set_version: '2021-06-08T21:46:45.901383+00:00' | |
| - enum_CCDH_Quantity_valueCodeableConcept: | |
| - name: enum_CCDH_Quantity_valueCodeableConcept | |
| - description: Autogenerated Enumeration for CRDC-H Quantity valueCodeableConcept | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.Quantity.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Quantity.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:46.052607+00:00' | |
| + code_set_version: '2021-09-16T18:44:44.628806+00:00' | |
| + enum_CRDCH_Quantity_value_enum: | |
| + name: enum_CRDCH_Quantity_value_enum | |
| + description: Autogenerated Enumeration for CRDC-H Quantity value_enum | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.Quantity.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Quantity.value_enum | |
| + code_set_version: '2021-09-16T18:44:44.733215+00:00' | |
| + enum_CRDCH_Quantity_unit: | |
| + name: enum_CRDCH_Quantity_unit | |
| + description: The unit for a value | |
| + notes: | |
| + - Derived from [Quantity.unit in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| permissible_values: | |
| - Not Reported: | |
| - text: Not Reported | |
| - description: Not Reported | |
| - Distal (>2cm): | |
| - text: Distal (>2cm) | |
| - description: Distal | |
| - Unknown: | |
| - text: Unknown | |
| - description: Unknown | |
| - Adjacent (< or = 2cm): | |
| - text: Adjacent (< or = 2cm) | |
| - description: Adjacent | |
| - enum_CCDH_Quantity_unit: | |
| - name: enum_CCDH_Quantity_unit | |
| - description: Autogenerated Enumeration for CRDC-H Quantity unit | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.Quantity.unit"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Quantity.unit | |
| - code_set_version: '2021-06-08T21:46:46.203685+00:00' | |
| - enum_CCDH_ResearchProject_research_project_type: | |
| - name: enum_CCDH_ResearchProject_research_project_type | |
| + milligrams: | |
| + text: milligrams | |
| + description: '' | |
| + days: | |
| + text: days | |
| + description: '' | |
| + minutes: | |
| + text: minutes | |
| + description: '' | |
| + enum_CRDCH_ResearchProject_research_project_type: | |
| + name: enum_CRDCH_ResearchProject_research_project_type | |
| description: A high-level type of research activity | |
| notes: | |
| - Derived from [ResearchProject.research_project_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| @@ -10683,13 +10054,13 @@ | |
| text: Clinical Trial | |
| description: A research study that prospectively assigns participants to one | |
| or more health-related interventions to evaluate the effects on health outcomes. | |
| - enum_CCDH_ResearchSubject_primary_diagnosis_condition: | |
| - name: enum_CCDH_ResearchSubject_primary_diagnosis_condition | |
| + enum_CRDCH_ResearchSubject_primary_diagnosis_condition: | |
| + name: enum_CRDCH_ResearchSubject_primary_diagnosis_condition | |
| description: Autogenerated Enumeration for CRDC-H ResearchSubject primary_diagnosis_condition | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.ResearchSubject.primary_diagnosis_condition"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ResearchSubject.primary_diagnosis_condition | |
| - code_set_version: '2021-06-08T21:46:46.513868+00:00' | |
| + code_set_version: '2021-09-16T18:44:45.043777+00:00' | |
| permissible_values: | |
| Soft Tissue Tumors and Sarcomas, NOS: | |
| text: Soft Tissue Tumors and Sarcomas, NOS | |
| @@ -10974,13 +10345,13 @@ | |
| text: Colon Adenocarcinoma | |
| Other: | |
| text: Other | |
| - enum_CCDH_ResearchSubject_index_timepoint: | |
| - name: enum_CCDH_ResearchSubject_index_timepoint | |
| + enum_CRDCH_ResearchSubject_index_timepoint: | |
| + name: enum_CRDCH_ResearchSubject_index_timepoint | |
| description: Autogenerated Enumeration for CRDC-H ResearchSubject index_timepoint | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.ResearchSubject.index_timepoint"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.ResearchSubject.index_timepoint | |
| - code_set_version: '2021-06-08T21:46:46.740283+00:00' | |
| + code_set_version: '2021-09-16T18:44:45.263369+00:00' | |
| permissible_values: | |
| Diagnosis: | |
| text: Diagnosis | |
| @@ -11000,15 +10371,15 @@ | |
| text: Initial Genomic Sequencing | |
| Recurrence: | |
| text: Recurrence | |
| - enum_CCDH_Specimen_specimen_type: | |
| - name: enum_CCDH_Specimen_specimen_type | |
| + enum_CRDCH_Specimen_specimen_type: | |
| + name: enum_CRDCH_Specimen_specimen_type | |
| description: A high-level type of specimen, based on its derivation provenance | |
| (i.e. how far removed it is from the original sample extracted from a source). | |
| notes: | |
| - Derived from [Specimen.specimen_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| permissible_values: | |
| - initial sample: | |
| - text: initial sample | |
| + Fresh Specimen: | |
| + text: Fresh Specimen | |
| description: A specimen representing the material that was directly collected | |
| from a subject (i.e. not generated through portioning, aliquoting, or analyte | |
| extraction from an existing specimen). | |
| @@ -11028,13 +10399,13 @@ | |
| text: slide | |
| description: A specimen that is mounted on a slide or coverslip for microscopic | |
| analysis. | |
| - enum_CCDH_Specimen_analyte_type: | |
| - name: enum_CCDH_Specimen_analyte_type | |
| + enum_CRDCH_Specimen_analyte_type: | |
| + name: enum_CRDCH_Specimen_analyte_type | |
| description: Autogenerated Enumeration for CRDC-H Specimen analyte_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Specimen.analyte_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.analyte_type | |
| - code_set_version: '2021-06-08T21:46:47.056667+00:00' | |
| + code_set_version: '2021-09-16T18:44:45.492060+00:00' | |
| permissible_values: | |
| Repli-G (Qiagen) DNA: | |
| text: Repli-G (Qiagen) DNA | |
| @@ -11099,13 +10470,13 @@ | |
| Protein: | |
| text: Protein | |
| description: Protein | |
| - enum_CCDH_Specimen_source_material_type: | |
| - name: enum_CCDH_Specimen_source_material_type | |
| + enum_CRDCH_Specimen_source_material_type: | |
| + name: enum_CRDCH_Specimen_source_material_type | |
| description: Autogenerated Enumeration for CRDC-H Specimen source_material_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Specimen.source_material_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.source_material_type | |
| - code_set_version: '2021-06-08T21:46:47.234524+00:00' | |
| + code_set_version: '2021-09-16T18:44:45.626640+00:00' | |
| permissible_values: | |
| Recurrent Blood Derived Cancer - Bone Marrow: | |
| text: Recurrent Blood Derived Cancer - Bone Marrow | |
| @@ -11280,13 +10651,13 @@ | |
| text: '12' | |
| '40': | |
| text: '40' | |
| - enum_CCDH_Specimen_tumor_status_at_collection: | |
| - name: enum_CCDH_Specimen_tumor_status_at_collection | |
| + enum_CRDCH_Specimen_tumor_status_at_collection: | |
| + name: enum_CRDCH_Specimen_tumor_status_at_collection | |
| description: Autogenerated Enumeration for CRDC-H Specimen tumor_status_at_collection | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Specimen.tumor_status_at_collection"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.tumor_status_at_collection | |
| - code_set_version: '2021-06-08T21:46:47.439050+00:00' | |
| + code_set_version: '2021-09-16T18:44:45.811497+00:00' | |
| permissible_values: | |
| recurrence: | |
| text: recurrence | |
| @@ -11325,13 +10696,13 @@ | |
| text: Not Reported | |
| Progression: | |
| text: Progression | |
| - enum_CCDH_Specimen_cellular_composition_type: | |
| - name: enum_CCDH_Specimen_cellular_composition_type | |
| + enum_CRDCH_Specimen_cellular_composition_type: | |
| + name: enum_CRDCH_Specimen_cellular_composition_type | |
| description: Autogenerated Enumeration for CRDC-H Specimen cellular_composition_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Specimen.cellular_composition_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.cellular_composition_type | |
| - code_set_version: '2021-06-08T21:46:47.605875+00:00' | |
| + code_set_version: '2021-09-16T18:44:45.947569+00:00' | |
| permissible_values: | |
| Lymphocytes: | |
| text: Lymphocytes | |
| @@ -11422,177 +10793,56 @@ | |
| description: Serum | |
| Not Allowed To Collect: | |
| text: Not Allowed To Collect | |
| - enum_CCDH_Specimen_general_tissue_morphology: | |
| - name: enum_CCDH_Specimen_general_tissue_morphology | |
| - description: Autogenerated Enumeration for CRDC-H Specimen general_tissue_morphology | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.Specimen.general_tissue_morphology"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.general_tissue_morphology | |
| - code_set_version: '2021-06-08T21:46:47.794493+00:00' | |
| - permissible_values: | |
| - Peritumoral: | |
| - text: Peritumoral | |
| - description: Peritumoral | |
| - Abnormal: | |
| - text: Abnormal | |
| - description: Abnormal | |
| - Normal: | |
| - text: Normal | |
| - description: Normal | |
| - Not Allowed To Collect: | |
| - text: Not Allowed To Collect | |
| - Unknown: | |
| - text: Unknown | |
| - description: Unknown | |
| - Tumor: | |
| - text: Tumor | |
| - description: Malignant Neoplasm | |
| - Not Reported: | |
| - text: Not Reported | |
| - enum_CCDH_Specimen_specific_tissue_morphology: | |
| - name: enum_CCDH_Specimen_specific_tissue_morphology | |
| - description: Autogenerated Enumeration for CRDC-H Specimen specific_tissue_morphology | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.Specimen.specific_tissue_morphology"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.specific_tissue_morphology | |
| - code_set_version: '2021-06-08T21:46:47.955393+00:00' | |
| - permissible_values: | |
| - '61': | |
| - text: '61' | |
| - '70': | |
| - text: '70' | |
| - '30': | |
| - text: '30' | |
| - '63': | |
| - text: '63' | |
| - '71': | |
| - text: '71' | |
| - '51': | |
| - text: '51' | |
| - '80': | |
| - text: '80' | |
| - '02': | |
| - text: '02' | |
| - '65': | |
| - text: '65' | |
| - '04': | |
| - text: '04' | |
| - '60': | |
| - text: '60' | |
| - '03': | |
| - text: '03' | |
| - '50': | |
| - text: '50' | |
| - '52': | |
| - text: '52' | |
| - '15': | |
| - text: '15' | |
| - '10': | |
| - text: '10' | |
| - '00': | |
| - text: '00' | |
| - '01': | |
| - text: '01' | |
| - '21': | |
| - text: '21' | |
| - '20': | |
| - text: '20' | |
| - '62': | |
| - text: '62' | |
| - '40': | |
| - text: '40' | |
| - '64': | |
| - text: '64' | |
| - '81': | |
| - text: '81' | |
| - '41': | |
| - text: '41' | |
| - Rhabdoid tumor (kidney) (RT): | |
| - text: Rhabdoid tumor (kidney) (RT) | |
| - Acute myeloid leukemia (AML): | |
| - text: Acute myeloid leukemia (AML) | |
| - Anal Cancer (all types): | |
| - text: Anal Cancer (all types) | |
| - Non cancerous tissue: | |
| - text: Non cancerous tissue | |
| - CNS, low grade glioma (LGG): | |
| - text: CNS, low grade glioma (LGG) | |
| - Lung Cancer (all types): | |
| - text: Lung Cancer (all types) | |
| - CNS, ependymoma: | |
| - text: CNS, ependymoma | |
| - Rhabdomyosarcoma: | |
| - text: Rhabdomyosarcoma | |
| - Induction Failure AML (AML-IF): | |
| - text: Induction Failure AML (AML-IF) | |
| - Soft tissue sarcoma, non-rhabdomyosarcoma: | |
| - text: Soft tissue sarcoma, non-rhabdomyosarcoma | |
| - NHL, Burkitt lymphoma (BL): | |
| - text: NHL, Burkitt lymphoma (BL) | |
| - Neuroblastoma (NBL): | |
| - text: Neuroblastoma (NBL) | |
| - Diffuse Large B-Cell Lymphoma (DLBCL): | |
| - text: Diffuse Large B-Cell Lymphoma (DLBCL) | |
| - Acute lymphoblastic leukemia (ALL): | |
| - text: Acute lymphoblastic leukemia (ALL) | |
| - CNS, rhabdoid tumor: | |
| - text: CNS, rhabdoid tumor | |
| - CNS, medulloblastoma: | |
| - text: CNS, medulloblastoma | |
| - Cervical Cancer (all types): | |
| - text: Cervical Cancer (all types) | |
| - NHL, anaplastic large cell lymphoma: | |
| - text: NHL, anaplastic large cell lymphoma | |
| - Clear cell sarcoma of the kidney (CCSK): | |
| - text: Clear cell sarcoma of the kidney (CCSK) | |
| - CNS, glioblastoma (GBM): | |
| - text: CNS, glioblastoma (GBM) | |
| - Acute Leukemia of Ambiguous Lineage (ALAL): | |
| - text: Acute Leukemia of Ambiguous Lineage (ALAL) | |
| - CNS, other: | |
| - text: CNS, other | |
| - Ewing sarcoma: | |
| - text: Ewing sarcoma | |
| - Osteosarcoma (OS): | |
| - text: Osteosarcoma (OS) | |
| - Wilms tumor (WT): | |
| - text: Wilms tumor (WT) | |
| - enum_CCDH_Specimen_preinvasive_tissue_morphology: | |
| - name: enum_CCDH_Specimen_preinvasive_tissue_morphology | |
| + enum_CRDCH_Specimen_general_tissue_pathology: | |
| + name: enum_CRDCH_Specimen_general_tissue_pathology | |
| + description: Autogenerated Enumeration for CRDC-H Specimen general_tissue_pathology | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.Specimen.general_tissue_pathology"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.general_tissue_pathology | |
| + code_set_version: '2021-09-16T18:44:46.109470+00:00' | |
| + enum_CRDCH_Specimen_specific_tissue_pathology: | |
| + name: enum_CRDCH_Specimen_specific_tissue_pathology | |
| + description: Autogenerated Enumeration for CRDC-H Specimen specific_tissue_pathology | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.Specimen.specific_tissue_pathology"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.specific_tissue_pathology | |
| + code_set_version: '2021-09-16T18:44:46.222414+00:00' | |
| + enum_CRDCH_Specimen_preinvasive_tissue_morphology: | |
| + name: enum_CRDCH_Specimen_preinvasive_tissue_morphology | |
| description: Autogenerated Enumeration for CRDC-H Specimen preinvasive_tissue_morphology | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Specimen.preinvasive_tissue_morphology"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.preinvasive_tissue_morphology | |
| - code_set_version: '2021-06-08T21:46:48.139512+00:00' | |
| - enum_CCDH_Specimen_morphology_assessor_role: | |
| - name: enum_CCDH_Specimen_morphology_assessor_role | |
| + code_set_version: '2021-09-16T18:44:46.326774+00:00' | |
| + enum_CRDCH_Specimen_morphology_assessor_role: | |
| + name: enum_CRDCH_Specimen_morphology_assessor_role | |
| description: Autogenerated Enumeration for CRDC-H Specimen morphology_assessor_role | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Specimen.morphology_assessor_role"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.morphology_assessor_role | |
| - code_set_version: '2021-06-08T21:46:48.295277+00:00' | |
| - enum_CCDH_Specimen_morphlogy_assessment_method: | |
| - name: enum_CCDH_Specimen_morphlogy_assessment_method | |
| - description: Autogenerated Enumeration for CRDC-H Specimen morphlogy_assessment_method | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.Specimen.morphlogy_assessment_method"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.morphlogy_assessment_method | |
| - code_set_version: '2021-06-08T21:46:48.451184+00:00' | |
| - enum_CCDH_Specimen_degree_of_dysplasia: | |
| - name: enum_CCDH_Specimen_degree_of_dysplasia | |
| + code_set_version: '2021-09-16T18:44:46.437604+00:00' | |
| + enum_CRDCH_Specimen_morphology_assessment_method: | |
| + name: enum_CRDCH_Specimen_morphology_assessment_method | |
| + description: Autogenerated Enumeration for CRDC-H Specimen morphology_assessment_method | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.Specimen.morphology_assessment_method"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.morphology_assessment_method | |
| + code_set_version: '2021-09-16T18:44:46.622724+00:00' | |
| + enum_CRDCH_Specimen_degree_of_dysplasia: | |
| + name: enum_CRDCH_Specimen_degree_of_dysplasia | |
| description: Autogenerated Enumeration for CRDC-H Specimen degree_of_dysplasia | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Specimen.degree_of_dysplasia"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Specimen.degree_of_dysplasia | |
| - code_set_version: '2021-06-08T21:46:48.596314+00:00' | |
| - enum_CCDH_Specimen_section_location: | |
| - name: enum_CCDH_Specimen_section_location | |
| + code_set_version: '2021-09-16T18:44:46.733576+00:00' | |
| + enum_CRDCH_Specimen_section_location: | |
| + name: enum_CRDCH_Specimen_section_location | |
| + related_mappings: | |
| + - GDC:Sample.section_location | |
| description: The location in a parent specimen from which a section/portion was | |
| excised. | |
| notes: | |
| - Derived from [Specimen.section_location in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| - related_mappings: | |
| - - GDC:Sample.section_location | |
| permissible_values: | |
| top: | |
| text: top | |
| @@ -11605,15 +10855,15 @@ | |
| text: bottom | |
| description: The part of a specimen designated as its 'bottom' based on specified | |
| orientation criteria. | |
| - enum_CCDH_SpecimenContainer_container_type: | |
| - name: enum_CCDH_SpecimenContainer_container_type | |
| + enum_CRDCH_SpecimenContainer_container_type: | |
| + name: enum_CRDCH_SpecimenContainer_container_type | |
| description: Autogenerated Enumeration for CRDC-H SpecimenContainer container_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.SpecimenContainer.container_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenContainer.container_type | |
| - code_set_version: '2021-06-08T21:46:48.901516+00:00' | |
| - enum_CCDH_SpecimenCreationActivity_activity_type: | |
| - name: enum_CCDH_SpecimenCreationActivity_activity_type | |
| + code_set_version: '2021-09-16T18:44:46.954707+00:00' | |
| + enum_CRDCH_SpecimenCreationActivity_activity_type: | |
| + name: enum_CRDCH_SpecimenCreationActivity_activity_type | |
| description: The high-level type of activity through which the specimen was generated | |
| (i.e. via collection from the original source, or via derivation from an existing | |
| specimen) | |
| @@ -11627,13 +10877,13 @@ | |
| derivation from specimen: | |
| text: derivation from specimen | |
| description: An activity that derives a new specimen from an existing one. | |
| - enum_CCDH_SpecimenCreationActivity_collection_method_type: | |
| - name: enum_CCDH_SpecimenCreationActivity_collection_method_type | |
| + enum_CRDCH_SpecimenCreationActivity_collection_method_type: | |
| + name: enum_CRDCH_SpecimenCreationActivity_collection_method_type | |
| description: Autogenerated Enumeration for CRDC-H SpecimenCreationActivity collection_method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.SpecimenCreationActivity.collection_method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenCreationActivity.collection_method_type | |
| - code_set_version: '2021-06-08T21:46:49.208449+00:00' | |
| + code_set_version: '2021-09-16T18:44:47.169555+00:00' | |
| permissible_values: | |
| 'Yes': | |
| text: 'Yes' | |
| @@ -11845,22 +11095,22 @@ | |
| text: Transoral Laser Excision | |
| Palatectomy: | |
| text: Palatectomy | |
| - enum_CCDH_SpecimenCreationActivity_derivation_method_type: | |
| - name: enum_CCDH_SpecimenCreationActivity_derivation_method_type | |
| + enum_CRDCH_SpecimenCreationActivity_derivation_method_type: | |
| + name: enum_CRDCH_SpecimenCreationActivity_derivation_method_type | |
| description: Autogenerated Enumeration for CRDC-H SpecimenCreationActivity derivation_method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.SpecimenCreationActivity.derivation_method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenCreationActivity.derivation_method_type | |
| - code_set_version: '2021-06-08T21:46:49.420777+00:00' | |
| - enum_CCDH_SpecimenQualityObservation_category: | |
| - name: enum_CCDH_SpecimenQualityObservation_category | |
| + code_set_version: '2021-09-16T18:44:47.388112+00:00' | |
| + enum_CRDCH_SpecimenQualityObservation_category: | |
| + name: enum_CRDCH_SpecimenQualityObservation_category | |
| description: Autogenerated Enumeration for CRDC-H SpecimenQualityObservation category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.SpecimenQualityObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenQualityObservation.category | |
| - code_set_version: '2021-06-08T21:46:49.572402+00:00' | |
| - enum_CCDH_SpecimenQualityObservation_observation_type: | |
| - name: enum_CCDH_SpecimenQualityObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:47.497278+00:00' | |
| + enum_CRDCH_SpecimenQualityObservation_observation_type: | |
| + name: enum_CRDCH_SpecimenQualityObservation_observation_type | |
| description: Types of measurements that reflect the quality of a specimen or its | |
| suitability for use. | |
| notes: | |
| @@ -11873,14 +11123,14 @@ | |
| ribosomal_rna_28s_16s_ratio: | |
| text: ribosomal_rna_28s_16s_ratio | |
| description: Ratio of quantity of 28s RNA over that of 16s RNA. | |
| - enum_CCDH_SpecimenQualityObservation_method_type: | |
| - name: enum_CCDH_SpecimenQualityObservation_method_type | |
| - description: A type of method used in determining the quantity of a specimen. | |
| - notes: | |
| - - Derived from [SpecimenQualityObservation.method_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| + enum_CRDCH_SpecimenQualityObservation_method_type: | |
| + name: enum_CRDCH_SpecimenQualityObservation_method_type | |
| related_mappings: | |
| - GDC:Analyte.spectrophotometer_method | |
| - PDC:Analyte.spectrophotometer_method | |
| + description: A type of method used in determining the quantity of a specimen. | |
| + notes: | |
| + - Derived from [SpecimenQualityObservation.method_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| permissible_values: | |
| UV Spec: | |
| text: UV Spec | |
| @@ -11891,16 +11141,16 @@ | |
| description: A technique applying the Pico488 fluorescent sensor dye that | |
| is used for quantifying the amount of double-stranded DNA (dsDNA) present | |
| in a given sample. | |
| - enum_CCDH_SpecimenQuantityObservation_category: | |
| - name: enum_CCDH_SpecimenQuantityObservation_category | |
| + enum_CRDCH_SpecimenQuantityObservation_category: | |
| + name: enum_CRDCH_SpecimenQuantityObservation_category | |
| description: Autogenerated Enumeration for CRDC-H SpecimenQuantityObservation | |
| category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.SpecimenQuantityObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenQuantityObservation.category | |
| - code_set_version: '2021-06-08T21:46:50.036695+00:00' | |
| - enum_CCDH_SpecimenQuantityObservation_observation_type: | |
| - name: enum_CCDH_SpecimenQuantityObservation_observation_type | |
| + code_set_version: '2021-09-16T18:44:47.817007+00:00' | |
| + enum_CRDCH_SpecimenQuantityObservation_observation_type: | |
| + name: enum_CRDCH_SpecimenQuantityObservation_observation_type | |
| description: Measures related to the quantity of a specimen or analyte it currently | |
| contains - e.g. its weight, volume, or concentration. | |
| notes: | |
| @@ -11919,16 +11169,16 @@ | |
| a specimen (specifically, in a specimen of type 'analyte', or an 'aliquot' | |
| derived from an analyte). For example, the concentration of DNA in a specimen | |
| created through extracting DNA from a blood sample. | |
| - enum_CCDH_SpecimenQuantityObservation_method_type: | |
| - name: enum_CCDH_SpecimenQuantityObservation_method_type | |
| + enum_CRDCH_SpecimenQuantityObservation_method_type: | |
| + name: enum_CRDCH_SpecimenQuantityObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H SpecimenQuantityObservation | |
| method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.SpecimenQuantityObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenQuantityObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:50.338589+00:00' | |
| - enum_CCDH_SpecimenProcessingActivity_activity_type: | |
| - name: enum_CCDH_SpecimenProcessingActivity_activity_type | |
| + code_set_version: '2021-09-16T18:44:48.040089+00:00' | |
| + enum_CRDCH_SpecimenProcessingActivity_activity_type: | |
| + name: enum_CRDCH_SpecimenProcessingActivity_activity_type | |
| description: The high-level type of processing activity performed. | |
| notes: | |
| - Derived from [SpecimenProcessingActivity.activity_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| @@ -11947,12 +11197,8 @@ | |
| Preservation: | |
| text: Preservation | |
| description: A processing activity that aims to preserve a specimen. | |
| - enum_CCDH_SpecimenProcessingActivity_method_type: | |
| - name: enum_CCDH_SpecimenProcessingActivity_method_type | |
| - description: A type of method used to process a specimen (e.g. freezing, fixing, | |
| - treating, preserving, labeling, etc.). | |
| - notes: | |
| - - Derived from [SpecimenProcessingActivity.method_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| + enum_CRDCH_SpecimenProcessingActivity_method_type: | |
| + name: enum_CRDCH_SpecimenProcessingActivity_method_type | |
| related_mappings: | |
| - GDC:Sample.freezing_method | |
| - GDC:Sample.preservation_method | |
| @@ -11965,9 +11211,13 @@ | |
| - GDC:Portion.is_ffpe | |
| - PDC:Sample.oct_embedded | |
| - HTAN:Biospecimen.PRESERVATION_METHOD | |
| + description: A type of method used to process a specimen (e.g. freezing, fixing, | |
| + treating, preserving, labeling, etc.). | |
| + notes: | |
| + - Derived from [SpecimenProcessingActivity.method_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| permissible_values: | |
| - '-80': | |
| - text: '-80' | |
| + Minues 80 Degrees Celsius Freezer: | |
| + text: Minues 80 Degrees Celsius Freezer | |
| description: Freezing at -80 degrees celcius | |
| '-20': | |
| text: '-20' | |
| @@ -11978,15 +11228,15 @@ | |
| isopentane: | |
| text: isopentane | |
| description: Freezing in isopentane. | |
| - enum_CCDH_SpecimenStorageActivity_method_type: | |
| - name: enum_CCDH_SpecimenStorageActivity_method_type | |
| + enum_CRDCH_SpecimenStorageActivity_method_type: | |
| + name: enum_CRDCH_SpecimenStorageActivity_method_type | |
| description: Autogenerated Enumeration for CRDC-H SpecimenStorageActivity method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.SpecimenStorageActivity.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.SpecimenStorageActivity.method_type | |
| - code_set_version: '2021-06-08T21:46:50.822681+00:00' | |
| - enum_CCDH_Subject_species: | |
| - name: enum_CCDH_Subject_species | |
| + code_set_version: '2021-09-16T18:44:48.356981+00:00' | |
| + enum_CRDCH_Subject_species: | |
| + name: enum_CRDCH_Subject_species | |
| description: The scientific binomial name for the species of the subject | |
| notes: | |
| - Derived from [Subject.species in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| @@ -12000,8 +11250,8 @@ | |
| Mus musculus: | |
| text: Mus musculus | |
| description: '' | |
| - enum_CCDH_Subject_breed: | |
| - name: enum_CCDH_Subject_breed | |
| + enum_CRDCH_Subject_breed: | |
| + name: enum_CRDCH_Subject_breed | |
| description: A label given to a group of animals homogeneous in appearance and | |
| other characteristics that distinguish it from other animals of the same species. | |
| notes: | |
| @@ -12148,13 +11398,13 @@ | |
| Yorkshire Terrier: | |
| text: Yorkshire Terrier | |
| description: '' | |
| - enum_CCDH_Subject_sex: | |
| - name: enum_CCDH_Subject_sex | |
| + enum_CRDCH_Subject_sex: | |
| + name: enum_CRDCH_Subject_sex | |
| description: Autogenerated Enumeration for CRDC-H Subject sex | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Subject.sex"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.sex | |
| - code_set_version: '2021-06-08T21:46:51.289679+00:00' | |
| + code_set_version: '2021-09-16T18:44:48.652885+00:00' | |
| permissible_values: | |
| unknown: | |
| text: unknown | |
| @@ -12166,13 +11416,13 @@ | |
| text: male | |
| unspecified: | |
| text: unspecified | |
| - enum_CCDH_Subject_ethnicity: | |
| - name: enum_CCDH_Subject_ethnicity | |
| + enum_CRDCH_Subject_ethnicity: | |
| + name: enum_CRDCH_Subject_ethnicity | |
| description: Autogenerated Enumeration for CRDC-H Subject ethnicity | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Subject.ethnicity"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.ethnicity | |
| - code_set_version: '2021-06-08T21:46:51.443978+00:00' | |
| + code_set_version: '2021-09-16T18:44:48.760719+00:00' | |
| permissible_values: | |
| not hispanic or latino: | |
| text: not hispanic or latino | |
| @@ -12187,13 +11437,13 @@ | |
| text: unknown | |
| not allowed to collect: | |
| text: not allowed to collect | |
| - enum_CCDH_Subject_race: | |
| - name: enum_CCDH_Subject_race | |
| + enum_CRDCH_Subject_race: | |
| + name: enum_CRDCH_Subject_race | |
| description: Autogenerated Enumeration for CRDC-H Subject race | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Subject.race"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.race | |
| - code_set_version: '2021-06-08T21:46:51.596778+00:00' | |
| + code_set_version: '2021-09-16T18:44:48.869614+00:00' | |
| permissible_values: | |
| not allowed to collect: | |
| text: not allowed to collect | |
| @@ -12216,13 +11466,13 @@ | |
| text: other | |
| black or african american: | |
| text: black or african american | |
| - enum_CCDH_Subject_vital_status: | |
| - name: enum_CCDH_Subject_vital_status | |
| + enum_CRDCH_Subject_vital_status: | |
| + name: enum_CRDCH_Subject_vital_status | |
| description: Autogenerated Enumeration for CRDC-H Subject vital_status | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Subject.vital_status"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.vital_status | |
| - code_set_version: '2021-06-08T21:46:51.757431+00:00' | |
| + code_set_version: '2021-09-16T18:44:48.986501+00:00' | |
| permissible_values: | |
| Unknown: | |
| text: Unknown | |
| @@ -12236,13 +11486,13 @@ | |
| Alive: | |
| text: Alive | |
| description: ALIVE | |
| - enum_CCDH_Subject_cause_of_death: | |
| - name: enum_CCDH_Subject_cause_of_death | |
| + enum_CRDCH_Subject_cause_of_death: | |
| + name: enum_CRDCH_Subject_cause_of_death | |
| description: Autogenerated Enumeration for CRDC-H Subject cause_of_death | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Subject.cause_of_death"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Subject.cause_of_death | |
| - code_set_version: '2021-06-08T21:46:51.915847+00:00' | |
| + code_set_version: '2021-09-16T18:44:49.093068+00:00' | |
| permissible_values: | |
| Infection: | |
| text: Infection | |
| @@ -12275,13 +11525,13 @@ | |
| Unknown: | |
| text: Unknown | |
| description: Unknown | |
| - enum_CCDH_Substance_substance_type: | |
| - name: enum_CCDH_Substance_substance_type | |
| + enum_CRDCH_Substance_substance_type: | |
| + name: enum_CRDCH_Substance_substance_type | |
| description: Autogenerated Enumeration for CRDC-H Substance substance_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Substance.substance_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Substance.substance_type | |
| - code_set_version: '2021-06-08T21:46:52.078830+00:00' | |
| + code_set_version: '2021-09-16T18:44:49.206692+00:00' | |
| permissible_values: | |
| Anti-PTK7/Auristatin-0101 Antibody-drug Conjugate PF-06647020: | |
| text: Anti-PTK7/Auristatin-0101 Antibody-drug Conjugate PF-06647020 | |
| @@ -21279,124 +20529,94 @@ | |
| text: Phosphatidylcholine-Bound Silybin | |
| Anti-CSF1 Monoclonal Antibody PD-0360324: | |
| text: Anti-CSF1 Monoclonal Antibody PD-0360324 | |
| - enum_CCDH_Substance_role: | |
| - name: enum_CCDH_Substance_role | |
| + enum_CRDCH_Substance_role: | |
| + name: enum_CRDCH_Substance_role | |
| description: Autogenerated Enumeration for CRDC-H Substance role | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Substance.role"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Substance.role | |
| - code_set_version: '2021-06-08T21:46:54.954840+00:00' | |
| - enum_CCDH_TimePoint_eventType: | |
| - name: enum_CCDH_TimePoint_eventType | |
| - description: A specific type of event for which a timepoint is captured | |
| - notes: | |
| - - Derived from [TimePoint.eventType in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| - permissible_values: | |
| - IACUC approval: | |
| - text: IACUC approval | |
| - description: The date that the Institutional Animal Care and Use Committee | |
| - (IACUC) approved an animal study protocol. This date cannot be released | |
| - to funding agencies until congruency between the animal use in the funding | |
| - proposal and the IACUC approved protocol has been verified. | |
| - IRB approval: | |
| - text: IRB approval | |
| - description: The date that the Institutional Review Board (IRB) approved a | |
| - study protocol | |
| - Histological confirmation of diagnosis: | |
| - text: Histological confirmation of diagnosis | |
| - description: The date that a histological diagnosis was confirmed. | |
| - enum_CCDH_TobaccoExposureObservation_category: | |
| - name: enum_CCDH_TobaccoExposureObservation_category | |
| + code_set_version: '2021-09-16T18:44:53.487954+00:00' | |
| + enum_CRDCH_TimePoint_event_type: | |
| + name: enum_CRDCH_TimePoint_event_type | |
| + description: Autogenerated Enumeration for CRDC-H TimePoint event_type | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.TimePoint.event_type"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TimePoint.event_type | |
| + code_set_version: '2021-09-16T18:44:53.604314+00:00' | |
| + enum_CRDCH_TobaccoExposureObservation_category: | |
| + name: enum_CRDCH_TobaccoExposureObservation_category | |
| description: Autogenerated Enumeration for CRDC-H TobaccoExposureObservation category | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.category"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.category | |
| - code_set_version: '2021-06-08T21:46:55.266549+00:00' | |
| - enum_CCDH_TobaccoExposureObservation_observation_type: | |
| - name: enum_CCDH_TobaccoExposureObservation_observation_type | |
| - description: Autogenerated Enumeration for CRDC-H TobaccoExposureObservation observation_type | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.observation_type"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.observation_type | |
| - code_set_version: '2021-06-08T21:46:55.415486+00:00' | |
| - enum_CCDH_TobaccoExposureObservation_method_type: | |
| - name: enum_CCDH_TobaccoExposureObservation_method_type | |
| + code_set_version: '2021-09-16T18:44:53.718414+00:00' | |
| + enum_CRDCH_TobaccoExposureObservation_observation_type: | |
| + name: enum_CRDCH_TobaccoExposureObservation_observation_type | |
| + description: Types of observations about a Subject's exposure to or use of tobacco. | |
| + notes: | |
| + - Derived from [TobaccoExposureObservation.observation_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| + permissible_values: | |
| + cigarettes_per_day: | |
| + text: cigarettes_per_day | |
| + description: The average number of cigarettes smoked per day. | |
| + pack_years_smoked: | |
| + text: pack_years_smoked | |
| + description: Numeric computed value to represent lifetime tobacco exposure | |
| + defined as number of cigarettes smoked per day x number of years smoked | |
| + divided by 20. | |
| + tobacco_smoking_onset_year: | |
| + text: tobacco_smoking_onset_year | |
| + description: The year in which the participant began smoking. | |
| + tobacco_smoking_quit_year: | |
| + text: tobacco_smoking_quit_year | |
| + description: The year in which the participant quit smoking. | |
| + years_smoked: | |
| + text: years_smoked | |
| + description: Numeric value (or unknown) to represent the number of years a | |
| + person has been smoking. | |
| + smoking_frequency: | |
| + text: smoking_frequency | |
| + description: The text term used to generally describe how often the patient | |
| + smokes. | |
| + time_between_waking_and_first_smoke: | |
| + text: time_between_waking_and_first_smoke | |
| + description: The text term used to describe the approximate amount of time | |
| + elapsed between the time the patient wakes up in the morning to the time | |
| + they smoke their first cigarette. | |
| + environmental_tobacco_smoke_exposure: | |
| + text: environmental_tobacco_smoke_exposure | |
| + description: The yes/no/unknown indicator used to describe whether a patient | |
| + was exposed to smoke that is emitted from burning tobacco, including cigarettes, | |
| + pipes, and cigars. This includes tobacco smoke exhaled by smokers. | |
| + tobacco_smoking_status: | |
| + text: tobacco_smoking_status | |
| + description: Category describing current smoking status and smoking history | |
| + as self-reported by a patient. | |
| + type_of_tobacco_used: | |
| + text: type_of_tobacco_used | |
| + description: The text term used to describe the specific type of tobacco used | |
| + by the patient. | |
| + enum_CRDCH_TobaccoExposureObservation_method_type: | |
| + name: enum_CRDCH_TobaccoExposureObservation_method_type | |
| description: Autogenerated Enumeration for CRDC-H TobaccoExposureObservation method_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.method_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.method_type | |
| - code_set_version: '2021-06-08T21:46:55.566032+00:00' | |
| - enum_CCDH_TobaccoExposureObservation_valueCodeableConcept: | |
| - name: enum_CCDH_TobaccoExposureObservation_valueCodeableConcept | |
| - description: Autogenerated Enumeration for CRDC-H TobaccoExposureObservation valueCodeableConcept | |
| - comments: | |
| - - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.valueCodeableConcept"' | |
| - code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.valueCodeableConcept | |
| - code_set_version: '2021-06-08T21:46:55.716410+00:00' | |
| - permissible_values: | |
| - Some days: | |
| - text: Some days | |
| - Every day: | |
| - text: Every day | |
| - Unknown: | |
| - text: Unknown | |
| - description: Unknown | |
| - After 60 Minutes: | |
| - text: After 60 Minutes | |
| - Within 5 Minutes: | |
| - text: Within 5 Minutes | |
| - 6-30 Minutes: | |
| - text: 6-30 Minutes | |
| - 31-60 Minutes: | |
| - text: 31-60 Minutes | |
| - Electronic Cigarette: | |
| - text: Electronic Cigarette | |
| - Smokeless Tobacco: | |
| - text: Smokeless Tobacco | |
| - Other: | |
| - text: Other | |
| - Cigar: | |
| - text: Cigar | |
| - Cigarette: | |
| - text: Cigarette | |
| - Pipe: | |
| - text: Pipe | |
| - Not Reported: | |
| - text: Not Reported | |
| - '1': | |
| - text: '1' | |
| - description: Lifelong Non-Smoker | |
| - '7': | |
| - text: '7' | |
| - description: Smoking history not documented | |
| - '2': | |
| - text: '2' | |
| - description: Current Smoker | |
| - '3': | |
| - text: '3' | |
| - description: Current Reformed Smoker for > 15 yrs | |
| - '5': | |
| - text: '5' | |
| - description: Current Reformed Smoker, Duration Not Specified | |
| - '4': | |
| - text: '4' | |
| - description: Current Reformed Smoker for < or = 15 yrs | |
| - 'Yes': | |
| - text: 'Yes' | |
| - 'No': | |
| - text: 'No' | |
| - '6': | |
| - text: '6' | |
| - description: Smoker at Diagnosis | |
| - Cigarettes: | |
| - text: Cigarettes | |
| - enum_CCDH_Treatment_treatment_type: | |
| - name: enum_CCDH_Treatment_treatment_type | |
| + code_set_version: '2021-09-16T18:44:53.933778+00:00' | |
| + enum_CRDCH_TobaccoExposureObservation_value_enum: | |
| + name: enum_CRDCH_TobaccoExposureObservation_value_enum | |
| + description: Autogenerated Enumeration for CRDC-H TobaccoExposureObservation value_enum | |
| + comments: | |
| + - 'Name according to TCCM: "CRDC-H.TobaccoExposureObservation.value_enum"' | |
| + code_set: https://terminology.ccdh.io/enumerations/CRDC-H.TobaccoExposureObservation.value_enum | |
| + code_set_version: '2021-09-16T18:44:54.042936+00:00' | |
| + enum_CRDCH_Treatment_treatment_type: | |
| + name: enum_CRDCH_Treatment_treatment_type | |
| description: Autogenerated Enumeration for CRDC-H Treatment treatment_type | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Treatment.treatment_type"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_type | |
| - code_set_version: '2021-06-08T21:46:55.875375+00:00' | |
| + code_set_version: '2021-09-16T18:44:54.151531+00:00' | |
| permissible_values: | |
| Radiation, Cyberknife: | |
| text: Radiation, Cyberknife | |
| @@ -21533,13 +20753,13 @@ | |
| text: Radioembolization | |
| Radiation, Radioisotope: | |
| text: Radiation, Radioisotope | |
| - enum_CCDH_Treatment_treatment_end_reason: | |
| - name: enum_CCDH_Treatment_treatment_end_reason | |
| + enum_CRDCH_Treatment_treatment_end_reason: | |
| + name: enum_CRDCH_Treatment_treatment_end_reason | |
| description: Autogenerated Enumeration for CRDC-H Treatment treatment_end_reason | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Treatment.treatment_end_reason"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_end_reason | |
| - code_set_version: '2021-06-08T21:46:56.055466+00:00' | |
| + code_set_version: '2021-09-16T18:44:54.319428+00:00' | |
| permissible_values: | |
| Other: | |
| text: Other | |
| @@ -21553,20 +20773,20 @@ | |
| text: Course of Therapy Completed | |
| Death: | |
| text: Death | |
| - enum_CCDH_Treatment_regimen: | |
| - name: enum_CCDH_Treatment_regimen | |
| + enum_CRDCH_Treatment_regimen: | |
| + name: enum_CRDCH_Treatment_regimen | |
| description: Autogenerated Enumeration for CRDC-H Treatment regimen | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Treatment.regimen"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.regimen | |
| - code_set_version: '2021-06-08T21:46:56.205483+00:00' | |
| - enum_CCDH_Treatment_treatment_frequency: | |
| - name: enum_CCDH_Treatment_treatment_frequency | |
| + code_set_version: '2021-09-16T18:44:54.439059+00:00' | |
| + enum_CRDCH_Treatment_treatment_frequency: | |
| + name: enum_CRDCH_Treatment_treatment_frequency | |
| description: Autogenerated Enumeration for CRDC-H Treatment treatment_frequency | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Treatment.treatment_frequency"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_frequency | |
| - code_set_version: '2021-06-08T21:46:56.354022+00:00' | |
| + code_set_version: '2021-09-16T18:44:54.547884+00:00' | |
| permissible_values: | |
| Every Other Day: | |
| text: Every Other Day | |
| @@ -21590,13 +20810,13 @@ | |
| text: Every 24 Hours | |
| Four Times Daily: | |
| text: Four Times Daily | |
| - enum_CCDH_Treatment_treatment_intent: | |
| - name: enum_CCDH_Treatment_treatment_intent | |
| + enum_CRDCH_Treatment_treatment_intent: | |
| + name: enum_CRDCH_Treatment_treatment_intent | |
| description: Autogenerated Enumeration for CRDC-H Treatment treatment_intent | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Treatment.treatment_intent"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_intent | |
| - code_set_version: '2021-06-08T21:46:56.511599+00:00' | |
| + code_set_version: '2021-09-16T18:44:54.673825+00:00' | |
| permissible_values: | |
| Neoadjuvant: | |
| text: Neoadjuvant | |
| @@ -21623,13 +20843,13 @@ | |
| Palliative: | |
| text: Palliative | |
| description: Palliative | |
| - enum_CCDH_Treatment_treatment_effect: | |
| - name: enum_CCDH_Treatment_treatment_effect | |
| + enum_CRDCH_Treatment_treatment_effect: | |
| + name: enum_CRDCH_Treatment_treatment_effect | |
| description: Autogenerated Enumeration for CRDC-H Treatment treatment_effect | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Treatment.treatment_effect"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_effect | |
| - code_set_version: '2021-06-08T21:46:56.684600+00:00' | |
| + code_set_version: '2021-09-16T18:44:54.792575+00:00' | |
| permissible_values: | |
| 'Yes': | |
| text: 'Yes' | |
| @@ -21649,13 +20869,13 @@ | |
| text: No Known Treatment Effect | |
| Complete Necrosis (No Viable Tumor): | |
| text: Complete Necrosis (No Viable Tumor) | |
| - enum_CCDH_Treatment_treatment_outcome: | |
| - name: enum_CCDH_Treatment_treatment_outcome | |
| + enum_CRDCH_Treatment_treatment_outcome: | |
| + name: enum_CRDCH_Treatment_treatment_outcome | |
| description: Autogenerated Enumeration for CRDC-H Treatment treatment_outcome | |
| comments: | |
| - 'Name according to TCCM: "CRDC-H.Treatment.treatment_outcome"' | |
| code_set: https://terminology.ccdh.io/enumerations/CRDC-H.Treatment.treatment_outcome | |
| - code_set_version: '2021-06-08T21:46:56.843366+00:00' | |
| + code_set_version: '2021-09-16T18:44:54.911782+00:00' | |
| permissible_values: | |
| Treatment Ongoing: | |
| text: Treatment Ongoing | |
| @@ -21694,45 +20914,15 @@ | |
| No Response: | |
| text: No Response | |
| description: No Response | |
| - enum_CCDH_ExecutionConditionObservation: | |
| - name: enum_CCDH_ExecutionConditionObservation | |
| - description: Types of observations about the environmental conditions under which | |
| - specific aspects of an activity were performed. | |
| - notes: | |
| - - Derived from [ExecutionConditionObservation in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| - permissible_values: | |
| - ischemic_temperature: | |
| - text: ischemic_temperature | |
| - description: A term describing the temperature of a specimen when it experienced | |
| - ischemia. | |
| - enum_CCDH_ExecutionTimeObservation: | |
| - name: enum_CCDH_ExecutionTimeObservation | |
| - description: An observation about the duration of specific aspects / parts of | |
| - an activity. | |
| - notes: | |
| - - Derived from [ExecutionTimeObservation in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| - permissible_values: | |
| - time_between_excision_and_freezing: | |
| - text: time_between_excision_and_freezing | |
| - description: The elapsed time between the excision and freezing of the specimen | |
| - from its subject/source. | |
| - time_between_clamping_and_freezing: | |
| - text: time_between_clamping_and_freezing | |
| - description: The elapsed time between the clamping of blood supply and freezing | |
| - of the specimen from its subject/source. | |
| - ischemic_time: | |
| - text: ischemic_time | |
| - description: Duration of time, in seconds, between when the specimen stopped | |
| - receiving oxygen and when it was preserved or processed. | |
| - enum_CCDH_ResearchProject_primary_anatomic_site: | |
| - name: enum_CCDH_ResearchProject_primary_anatomic_site | |
| + enum_CRDCH_ResearchProject_primary_anatomic_site: | |
| + name: enum_CRDCH_ResearchProject_primary_anatomic_site | |
| description: The text term used to describe the general location of the malignant | |
| disease, as categorized by the World Health Organization's (WHO) International | |
| Classification of Diseases for Oncology (ICD-O). | |
| notes: | |
| - Derived from [ResearchProject.primary_anatomic_site in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| - enum_CCDH_Substance__role: | |
| - name: enum_CCDH_Substance__role | |
| + enum_CRDCH_Substance__role: | |
| + name: enum_CRDCH_Substance__role | |
| description: A role played by the substance in a particular application (e.g. | |
| the role of a lysis buffer when applied in a specimen creation activity, or | |
| the role of fixative when applied in specimen processing) | |
| @@ -21755,52 +20945,25 @@ | |
| text: collection media | |
| description: A substance applied to stabilize or support the growth/metabolic | |
| activity of a specimen or derived product such as a cell line. | |
| - enum_CCDH_TobbaccoExposureObservation_observation_type: | |
| - name: enum_CCDH_TobbaccoExposureObservation_observation_type | |
| - description: Types of observations about a Subject's exposure to or use of tobacco. | |
| + enum_CRDCH_TimePoint_eventType: | |
| + name: enum_CRDCH_TimePoint_eventType | |
| + description: A specific type of event for which a timepoint is captured | |
| notes: | |
| - - Derived from [TobbaccoExposureObservation.observation_type in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| + - Derived from [TimePoint.eventType in sheet O_CCDH Enums](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=196972368) | |
| permissible_values: | |
| - cigarettes_per_day: | |
| - text: cigarettes_per_day | |
| - description: The average number of cigarettes smoked per day. | |
| - pack_years_smoked: | |
| - text: pack_years_smoked | |
| - description: Numeric computed value to represent lifetime tobacco exposure | |
| - defined as number of cigarettes smoked per day x number of years smoked | |
| - divided by 20. | |
| - tobacco_smoking_onset_year: | |
| - text: tobacco_smoking_onset_year | |
| - description: The year in which the participant began smoking. | |
| - tobacco_smoking_quit_year: | |
| - text: tobacco_smoking_quit_year | |
| - description: The year in which the participant quit smoking. | |
| - years_smoked: | |
| - text: years_smoked | |
| - description: Numeric value (or unknown) to represent the number of years a | |
| - person has been smoking. | |
| - smoking_frequency: | |
| - text: smoking_frequency | |
| - description: The text term used to generally describe how often the patient | |
| - smokes. | |
| - time_between_waking_and_first_smoke: | |
| - text: time_between_waking_and_first_smoke | |
| - description: The text term used to describe the approximate amount of time | |
| - elapsed between the time the patient wakes up in the morning to the time | |
| - they smoke their first cigarette. | |
| - environmental_tobacco_smoke_exposure: | |
| - text: environmental_tobacco_smoke_exposure | |
| - description: The yes/no/unknown indicator used to describe whether a patient | |
| - was exposed to smoke that is emitted from burning tobacco, including cigarettes, | |
| - pipes, and cigars. This includes tobacco smoke exhaled by smokers. | |
| - tobacco_smoking_status: | |
| - text: tobacco_smoking_status | |
| - description: Category describing current smoking status and smoking history | |
| - as self-reported by a patient. | |
| - type_of_tobacco_used: | |
| - text: type_of_tobacco_used | |
| - description: The text term used to describe the specific type of tobacco used | |
| - by the patient. | |
| + IACUC approval: | |
| + text: IACUC approval | |
| + description: The date that the Institutional Animal Care and Use Committee | |
| + (IACUC) approved an animal study protocol. This date cannot be released | |
| + to funding agencies until congruency between the animal use in the funding | |
| + proposal and the IACUC approved protocol has been verified. | |
| + IRB approval: | |
| + text: IRB approval | |
| + description: The date that the Institutional Review Board (IRB) approved a | |
| + study protocol | |
| + Histological confirmation of diagnosis: | |
| + text: Histological confirmation of diagnosis | |
| + description: The date that a histological diagnosis was confirmed. | |
| classes: | |
| AlcoholExposureObservation: | |
| name: AlcoholExposureObservation | |
| @@ -21839,7 +21002,7 @@ | |
| examples: | |
| - value: '' | |
| domain: AlcoholExposureObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -21850,7 +21013,7 @@ | |
| examples: | |
| - value: '' | |
| domain: AlcoholExposureObservation | |
| - range: enum_CCDH_AlcoholExposureObservation_category | |
| + range: enum_CRDCH_AlcoholExposureObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -21868,7 +21031,7 @@ | |
| - value: alcohol_history | |
| - value: alcohol_intensity | |
| domain: AlcoholExposureObservation | |
| - range: enum_CCDH_AlcoholExposureObservation_observation_type | |
| + range: enum_CRDCH_AlcoholExposureObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -21886,7 +21049,7 @@ | |
| examples: | |
| - value: '' | |
| domain: AlcoholExposureObservation | |
| - range: enum_CCDH_AlcoholExposureObservation_method_type | |
| + range: enum_CRDCH_AlcoholExposureObservation_method_type | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -21932,8 +21095,13 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueInteger: | |
| - name: valueInteger | |
| + value_integer: | |
| + name: value_integer | |
| + exact_mappings: | |
| + - GDC:Exposure.alcohol_days_per_week | |
| + - PDC:Exposure.alcohol_days_per_week | |
| + - GDC:Exposure.alcohol_drinks_per_day | |
| + - PDC:Exposure.alcohol_drinks_per_day | |
| description: The result of the observation, encoded as an integer. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -21941,17 +21109,17 @@ | |
| - One and only one of the value(x) fields must be populated. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Exposure.alcohol_days_per_week | |
| - - PDC:Exposure.alcohol_days_per_week | |
| - - GDC:Exposure.alcohol_drinks_per_day | |
| - - PDC:Exposure.alcohol_drinks_per_day | |
| domain: AlcoholExposureObservation | |
| - range: ccdh_integer | |
| + range: crdch_integer | |
| multivalued: false | |
| required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| + value_enum: | |
| + name: value_enum | |
| + exact_mappings: | |
| + - GDC:Exposure.alcohol_history | |
| + - PDC:Exposure.alcohol_history | |
| + - GDC:Exposure.alcohol_intensity | |
| + - PDC:Exposure.alcohol_intensity | |
| description: The result of the observation, encoded as a CodeableConcept. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -21959,13 +21127,8 @@ | |
| - One and only one of the value(x) fields must be populated. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Exposure.alcohol_history | |
| - - PDC:Exposure.alcohol_history | |
| - - GDC:Exposure.alcohol_intensity | |
| - - PDC:Exposure.alcohol_intensity | |
| domain: AlcoholExposureObservation | |
| - range: enum_CCDH_AlcoholExposureObservation_valueCodeableConcept | |
| + range: enum_CRDCH_AlcoholExposureObservation_value_enum | |
| multivalued: false | |
| required: false | |
| BodySite: | |
| @@ -21980,13 +21143,6 @@ | |
| attributes: | |
| site: | |
| name: site | |
| - description: A term describing any site in the body. | |
| - notes: | |
| - - 'Cardinality: 1..1' | |
| - examples: | |
| - - value: Adenoid | |
| - - value: Adipose | |
| - - value: Adrenal | |
| exact_mappings: | |
| - GDC:Sample.biospecimen_anatomic_site | |
| - PDC:Sample.biospecimen_anatomic_site | |
| @@ -21999,12 +21155,22 @@ | |
| - PDC:Treatment.treatment_anatomic_site | |
| - GDC:Diagnosis.site_of_resection_or_biopsy | |
| - PDC:Diagnosis.site_of_resection_or_biopsy | |
| + description: A term describing any site in the body. | |
| + notes: | |
| + - 'Cardinality: 1..1' | |
| + examples: | |
| + - value: Adenoid | |
| + - value: Adipose | |
| + - value: Adrenal | |
| domain: BodySite | |
| - range: enum_CCDH_BodySite_site | |
| + range: enum_CRDCH_BodySite_site | |
| multivalued: false | |
| required: true | |
| qualifier: | |
| name: qualifier | |
| + exact_mappings: | |
| + - GDC:Sample.biospecimen_laterality | |
| + - PDC:Sample.biospecimen_laterality | |
| description: A qualifier that further refines or specifies the location of | |
| the body site (e.g. to indicate laterality, upper v. lower, containment, | |
| etc). | |
| @@ -22014,11 +21180,8 @@ | |
| - value: left | |
| - value: right | |
| - value: bilateral | |
| - exact_mappings: | |
| - - GDC:Sample.biospecimen_laterality | |
| - - PDC:Sample.biospecimen_laterality | |
| domain: BodySite | |
| - range: enum_CCDH_BodySite_qualifier | |
| + range: enum_CRDCH_BodySite_qualifier | |
| multivalued: true | |
| required: false | |
| BiologicProduct: | |
| @@ -22058,7 +21221,7 @@ | |
| examples: | |
| - value: '' | |
| domain: BiologicProduct | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| identifier: | |
| @@ -22086,6 +21249,7 @@ | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| description: | |
| name: description | |
| description: A free text field to capture additional info/explanation about | |
| @@ -22095,7 +21259,7 @@ | |
| examples: | |
| - value: '' | |
| domain: BiologicProduct | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| product_type: | |
| @@ -22110,38 +21274,40 @@ | |
| - value: tissue culture | |
| - value: organoid | |
| domain: BiologicProduct | |
| - range: enum_CCDH_BiologicProduct_product_type | |
| + range: enum_CRDCH_BiologicProduct_product_type | |
| multivalued: false | |
| required: false | |
| passage_number: | |
| name: passage_number | |
| + exact_mappings: | |
| + - GDC:Sample.passage_count | |
| + - PDC:Sample.passage_count | |
| description: When the specimen an actively growing model system, such as a | |
| cell or tissue culture, this property captures its passage number. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Sample.passage_count | |
| - - PDC:Sample.passage_count | |
| domain: BiologicProduct | |
| - range: ccdh_integer | |
| + range: crdch_integer | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| growth_rate: | |
| name: growth_rate | |
| + exact_mappings: | |
| + - GDC:Sample.growth_rate | |
| + - PDC:Sample.growth_rate | |
| description: When the specimen an actively growing model system, such as a | |
| cell or tissue culture, this property captures its rate of growth. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Sample.growth_rate | |
| - - PDC:Sample.growth_rate | |
| domain: BiologicProduct | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| CancerGradeObservation: | |
| name: CancerGradeObservation | |
| - description: A data structure with key (observation_type) and value (valueCodeableConcept) | |
| + description: A data structure with key (observation_type) and value (value_enum) | |
| attributes that represents a single cancer grade observation | |
| notes: | |
| - Derived from [CancerGradeObservation in sheet CancerGradeObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1099484640) | |
| @@ -22175,7 +21341,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerGradeObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -22186,7 +21352,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerGradeObservation | |
| - range: enum_CCDH_CancerGradeObservation_category | |
| + range: enum_CRDCH_CancerGradeObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -22207,7 +21373,7 @@ | |
| - value: secondary_gleason_grade | |
| - value: tumor_grade | |
| domain: CancerGradeObservation | |
| - range: enum_CCDH_CancerGradeObservation_observation_type | |
| + range: enum_CRDCH_CancerGradeObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -22225,7 +21391,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerGradeObservation | |
| - range: enum_CCDH_CancerGradeObservation_method_type | |
| + range: enum_CRDCH_CancerGradeObservation_method_type | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -22260,16 +21426,8 @@ | |
| range: Subject | |
| multivalued: false | |
| required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| - description: The value from the grade classification system that classifies | |
| - the cancer (e.g. Poorly differentiated, differentiated, etc.) | |
| - notes: | |
| - - 'Cardinality: 1..1' | |
| - comments: | |
| - - One and only one of the value(x) fields must be populated. | |
| - examples: | |
| - - value: '' | |
| + value_enum: | |
| + name: value_enum | |
| exact_mappings: | |
| - GDC:Diagnosis.enneking_msts_grade | |
| - PDC:Diagnosis.enneking_msts_grade | |
| @@ -22290,8 +21448,16 @@ | |
| - PDC:Diagnosis.tumor_grade | |
| - HTAN:Diagnosis.TumorGrade | |
| - ICDC:Diagnosis.histological_grade | |
| + description: The value from the grade classification system that classifies | |
| + the cancer (e.g. Poorly differentiated, differentiated, etc.) | |
| + notes: | |
| + - 'Cardinality: 1..1' | |
| + comments: | |
| + - One and only one of the value(x) fields must be populated. | |
| + examples: | |
| + - value: '' | |
| domain: CancerGradeObservation | |
| - range: enum_CCDH_CancerGradeObservation_valueCodeableConcept | |
| + range: enum_CRDCH_CancerGradeObservation_value_enum | |
| multivalued: false | |
| required: true | |
| CancerGradeObservationSet: | |
| @@ -22330,7 +21496,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerGradeObservationSet | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -22347,7 +21513,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerGradeObservationSet | |
| - range: enum_CCDH_CancerGradeObservationSet_category | |
| + range: enum_CRDCH_CancerGradeObservationSet_category | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -22368,6 +21534,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -22400,7 +21567,7 @@ | |
| - value: INPC | |
| - value: Unspecified grading system | |
| domain: CancerGradeObservationSet | |
| - range: enum_CCDH_CancerGradeObservationSet_method_type | |
| + range: enum_CRDCH_CancerGradeObservationSet_method_type | |
| multivalued: true | |
| required: false | |
| performed_by: | |
| @@ -22427,9 +21594,10 @@ | |
| range: CancerGradeObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| CancerStageObservation: | |
| name: CancerStageObservation | |
| - description: A data structure with key (observation_type) and value (valueCodeableConcept) | |
| + description: A data structure with key (observation_type) and value (value_enum) | |
| attributes that represents a single cancer staging observation, such as the | |
| Clinical Metastasis (M) component of a clinical TNM staging. | |
| notes: | |
| @@ -22464,7 +21632,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerStageObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -22475,7 +21643,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerStageObservation | |
| - range: enum_CCDH_CancerStageObservation_category | |
| + range: enum_CRDCH_CancerStageObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -22507,7 +21675,7 @@ | |
| - value: Pathological Metastasis (M) | |
| - value: Ann Arbor Modifier | |
| domain: CancerStageObservation | |
| - range: enum_CCDH_CancerStageObservation_observation_type | |
| + range: enum_CRDCH_CancerStageObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -22525,7 +21693,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerStageObservation | |
| - range: enum_CCDH_CancerStageObservation_method_type | |
| + range: enum_CRDCH_CancerStageObservation_method_type | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -22571,8 +21739,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueEntity: | |
| - name: valueEntity | |
| + value_entity: | |
| + name: value_entity | |
| description: The value of an observation | |
| notes: | |
| - 'Cardinality: 0..0' | |
| @@ -22582,21 +21750,8 @@ | |
| range: Entity | |
| multivalued: false | |
| required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| - description: The value for a cancer staging component being represented (e.g. | |
| - 'M1'), encoded as a CodeableConcept. | |
| - notes: | |
| - - 'Cardinality: 1..1' | |
| - comments: | |
| - - One and only one of the value(x) fields must be populated. | |
| - examples: | |
| - - value: M0 | |
| - - value: M1 | |
| - - value: M1a | |
| - - value: N0 | |
| - - value: N0 (i+) | |
| - - value: N0 (i-) | |
| + value_enum: | |
| + name: value_enum | |
| exact_mappings: | |
| - GDC:Diagnosis.ajcc_clinical_m | |
| - PDC:Diagnosis.ajcc_clinical_m | |
| @@ -22614,6 +21769,7 @@ | |
| - HTAN:Diagnosis.AJCCPathologicN | |
| - HTAN:Diagnosis.AJCCPathologicT | |
| - HTAN:Diagnosis.AJCCPathologicStage | |
| + - GDC:Diagnosis.tumor_stage | |
| - PDC:Diagnosis.tumor_stage | |
| - ICDC:Diagnosis.stage_of_disease | |
| - GDC:Diagnosis.ajcc_pathologic_m | |
| @@ -22658,8 +21814,21 @@ | |
| - PDC:Diagnosis.ann_arbor_b_symptoms | |
| - GDC:Diagnosis.ann_arbor_extranodal_involvement | |
| - PDC:Diagnosis.ann_arbor_extranodal_involvement | |
| + description: The value for a cancer staging component being represented (e.g. | |
| + 'M1'), encoded as a CodeableConcept. | |
| + notes: | |
| + - 'Cardinality: 1..1' | |
| + comments: | |
| + - One and only one of the value(x) fields must be populated. | |
| + examples: | |
| + - value: M0 | |
| + - value: M1 | |
| + - value: M1a | |
| + - value: N0 | |
| + - value: N0 (i+) | |
| + - value: N0 (i-) | |
| domain: CancerStageObservation | |
| - range: enum_CCDH_CancerStageObservation_valueCodeableConcept | |
| + range: enum_CRDCH_CancerStageObservation_value_enum | |
| multivalued: false | |
| required: true | |
| CancerStageObservationSet: | |
| @@ -22698,7 +21867,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerStageObservationSet | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -22715,7 +21884,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CancerStageObservationSet | |
| - range: enum_CCDH_CancerStageObservationSet_category | |
| + range: enum_CRDCH_CancerStageObservationSet_category | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -22736,6 +21905,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -22752,6 +21922,10 @@ | |
| required: false | |
| method_type: | |
| name: method_type | |
| + close_mappings: | |
| + - GDC:Diagnosis.ajcc_staging_system_edition | |
| + - PDC:Diagnosis.ajcc_staging_system_edition | |
| + - HTAN:Diagnosis.AJCCStagingSystemEdition | |
| description: A type of method used in generating each of the Observations | |
| bundled in the set, in this case, the particular staging system being used | |
| to classify the cancer. | |
| @@ -22785,12 +21959,8 @@ | |
| - value: ISS staging system | |
| - value: Masaoka staging system | |
| - value: Unspecified staging system | |
| - close_mappings: | |
| - - GDC:Diagnosis.ajcc_staging_system_edition | |
| - - PDC:Diagnosis.ajcc_staging_system_edition | |
| - - HTAN:Diagnosis.AJCCStagingSystemEdition | |
| domain: CancerStageObservationSet | |
| - range: enum_CCDH_CancerStageObservationSet_method_type | |
| + range: enum_CRDCH_CancerStageObservationSet_method_type | |
| multivalued: true | |
| required: false | |
| performed_by: | |
| @@ -22816,6 +21986,7 @@ | |
| range: CancerStageObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| CodeableConcept: | |
| name: CodeableConcept | |
| description: A representation of a concept that may be defined by or mapped to | |
| @@ -22846,6 +22017,7 @@ | |
| range: Coding | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| text: | |
| name: text | |
| description: A human language representation of the concept represented by | |
| @@ -22860,7 +22032,7 @@ | |
| examples: | |
| - value: '' | |
| domain: CodeableConcept | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| Coding: | |
| @@ -22879,53 +22051,78 @@ | |
| examples: | |
| - value: '' | |
| domain: Coding | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| + label: | |
| + name: label | |
| + description: A human-readable name for the code, as defined by the code system. | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + examples: | |
| + - value: '' | |
| + domain: Coding | |
| + range: crdch_string | |
| + multivalued: false | |
| + required: false | |
| system: | |
| name: system | |
| - description: The code system where the code is defined. | |
| + description: The URL of the code system where the code is defined. | |
| notes: | |
| - 'Cardinality: 1..1' | |
| examples: | |
| - value: '' | |
| domain: Coding | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| - label: | |
| - name: label | |
| - description: A human-readable name for the code, as defined by the code system. | |
| + system_version: | |
| + name: system_version | |
| + description: The version of the code system. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| domain: Coding | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| - systemURL: | |
| - name: systemURL | |
| - description: A URL where the code system can be found. | |
| + value_set: | |
| + name: value_set | |
| + description: The identifier of the enumeration / value set that the code is | |
| + a part of in the context of this element | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| domain: Coding | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| - systemVersion: | |
| - name: systemVersion | |
| - description: The version of the code system. | |
| + value_set_version: | |
| + name: value_set_version | |
| + description: The version of the enuemration / value set the code is pulled | |
| + from | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| domain: Coding | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| + tag: | |
| + name: tag | |
| + description: original value | harmonized value | | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| + domain: Coding | |
| + range: crdch_string | |
| + multivalued: true | |
| + required: false | |
| + inlined_as_list: true | |
| Diagnosis: | |
| name: Diagnosis | |
| description: A collection of characteristics that describe an abnormal condition | |
| @@ -22937,6 +22134,9 @@ | |
| attributes: | |
| id: | |
| name: id | |
| + exact_mappings: | |
| + - GDC:Diagnosis.id | |
| + - PDC:Diagnosis.diagnosis_id | |
| description: The 'logical' identifier of the entity within the system of record. The | |
| simple value of this attribute stands for an identifier of this data object | |
| within the system, it can be used as a reference from other objects within | |
| @@ -22962,15 +22162,15 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Diagnosis.id | |
| - - PDC:Diagnosis.diagnosis_id | |
| domain: Diagnosis | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| identifier: | |
| name: identifier | |
| + exact_mappings: | |
| + - GDC:Diagnosis.submitter_id | |
| + - PDC:Diagnosis.diagnosis_submitter_id | |
| description: A 'business' identifier or accession number for the entity, typically | |
| as provided by an external system or authority, that are globally unique | |
| and persist across implementing systems. Also, since these identifiers are | |
| @@ -22990,13 +22190,11 @@ | |
| the identifier itself, along with metadata about its source. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Diagnosis.submitter_id | |
| - - PDC:Diagnosis.diagnosis_submitter_id | |
| domain: Diagnosis | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The subject of this diagnosis. | |
| @@ -23010,37 +22208,53 @@ | |
| required: false | |
| age_at_diagnosis: | |
| name: age_at_diagnosis | |
| + close_mappings: | |
| + - GDC:Diagnosis.age_at_diagnosis | |
| + - PDC:Diagnosis.age_at_diagnosis | |
| + - HTAN:Diagnosis.AgeatDiagnosis | |
| description: The age in days of the individual at the time of diagnosis | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Diagnosis.age_at_diagnosis | |
| - - PDC:Diagnosis.age_at_diagnosis | |
| - - HTAN:Diagnosis.AgeatDiagnosis | |
| domain: Diagnosis | |
| range: Quantity | |
| multivalued: false | |
| required: false | |
| - year_at_diagnosis: | |
| - name: year_at_diagnosis | |
| - description: Numeric value to represent the year of an individual's diagnosis. | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - examples: | |
| - - value: '' | |
| - exact_mappings: | |
| + diagnosis_date: | |
| + name: diagnosis_date | |
| + close_mappings: | |
| - GDC:Diagnosis.year_of_diagnosis | |
| + - GDC:Diagnosis.days_to_diagnosis | |
| - PDC:Diagnosis.year_of_diagnosis | |
| + - PDC:Diagnosis.days_to_diagnosis | |
| - HTAN:Diagnosis.YearofDiagnosis | |
| - ICDC:Diagnosis.date_of_diagnosis | |
| + description: When the diagnosis was made. | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + comments: | |
| + - 'A TimePoint object supports three ways to specify a point in time, each | |
| + of which might be used in the context of capturing a diagnosis date - as | |
| + source node data can report this date as an explicit year or date (e.g. | |
| + 2021-05-05), or an offset from an indexed point in time. See description | |
| + of the TimePoint entity for more information here. ' | |
| + examples: | |
| + - value: '' | |
| domain: Diagnosis | |
| - range: ccdh_integer | |
| + range: TimePoint | |
| multivalued: false | |
| required: false | |
| condition: | |
| name: condition | |
| + exact_mappings: | |
| + - GDC:Diagnosis.primary_diagnosis | |
| + - PDC:Diagnosis.primary_diagnosis | |
| + - HTAN:Diagnosis.PrimaryDiagnosis | |
| + - ICDC:Diagnosis.disease_term | |
| + - ICDC:Diagnosis.concurrent_disease_type | |
| + - GDC:Diagnosis.icd_10_code | |
| + - PDC:Diagnosis.icd_10_code | |
| description: Code that captures the condition being diagnosed (e.g. ICD-O, | |
| ICD-10, SNOMED, etc.) | |
| notes: | |
| @@ -23050,25 +22264,12 @@ | |
| ICD-10 classification systems. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Diagnosis.primary_diagnosis | |
| - - PDC:Diagnosis.primary_diagnosis | |
| - - HTAN:Diagnosis.PrimaryDiagnosis | |
| - - ICDC:Diagnosis.disease_term | |
| - - ICDC:Diagnosis.concurrent_disease_type | |
| - - GDC:Diagnosis.icd_10_code | |
| - - PDC:Diagnosis.icd_10_code | |
| domain: Diagnosis | |
| - range: enum_CCDH_Diagnosis_condition | |
| + range: enum_CRDCH_Diagnosis_condition | |
| multivalued: false | |
| required: false | |
| primary_site: | |
| name: primary_site | |
| - description: The anatomical location of the primary condition | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Diagnosis.tissue_or_organ_of_origin | |
| - PDC:Diagnosis.tissue_or_organ_of_origin | |
| @@ -23079,10 +22280,16 @@ | |
| - GDC:Diagnosis.site_of_resection_or_biopsy | |
| - PDC:Diagnosis.site_of_resection_or_biopsy | |
| - HTAN:Diagnosis.SiteofResectionorBiopsy | |
| + description: The anatomical location of the primary condition | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| domain: Diagnosis | |
| range: BodySite | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| metastatic_site: | |
| name: metastatic_site | |
| description: The anatomical location(s) of metastatic disease | |
| @@ -23094,15 +22301,9 @@ | |
| range: BodySite | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| stage: | |
| name: stage | |
| - description: The extent of a cancer in the body. Staging is usually based | |
| - on the size of the tumor, whether lymph nodes contain cancer, and whether | |
| - the cancer has spread from the original site to other parts of the body. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Diagnosis.ajcc_clinical_m | |
| - PDC:Diagnosis.ajcc_clinical_m | |
| @@ -23112,6 +22313,7 @@ | |
| - PDC:Diagnosis.ajcc_clinical_t | |
| - GDC:Diagnosis.ajcc_clinical_stage | |
| - PDC:Diagnosis.ajcc_clinical_stage | |
| + - GDC:Diagnosis.tumor_stage | |
| - PDC:Diagnosis.tumor_stage | |
| - ICDC:Diagnosis.stage_of_disease | |
| - GDC:Diagnosis.ajcc_pathologic_m | |
| @@ -23152,25 +22354,20 @@ | |
| - PDC:Diagnosis.inrg_stage | |
| - GDC:Diagnosis.irs_stage | |
| - PDC:Diagnosis.irs_stage | |
| + description: The extent of a cancer in the body. Staging is usually based | |
| + on the size of the tumor, whether lymph nodes contain cancer, and whether | |
| + the cancer has spread from the original site to other parts of the body. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| domain: Diagnosis | |
| range: CancerStageObservationSet | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| grade: | |
| name: grade | |
| - description: The degree of abnormality of cancer cells, a measure of differentiation, | |
| - the extent to which cancer cells are similar in appearance and function | |
| - to healthy cells of the same tissue type. The degree of differentiation | |
| - often relates to the clinical behavior of the particular tumor. Based on | |
| - the microscopic findings, tumor grade is commonly described by one of four | |
| - degrees of severity. Histopathologic grade of a tumor may be used to plan | |
| - treatment and estimate the future course, outcome, and overall prognosis | |
| - of disease. Certain types of cancers, such as soft tissue sarcoma, primary | |
| - brain tumors, lymphomas, and breast have special grading systems. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Diagnosis.enneking_msts_grade | |
| - PDC:Diagnosis.enneking_msts_grade | |
| @@ -23190,12 +22387,30 @@ | |
| - ICDC:Diagnosis.histological_grade | |
| - GDC:Diagnosis.tumor_regression_grade | |
| - PDC:Diagnosis.tumor_regression_grade | |
| - domain: Diagnosis | |
| - range: CancerGradeObservationSet | |
| + description: The degree of abnormality of cancer cells, a measure of differentiation, | |
| + the extent to which cancer cells are similar in appearance and function | |
| + to healthy cells of the same tissue type. The degree of differentiation | |
| + often relates to the clinical behavior of the particular tumor. Based on | |
| + the microscopic findings, tumor grade is commonly described by one of four | |
| + degrees of severity. Histopathologic grade of a tumor may be used to plan | |
| + treatment and estimate the future course, outcome, and overall prognosis | |
| + of disease. Certain types of cancers, such as soft tissue sarcoma, primary | |
| + brain tumors, lymphomas, and breast have special grading systems. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| + domain: Diagnosis | |
| + range: CancerGradeObservationSet | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| morphology: | |
| name: morphology | |
| + exact_mappings: | |
| + - GDC:Diagnosis.morphology | |
| + - PDC:Diagnosis.morphology | |
| + - HTAN:Diagnosis.Morphology | |
| description: Code that represents the histology of the disease using the third | |
| edition of the International Classification of Diseases for Oncology, published | |
| in 2000, used principally in tumor and cancer registries for coding the | |
| @@ -23208,16 +22423,15 @@ | |
| - value: 8003/3 | |
| - value: 8004/3 | |
| - value: 8005/3 | |
| - exact_mappings: | |
| - - GDC:Diagnosis.morphology | |
| - - PDC:Diagnosis.morphology | |
| - - HTAN:Diagnosis.Morphology | |
| domain: Diagnosis | |
| - range: enum_CCDH_Diagnosis_morphology | |
| + range: enum_CRDCH_Diagnosis_morphology | |
| multivalued: false | |
| required: false | |
| disease_status: | |
| name: disease_status | |
| + exact_mappings: | |
| + - GDC:Treatment.initial_disease_status | |
| + - PDC:Treatment.initial_disease_status | |
| description: A term that refers to the nature and/or clinical outcome of a | |
| disease (e.g., primary disease, metastatic disease, recurrent disease, etc.) | |
| notes: | |
| @@ -23229,11 +22443,8 @@ | |
| - value: Residual Disease | |
| - value: Unknown | |
| - value: Not Reported | |
| - exact_mappings: | |
| - - GDC:Treatment.initial_disease_status | |
| - - PDC:Treatment.initial_disease_status | |
| domain: Diagnosis | |
| - range: enum_CCDH_Diagnosis_disease_status | |
| + range: enum_CRDCH_Diagnosis_disease_status | |
| multivalued: false | |
| required: false | |
| prior_diagnosis: | |
| @@ -23251,6 +22462,9 @@ | |
| required: false | |
| method_of_diagnosis: | |
| name: method_of_diagnosis | |
| + exact_mappings: | |
| + - GDC:Diagnosis.method_of_diagnosis | |
| + - PDC:Diagnosis.method_of_diagnosis | |
| description: The method used to confirm the patients malignant diagnosis | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -23261,11 +22475,8 @@ | |
| - value: Bone Marrow Aspirate | |
| - value: Core Biopsy | |
| - value: .. | |
| - exact_mappings: | |
| - - GDC:Diagnosis.method_of_diagnosis | |
| - - PDC:Diagnosis.method_of_diagnosis | |
| domain: Diagnosis | |
| - range: enum_CCDH_Diagnosis_method_of_diagnosis | |
| + range: enum_CRDCH_Diagnosis_method_of_diagnosis | |
| multivalued: false | |
| required: false | |
| related_specimen: | |
| @@ -23279,29 +22490,24 @@ | |
| range: Specimen | |
| multivalued: true | |
| required: false | |
| - dimensional_measure: | |
| - name: dimensional_measure | |
| - description: A set of one or more observations about the current physical | |
| - dimensions of an object (e.g. length, width, area). | |
| + inlined_as_list: true | |
| + primary_tumor_dimensional_measures: | |
| + name: primary_tumor_dimensional_measures | |
| + close_mappings: | |
| + - GDC:Diagnosis.tumor_largest_dimension_diameter | |
| + - PDC:Diagnosis.tumor_largest_dimension_diameter | |
| + description: Observations about the current physical dimensions of the primary | |
| + tumor. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Diagnosis.tumor_largest_dimension_diameter | |
| - - PDC:Diagnosis.tumor_largest_dimension_diameter | |
| domain: Diagnosis | |
| range: DimensionalObservationSet | |
| multivalued: false | |
| required: false | |
| supporting_observation: | |
| name: supporting_observation | |
| - description: One or more observations that capture information relevant to | |
| - this condition or diagnosis. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| exact_mappings: | |
| - GDC:Diagnosis.international_prognostic_index | |
| - PDC:Diagnosis.international_prognostic_index | |
| @@ -23311,10 +22517,17 @@ | |
| - PDC:Diagnosis.lymphatic_invasion_present | |
| - GDC:Diagnosis.metastasis_at_diagnosis | |
| - PDC:Diagnosis.metastasis_at_diagnosis | |
| + description: One or more observations that capture information relevant to | |
| + this condition or diagnosis. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| domain: Diagnosis | |
| range: Observation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| DimensionalObservation: | |
| name: DimensionalObservation | |
| description: A structured object that describes a single data item about the physical | |
| @@ -23358,7 +22571,7 @@ | |
| examples: | |
| - value: '' | |
| domain: DimensionalObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -23371,7 +22584,7 @@ | |
| examples: | |
| - value: '' | |
| domain: DimensionalObservation | |
| - range: enum_CCDH_DimensionalObservation_category | |
| + range: enum_CRDCH_DimensionalObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -23386,7 +22599,7 @@ | |
| examples: | |
| - value: '' | |
| domain: DimensionalObservation | |
| - range: enum_CCDH_DimensionalObservation_observation_type | |
| + range: enum_CRDCH_DimensionalObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -23404,7 +22617,7 @@ | |
| examples: | |
| - value: '' | |
| domain: DimensionalObservation | |
| - range: enum_CCDH_DimensionalObservation_method_type | |
| + range: enum_CRDCH_DimensionalObservation_method_type | |
| multivalued: true | |
| required: false | |
| focus: | |
| @@ -23425,6 +22638,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -23450,8 +22664,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueQuantity: | |
| - name: valueQuantity | |
| + value_quantity: | |
| + name: value_quantity | |
| description: The result of the observation, encoded as a free-text Quantity. | |
| notes: | |
| - 'Cardinality: 1..1' | |
| @@ -23497,7 +22711,7 @@ | |
| examples: | |
| - value: '' | |
| domain: DimensionalObservationSet | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -23514,7 +22728,7 @@ | |
| examples: | |
| - value: '' | |
| domain: DimensionalObservationSet | |
| - range: enum_CCDH_DimensionalObservationSet_category | |
| + range: enum_CRDCH_DimensionalObservationSet_category | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -23535,6 +22749,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -23551,6 +22766,10 @@ | |
| required: false | |
| method_type: | |
| name: method_type | |
| + exact_mappings: | |
| + - GDC:Analyte.spectrophotometer_method | |
| + - PDC:Analyte.spectrophotometer_method | |
| + - HTAN:Biospecimen.HistologyAssessmentMedium | |
| description: A type of method used in generating each of the Observations | |
| bundled in the set. | |
| notes: | |
| @@ -23564,12 +22783,8 @@ | |
| as that provided by the ACMG). | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Analyte.spectrophotometer_method | |
| - - PDC:Analyte.spectrophotometer_method | |
| - - HTAN:Biospecimen.HistologyAssessmentMedium | |
| domain: DimensionalObservationSet | |
| - range: enum_CCDH_DimensionalObservationSet_method_type | |
| + range: enum_CRDCH_DimensionalObservationSet_method_type | |
| multivalued: true | |
| required: false | |
| performed_by: | |
| @@ -23599,6 +22814,7 @@ | |
| range: DimensionalObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| Document: | |
| name: Document | |
| description: A collection of information intented to be understood together as | |
| @@ -23635,7 +22851,7 @@ | |
| examples: | |
| - value: '' | |
| domain: Document | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| identifier: | |
| @@ -23663,6 +22879,7 @@ | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| document_type: | |
| name: document_type | |
| description: The high-level type of the document (e.g. 'publication', 'pathology | |
| @@ -23672,7 +22889,7 @@ | |
| examples: | |
| - value: '' | |
| domain: Document | |
| - range: enum_CCDH_Document_document_type | |
| + range: enum_CRDCH_Document_document_type | |
| multivalued: false | |
| required: false | |
| description: | |
| @@ -23683,7 +22900,7 @@ | |
| examples: | |
| - value: '' | |
| domain: Document | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -23705,9 +22922,10 @@ | |
| examples: | |
| - value: '' | |
| domain: Document | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| Entity: | |
| name: Entity | |
| description: Any resource that has its own identifier | |
| @@ -23750,7 +22968,7 @@ | |
| examples: | |
| - value: '' | |
| domain: EnvironmentalExposureObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -23761,7 +22979,7 @@ | |
| examples: | |
| - value: '' | |
| domain: EnvironmentalExposureObservation | |
| - range: enum_CCDH_EnvironmentalExposureObservation_category | |
| + range: enum_CRDCH_EnvironmentalExposureObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -23781,7 +22999,7 @@ | |
| - value: respirable_crystalline_silica_exposure | |
| - value: type_of_smoke_exposure | |
| domain: EnvironmentalExposureObservation | |
| - range: enum_CCDH_EnvironmentalExposureObservation_observation_type | |
| + range: enum_CRDCH_EnvironmentalExposureObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -23799,7 +23017,7 @@ | |
| examples: | |
| - value: '' | |
| domain: EnvironmentalExposureObservation | |
| - range: enum_CCDH_EnvironmentalExposureObservation_method_type | |
| + range: enum_CRDCH_EnvironmentalExposureObservation_method_type | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -23845,15 +23063,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| - description: The result of the observation, encoded as a CodeableConcept. | |
| - notes: | |
| - - 'Cardinality: 1..1' | |
| - comments: | |
| - - One and only one of the value(x) fields must be populated. | |
| - examples: | |
| - - value: '' | |
| + value_enum: | |
| + name: value_enum | |
| exact_mappings: | |
| - GDC:Exposure.asbestos_exposure | |
| - PDC:Exposure.asbestos_exposure | |
| @@ -23865,12 +23076,19 @@ | |
| - PDC:Exposure.respirable_crystalline_silica_exposure | |
| - GDC:Exposure.type_of_smoke_exposure | |
| - PDC:Exposure.type_of_smoke_exposure | |
| + description: The result of the observation, encoded as a CodeableConcept. | |
| + notes: | |
| + - 'Cardinality: 1..1' | |
| + comments: | |
| + - One and only one of the value(x) fields must be populated. | |
| + examples: | |
| + - value: '' | |
| domain: EnvironmentalExposureObservation | |
| - range: enum_CCDH_EnvironmentalExposureObservation_valueCodeableConcept | |
| + range: enum_CRDCH_EnvironmentalExposureObservation_value_enum | |
| multivalued: false | |
| required: true | |
| - ExecutionTimeObservation: | |
| - name: ExecutionTimeObservation | |
| + ExecutionConditionObservation: | |
| + name: ExecutionConditionObservation | |
| description: 'A structured object that describes how long certain parts on an | |
| activity took to complete, as determined through a point-in-time observation | |
| or measurement. | |
| @@ -23879,7 +23097,7 @@ | |
| Information describing the environmental conditions in which an activity, or | |
| a specific part of an activity, was performed.' | |
| notes: | |
| - - Derived from [ExecutionTimeObservation in sheet ExecutionTimeObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=638866265) | |
| + - Derived from [ExecutionConditionObservation in sheet ExecutionConditionObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1598634433) | |
| is_a: Entity | |
| attributes: | |
| id: | |
| @@ -23909,8 +23127,8 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionTimeObservation | |
| - range: ccdh_string | |
| + domain: ExecutionConditionObservation | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -23920,8 +23138,8 @@ | |
| - 'Cardinality: 0..0' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionTimeObservation | |
| - range: enum_CCDH_ExecutionTimeObservation_category | |
| + domain: ExecutionConditionObservation | |
| + range: enum_CRDCH_ExecutionConditionObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -23936,8 +23154,8 @@ | |
| field and the relevant value(s) field. | |
| examples: | |
| - value: '' | |
| - domain: ExecutionTimeObservation | |
| - range: enum_CCDH_ExecutionTimeObservation_observation_type | |
| + domain: ExecutionConditionObservation | |
| + range: enum_CRDCH_ExecutionConditionObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -23954,8 +23172,8 @@ | |
| as that provided by the ACMG). | |
| examples: | |
| - value: '' | |
| - domain: ExecutionTimeObservation | |
| - range: enum_CCDH_ExecutionTimeObservation_method_type | |
| + domain: ExecutionConditionObservation | |
| + range: enum_CRDCH_ExecutionConditionObservation_method_type | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -23972,7 +23190,7 @@ | |
| can be determined from context. ' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionTimeObservation | |
| + domain: ExecutionConditionObservation | |
| range: Entity | |
| multivalued: false | |
| required: false | |
| @@ -23986,7 +23204,7 @@ | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionTimeObservation | |
| + domain: ExecutionConditionObservation | |
| range: Subject | |
| multivalued: false | |
| required: false | |
| @@ -23997,31 +23215,28 @@ | |
| - 'Cardinality: 0..0' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionTimeObservation | |
| + domain: ExecutionConditionObservation | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueQuantity: | |
| - name: valueQuantity | |
| - description: The result of the observation, encoded as a free-text Quantity. | |
| + value_enum: | |
| + name: value_enum | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.ISCHEMIC_TEMPERATURE | |
| + - HTAN:Biospecimen.SHIPPING_CONDITIONS | |
| + description: The result of the observation, encoded as a CodeableConcept. | |
| notes: | |
| - 'Cardinality: 1..1' | |
| comments: | |
| - One and only one of the value(x) fields must be populated. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Sample.time_between_excision_and_freezing | |
| - - GDC:Sample.time_between_clamping_and_freezing | |
| - - PDC:Sample.time_between_excision_and_freezing | |
| - - PDC:Sample.time_between_clamping_and_freezing | |
| - - HTAN:Biospecimen.ISCHEMIC_TIME | |
| - domain: ExecutionTimeObservation | |
| - range: Quantity | |
| + domain: ExecutionConditionObservation | |
| + range: enum_CRDCH_ExecutionConditionObservation_value_enum | |
| multivalued: false | |
| required: true | |
| - ExecutionConditionObservation: | |
| - name: ExecutionConditionObservation | |
| + ExecutionTimeObservation: | |
| + name: ExecutionTimeObservation | |
| description: 'A structured object that describes how long certain parts on an | |
| activity took to complete, as determined through a point-in-time observation | |
| or measurement. | |
| @@ -24030,7 +23245,7 @@ | |
| Information describing the environmental conditions in which an activity, or | |
| a specific part of an activity, was performed.' | |
| notes: | |
| - - Derived from [ExecutionConditionObservation in sheet ExecutionConditionObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1598634433) | |
| + - Derived from [ExecutionTimeObservation in sheet ExecutionTimeObservation](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=638866265) | |
| is_a: Entity | |
| attributes: | |
| id: | |
| @@ -24060,8 +23275,8 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionConditionObservation | |
| - range: ccdh_string | |
| + domain: ExecutionTimeObservation | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -24071,8 +23286,8 @@ | |
| - 'Cardinality: 0..0' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionConditionObservation | |
| - range: enum_CCDH_ExecutionConditionObservation_category | |
| + domain: ExecutionTimeObservation | |
| + range: enum_CRDCH_ExecutionTimeObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -24087,8 +23302,8 @@ | |
| field and the relevant value(s) field. | |
| examples: | |
| - value: '' | |
| - domain: ExecutionConditionObservation | |
| - range: enum_CCDH_ExecutionConditionObservation_observation_type | |
| + domain: ExecutionTimeObservation | |
| + range: enum_CRDCH_ExecutionTimeObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -24105,8 +23320,8 @@ | |
| as that provided by the ACMG). | |
| examples: | |
| - value: '' | |
| - domain: ExecutionConditionObservation | |
| - range: enum_CCDH_ExecutionConditionObservation_method_type | |
| + domain: ExecutionTimeObservation | |
| + range: enum_CRDCH_ExecutionTimeObservation_method_type | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -24123,7 +23338,7 @@ | |
| can be determined from context. ' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionConditionObservation | |
| + domain: ExecutionTimeObservation | |
| range: Entity | |
| multivalued: false | |
| required: false | |
| @@ -24137,7 +23352,7 @@ | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionConditionObservation | |
| + domain: ExecutionTimeObservation | |
| range: Subject | |
| multivalued: false | |
| required: false | |
| @@ -24148,24 +23363,27 @@ | |
| - 'Cardinality: 0..0' | |
| examples: | |
| - value: '' | |
| - domain: ExecutionConditionObservation | |
| + domain: ExecutionTimeObservation | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| - description: The result of the observation, encoded as a CodeableConcept. | |
| + value_quantity: | |
| + name: value_quantity | |
| + exact_mappings: | |
| + - GDC:Sample.time_between_excision_and_freezing | |
| + - GDC:Sample.time_between_clamping_and_freezing | |
| + - PDC:Sample.time_between_excision_and_freezing | |
| + - PDC:Sample.time_between_clamping_and_freezing | |
| + - HTAN:Biospecimen.ISCHEMIC_TIME | |
| + description: The result of the observation, encoded as a free-text Quantity. | |
| notes: | |
| - 'Cardinality: 1..1' | |
| comments: | |
| - One and only one of the value(x) fields must be populated. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.ISCHEMIC_TEMPERATURE | |
| - - HTAN:Biospecimen.SHIPPING_CONDITIONS | |
| - domain: ExecutionConditionObservation | |
| - range: enum_CCDH_ExecutionConditionObservation_valueCodeableConcept | |
| + domain: ExecutionTimeObservation | |
| + range: Quantity | |
| multivalued: false | |
| required: true | |
| Exposure: | |
| @@ -24179,6 +23397,9 @@ | |
| attributes: | |
| id: | |
| name: id | |
| + exact_mappings: | |
| + - GDC:Exposure.id | |
| + - PDC:Exposure.id | |
| description: The 'logical' identifier of the entity within the system of record. The | |
| simple value of this attribute stands for an identifier of this data object | |
| within the system, it can be used as a reference from other objects within | |
| @@ -24204,15 +23425,15 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Exposure.id | |
| - - PDC:Exposure.id | |
| domain: Exposure | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| identifier: | |
| name: identifier | |
| + close_mappings: | |
| + - GDC:Exposure.submitter_id | |
| + - PDC:Exposure.submitter_id | |
| description: A 'business' identifier or accession number for the entity, typically | |
| as provided by an external system or authority, that are globally unique | |
| and persist across implementing systems. Also, since these identifiers are | |
| @@ -24232,20 +23453,13 @@ | |
| the identifier itself, along with metadata about its source. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Exposure.submitter_id | |
| - - PDC:Exposure.submitter_id | |
| domain: Exposure | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| tobacco_exposure: | |
| name: tobacco_exposure | |
| - description: Observations about an individual's exposure to tobacco. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Exposure.cigarettes_per_day | |
| - PDC:Exposure.cigarettes_per_day | |
| @@ -24267,17 +23481,18 @@ | |
| - PDC:Exposure.type_of_tobacco_used | |
| - GDC:Exposure.years_smoked | |
| - PDC:Exposure.years_smoked | |
| + description: Observations about an individual's exposure to tobacco. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| domain: Exposure | |
| range: TobaccoExposureObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| alcohol_exposure: | |
| name: alcohol_exposure | |
| - description: Observations about an individual's exposure to alcohol. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Exposure.alcohol_days_per_week | |
| - PDC:Exposure.alcohol_days_per_week | |
| @@ -24287,18 +23502,18 @@ | |
| - PDC:Exposure.alcohol_history | |
| - GDC:Exposure.alcohol_intensity | |
| - PDC:Exposure.alcohol_intensity | |
| + description: Observations about an individual's exposure to alcohol. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| domain: Exposure | |
| range: AlcoholExposureObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| environmental_exposure: | |
| name: environmental_exposure | |
| - description: Observations about an individual's exposure to environmental | |
| - substances that may impact clinical outcomes. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Exposure.asbestos_exposure | |
| - PDC:Exposure.asbestos_exposure | |
| @@ -24310,10 +23525,17 @@ | |
| - PDC:Exposure.respirable_crystalline_silica_exposure | |
| - GDC:Exposure.type_of_smoke_exposure | |
| - PDC:Exposure.type_of_smoke_exposure | |
| + description: Observations about an individual's exposure to environmental | |
| + substances that may impact clinical outcomes. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| domain: Exposure | |
| range: EnvironmentalExposureObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: A reference to the Subject that is the subject of this Exposure | |
| @@ -24363,7 +23585,7 @@ | |
| examples: | |
| - value: '' | |
| domain: HistologicalCompositionObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -24376,7 +23598,7 @@ | |
| examples: | |
| - value: '' | |
| domain: HistologicalCompositionObservation | |
| - range: enum_CCDH_HistologicalCompositionObservation_category | |
| + range: enum_CRDCH_HistologicalCompositionObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -24391,7 +23613,7 @@ | |
| examples: | |
| - value: '' | |
| domain: HistologicalCompositionObservation | |
| - range: enum_CCDH_HistologicalCompositionObservation_observation_type | |
| + range: enum_CRDCH_HistologicalCompositionObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -24409,7 +23631,7 @@ | |
| examples: | |
| - value: '' | |
| domain: HistologicalCompositionObservation | |
| - range: enum_CCDH_HistologicalCompositionObservation_method_type | |
| + range: enum_CRDCH_HistologicalCompositionObservation_method_type | |
| multivalued: true | |
| required: false | |
| focus: | |
| @@ -24430,6 +23652,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -24455,8 +23678,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueQuantity: | |
| - name: valueQuantity | |
| + value_quantity: | |
| + name: value_quantity | |
| description: The result of the observation, encoded as a free-text Quantity. | |
| notes: | |
| - 'Cardinality: 1..1' | |
| @@ -24513,7 +23736,7 @@ | |
| examples: | |
| - value: '' | |
| domain: HistologicalCompositionObservationSet | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| category: | |
| @@ -24524,7 +23747,7 @@ | |
| examples: | |
| - value: '' | |
| domain: HistologicalCompositionObservationSet | |
| - range: enum_CCDH_HistologicalCompositionObservationSet_category | |
| + range: enum_CRDCH_HistologicalCompositionObservationSet_category | |
| multivalued: false | |
| required: true | |
| focus: | |
| @@ -24545,6 +23768,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -24575,7 +23799,7 @@ | |
| examples: | |
| - value: '' | |
| domain: HistologicalCompositionObservationSet | |
| - range: enum_CCDH_HistologicalCompositionObservationSet_method_type | |
| + range: enum_CRDCH_HistologicalCompositionObservationSet_method_type | |
| multivalued: true | |
| required: false | |
| performed_by: | |
| @@ -24605,6 +23829,7 @@ | |
| range: HistologicalCompositionObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| Identifier: | |
| name: Identifier | |
| description: An Identifier is associated with a unique object or entity within | |
| @@ -24618,11 +23843,6 @@ | |
| attributes: | |
| value: | |
| name: value | |
| - description: The value of the identifier, as defined by the system. | |
| - notes: | |
| - - 'Cardinality: 1..1' | |
| - examples: | |
| - - value: '' | |
| exact_mappings: | |
| - GDC:Sample.submitter_id | |
| - GDC:Analyte.submitter_id | |
| @@ -24643,8 +23863,13 @@ | |
| - ICDC:Study.clinical_study_designation | |
| - GDC:Case.submitter_id | |
| - PDC:Case.case_submitter_id | |
| + description: The value of the identifier, as defined by the system. | |
| + notes: | |
| + - 'Cardinality: 1..1' | |
| + examples: | |
| + - value: '' | |
| domain: Identifier | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| system: | |
| @@ -24655,7 +23880,7 @@ | |
| examples: | |
| - value: '' | |
| domain: Identifier | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| type: | |
| @@ -24666,7 +23891,7 @@ | |
| examples: | |
| - value: '' | |
| domain: Identifier | |
| - range: enum_CCDH_Identifier_type | |
| + range: enum_CRDCH_Identifier_type | |
| multivalued: false | |
| required: false | |
| Observation: | |
| @@ -24711,7 +23936,7 @@ | |
| examples: | |
| - value: '' | |
| domain: Observation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -24728,7 +23953,7 @@ | |
| - value: CellularCompositionMeasure | |
| - value: TobbaccoExposureMeasure | |
| domain: Observation | |
| - range: enum_CCDH_Observation_category | |
| + range: enum_CRDCH_Observation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -24747,11 +23972,15 @@ | |
| - value: width_of_tumor | |
| - value: time_between_excision_and_freezing | |
| domain: Observation | |
| - range: enum_CCDH_Observation_observation_type | |
| + range: enum_CRDCH_Observation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| name: method_type | |
| + exact_mappings: | |
| + - GDC:Analyte.spectrophotometer_method | |
| + - PDC:Analyte.spectrophotometer_method | |
| + - HTAN:Biospecimen.HistologyAssessmentMedium | |
| description: A type of method used in generating the Observation result. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| @@ -24764,12 +23993,8 @@ | |
| as that provided by the ACMG). | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Analyte.spectrophotometer_method | |
| - - PDC:Analyte.spectrophotometer_method | |
| - - HTAN:Biospecimen.HistologyAssessmentMedium | |
| domain: Observation | |
| - range: enum_CCDH_Observation_method_type | |
| + range: enum_CRDCH_Observation_method_type | |
| multivalued: true | |
| required: false | |
| focus: | |
| @@ -24790,6 +24015,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -24815,8 +24041,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueEntity: | |
| - name: valueEntity | |
| + value_entity: | |
| + name: value_entity | |
| description: The value of an observation | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24826,8 +24052,8 @@ | |
| range: Entity | |
| multivalued: false | |
| required: false | |
| - valueString: | |
| - name: valueString | |
| + value_string: | |
| + name: value_string | |
| description: The result of the observation, encoded as a free-text string. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24836,11 +24062,11 @@ | |
| examples: | |
| - value: '' | |
| domain: Observation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| - valueInteger: | |
| - name: valueInteger | |
| + value_integer: | |
| + name: value_integer | |
| description: The result of the observation, encoded as a decimal. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24849,11 +24075,11 @@ | |
| examples: | |
| - value: '' | |
| domain: Observation | |
| - range: ccdh_decimal | |
| + range: crdch_decimal | |
| multivalued: false | |
| required: false | |
| - valueDecimal: | |
| - name: valueDecimal | |
| + value_decimal: | |
| + name: value_decimal | |
| description: The result of the observation, encoded as a decimal. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24862,11 +24088,11 @@ | |
| examples: | |
| - value: '' | |
| domain: Observation | |
| - range: ccdh_decimal | |
| + range: crdch_decimal | |
| multivalued: false | |
| required: false | |
| - valueBoolean: | |
| - name: valueBoolean | |
| + value_boolean: | |
| + name: value_boolean | |
| description: The result of the observation, encoded as a boolean. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24875,11 +24101,11 @@ | |
| examples: | |
| - value: '' | |
| domain: Observation | |
| - range: ccdh_boolean | |
| + range: crdch_boolean | |
| multivalued: false | |
| required: false | |
| - valueDateTime: | |
| - name: valueDateTime | |
| + value_date_time: | |
| + name: value_date_time | |
| description: The result of the observation, encoded as a dateTime. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24888,11 +24114,11 @@ | |
| examples: | |
| - value: '' | |
| domain: Observation | |
| - range: ccdh_dateTime | |
| + range: crdch_dateTime | |
| multivalued: false | |
| required: false | |
| - valueQuantity: | |
| - name: valueQuantity | |
| + value_quantity: | |
| + name: value_quantity | |
| description: The result of the observation, encoded as a free-text Quantity. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24904,8 +24130,8 @@ | |
| range: Quantity | |
| multivalued: false | |
| required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| + value_enum: | |
| + name: value_enum | |
| description: The result of the observation, encoded as a CodeableConcept. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -24914,7 +24140,7 @@ | |
| examples: | |
| - value: '' | |
| domain: Observation | |
| - range: enum_CCDH_Observation_valueCodeableConcept | |
| + range: enum_CRDCH_Observation_value_enum | |
| multivalued: false | |
| required: false | |
| ObservationSet: | |
| @@ -24961,7 +24187,7 @@ | |
| examples: | |
| - value: '' | |
| domain: ObservationSet | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| category: | |
| @@ -24974,7 +24200,7 @@ | |
| - value: TissueCompositionMeasureSet | |
| - value: CellularCompositionMeasureSet | |
| domain: ObservationSet | |
| - range: enum_CCDH_ObservationSet_category | |
| + range: enum_CRDCH_ObservationSet_category | |
| multivalued: false | |
| required: true | |
| focus: | |
| @@ -24995,6 +24221,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -25011,6 +24238,10 @@ | |
| required: false | |
| method_type: | |
| name: method_type | |
| + exact_mappings: | |
| + - GDC:Analyte.spectrophotometer_method | |
| + - PDC:Analyte.spectrophotometer_method | |
| + - HTAN:Biospecimen.HistologyAssessmentMedium | |
| description: A type of method used in generating each of the Observations | |
| bundled in the set. | |
| notes: | |
| @@ -25024,12 +24255,8 @@ | |
| as that provided by the ACMG). | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Analyte.spectrophotometer_method | |
| - - PDC:Analyte.spectrophotometer_method | |
| - - HTAN:Biospecimen.HistologyAssessmentMedium | |
| domain: ObservationSet | |
| - range: enum_CCDH_ObservationSet_method_type | |
| + range: enum_CRDCH_ObservationSet_method_type | |
| multivalued: true | |
| required: false | |
| performed_by: | |
| @@ -25059,6 +24286,7 @@ | |
| range: Observation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| Organization: | |
| name: Organization | |
| description: A grouping of people or organizations with a common purpose such | |
| @@ -25069,6 +24297,8 @@ | |
| attributes: | |
| id: | |
| name: id | |
| + exact_mappings: | |
| + - GDC:Center.id | |
| description: The 'logical' identifier of the entity within the system of record. The | |
| simple value of this attribute stands for an identifier of this data object | |
| within the system, it can be used as a reference from other objects within | |
| @@ -25094,14 +24324,15 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Center.id | |
| domain: Organization | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| identifier: | |
| name: identifier | |
| + exact_mappings: | |
| + - GDC:Center.code | |
| + - HTAN:Biospecimen.SiteDataSource | |
| description: A 'business' identifier or accession number for the entity, typically | |
| as provided by an external system or authority, that are globally unique | |
| and persist across implementing systems. Also, since these identifiers are | |
| @@ -25121,55 +24352,55 @@ | |
| the identifier itself, along with metadata about its source. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Center.code | |
| - - HTAN:Biospecimen.SiteDataSource | |
| domain: Organization | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| name: | |
| name: name | |
| + exact_mappings: | |
| + - GDC:Center.name | |
| + - GDC:Aliquot.source_center | |
| + - HTAN:Biospecimen.SiteDataSource | |
| description: The full legal name by which the organization is known (e.g. | |
| 'National Cancer Institute') | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Center.name | |
| - - GDC:Aliquot.source_center | |
| - - HTAN:Biospecimen.SiteDataSource | |
| domain: Organization | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| alias: | |
| name: alias | |
| + exact_mappings: | |
| + - GDC:Center.short_name | |
| description: A secondary name for the organization such as a short name or | |
| abbreviation (e.g. 'NCI') | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Center.short_name | |
| domain: Organization | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| organization_type: | |
| name: organization_type | |
| + exact_mappings: | |
| + - GDC:Center.center_type | |
| description: The type of the organization (e.g. 'Cancer Genome Characterization | |
| Center') | |
| notes: | |
| - 'Cardinality: 0..1' | |
| + comments: | |
| + - See dev issues column | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Center.center_type | |
| domain: Organization | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| Quantity: | |
| @@ -25193,13 +24424,8 @@ | |
| most appropriate. | |
| is_a: Entity | |
| attributes: | |
| - valueDecimal: | |
| - name: valueDecimal | |
| - description: An amount, in the given units (if specified) | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - examples: | |
| - - value: '' | |
| + value_decimal: | |
| + name: value_decimal | |
| exact_mappings: | |
| - GDC:Sample.initial_weight | |
| - PDC:Sample.initial_weight | |
| @@ -25292,37 +24518,44 @@ | |
| - GDC:Diagnosis.age_at_diagnosis | |
| - PDC:Diagnosis.age_at_diagnosis | |
| - HTAN:Diagnosis.AgeatDiagnosis | |
| + - GDC:Diagnosis.days_to_diagnosis | |
| + - PDC:Diagnosis.days_to_diagnosis | |
| + description: An amount, in the given units (if specified) | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + examples: | |
| + - value: '' | |
| domain: Quantity | |
| - range: ccdh_decimal | |
| + range: crdch_decimal | |
| multivalued: false | |
| required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| + value_enum: | |
| + name: value_enum | |
| + exact_mappings: | |
| + - GDC:Sample.distance_normal_to_tumor | |
| + - PDC:Sample.distance_normal_to_tumor | |
| description: A coded value representing a quantity (e.g. "Adjacent (< or = | |
| 2cm)") | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Sample.distance_normal_to_tumor | |
| - - PDC:Sample.distance_normal_to_tumor | |
| domain: Quantity | |
| - range: enum_CCDH_Quantity_valueCodeableConcept | |
| + range: enum_CRDCH_Quantity_value_enum | |
| multivalued: false | |
| required: false | |
| unit: | |
| name: unit | |
| + exact_mappings: | |
| + - GDC:Treatment.treatment_dose_unit | |
| description: A coded or free text (in the .text field) representation of the | |
| unit. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Treatment.treatment_dose_unit | |
| domain: Quantity | |
| - range: enum_CCDH_Quantity_unit | |
| + range: enum_CRDCH_Quantity_unit | |
| multivalued: false | |
| required: false | |
| ResearchProject: | |
| @@ -25339,6 +24572,12 @@ | |
| attributes: | |
| id: | |
| name: id | |
| + exact_mappings: | |
| + - GDC:Program.id | |
| + - PDC:Program.program_id | |
| + - PDC:Project.project_id | |
| + - GDC:Project.id | |
| + - ICDC:Study.clinical_study_id | |
| description: The 'logical' identifier of the entity within the system of record. The | |
| simple value of this attribute stands for an identifier of this data object | |
| within the system, it can be used as a reference from other objects within | |
| @@ -25364,18 +24603,18 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Program.id | |
| - - PDC:Program.program_id | |
| - - PDC:Project.project_id | |
| - - GDC:Project.id | |
| - - ICDC:Study.clinical_study_id | |
| domain: ResearchProject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| identifier: | |
| name: identifier | |
| + close_mappings: | |
| + - GDC:Program.dbgap_accession_number | |
| + - GDC:Project.dbgap_accession_number | |
| + - PDC:Program.program_submitter_id | |
| + - PDC:Project.project_submitter_id | |
| + - ICDC:Study.clinical_study_designation | |
| description: A 'business' identifier or accession number for the entity, typically | |
| as provided by an external system or authority, that are globally unique | |
| and persist across implementing systems. Also, since these identifiers are | |
| @@ -25395,23 +24634,13 @@ | |
| the identifier itself, along with metadata about its source. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Program.dbgap_accession_number | |
| - - GDC:Project.dbgap_accession_number | |
| - - PDC:Program.program_submitter_id | |
| - - PDC:Project.project_submitter_id | |
| - - ICDC:Study.clinical_study_designation | |
| domain: ResearchProject | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| name: | |
| name: name | |
| - description: An unabridged name of a research program, project, or study. | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - examples: | |
| - - value: '' | |
| exact_mappings: | |
| - GDC:Program.name | |
| - PDC:Program.name | |
| @@ -25419,94 +24648,102 @@ | |
| - GDC:Project.name | |
| - PDC:Project.name | |
| - ICDC:Study.clinical_study_name | |
| + description: An unabridged name of a research program, project, or study. | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + examples: | |
| + - value: '' | |
| domain: ResearchProject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| name_shortened: | |
| name: name_shortened | |
| + exact_mappings: | |
| + - ICDC:Program.program_acronym | |
| + - PDC:Program.program_shortname | |
| description: An abbreviated name of a research program, project, or study. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - ICDC:Program.program_acronym | |
| - - PDC:Program.program_shortname | |
| domain: ResearchProject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| description: | |
| name: description | |
| + exact_mappings: | |
| + - ICDC:Program.program_full_description | |
| description: An unabridged description of a research program, project, or | |
| study. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - ICDC:Program.program_full_description | |
| domain: ResearchProject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| description_shortened: | |
| name: description_shortened | |
| + exact_mappings: | |
| + - ICDC:Program.program_short_description | |
| description: An abbreviated description of a research program, project, or | |
| study. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - ICDC:Program.program_short_description | |
| domain: ResearchProject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| sponsor: | |
| name: sponsor | |
| + exact_mappings: | |
| + - PDC:Program.sponsor | |
| description: An entity that is responsible for the initiation, management, | |
| and/or financing of a research project. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - PDC:Program.sponsor | |
| domain: ResearchProject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| date_started: | |
| name: date_started | |
| + close_mappings: | |
| + - ICDC:Study.dates_of_conduct | |
| description: The date when the research project began. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - ICDC:Study.dates_of_conduct | |
| domain: ResearchProject | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| date_ended: | |
| name: date_ended | |
| + close_mappings: | |
| + - ICDC:Study.dates_of_conduct | |
| description: The date when the research project ended. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - ICDC:Study.dates_of_conduct | |
| domain: ResearchProject | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| primary_anatomic_site: | |
| name: primary_anatomic_site | |
| + close_mappings: | |
| + - GDC:Project.primary_site | |
| description: The text term used to describe the general location of the malignant | |
| disease, as categorized by the World Health Organization's (WHO) International | |
| Classification of Diseases for Oncology (ICD-O). In the context of ResearchProject, | |
| @@ -25515,26 +24752,26 @@ | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Project.primary_site | |
| domain: ResearchProject | |
| range: BodySite | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| url: | |
| name: url | |
| + exact_mappings: | |
| + - ICDC:Program.program_external_url | |
| description: A URL address for a resource that provides information about | |
| a research program, project, or study. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - ICDC:Program.program_external_url | |
| domain: ResearchProject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| part_of: | |
| name: part_of | |
| description: A reference to a parent ResearchProject (e.g. a link to the overarching | |
| @@ -25547,17 +24784,9 @@ | |
| range: ResearchProject | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| research_project_type: | |
| name: research_project_type | |
| - description: The 'type' of ResearchProject represented (e.g. a broad-based | |
| - Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery | |
| - Study') | |
| - notes: | |
| - - 'Cardinality: 1..1' | |
| - examples: | |
| - - value: Program | |
| - - value: Project | |
| - - value: Clinical Trial | |
| exact_mappings: | |
| - ICDC:Study.clinical_study_type | |
| close_mappings: | |
| @@ -25567,12 +24796,23 @@ | |
| - PDC:Project | |
| - ICDC:Program | |
| - ICDC:Study | |
| + description: The 'type' of ResearchProject represented (e.g. a broad-based | |
| + Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery | |
| + Study') | |
| + notes: | |
| + - 'Cardinality: 1..1' | |
| + examples: | |
| + - value: Program | |
| + - value: Project | |
| + - value: Clinical Trial | |
| domain: ResearchProject | |
| - range: enum_CCDH_ResearchProject_research_project_type | |
| + range: enum_CRDCH_ResearchProject_research_project_type | |
| multivalued: false | |
| required: true | |
| associated_timepoint: | |
| name: associated_timepoint | |
| + close_mappings: | |
| + - ICDC:Study.date_of_iacuc_approval | |
| description: A collection of timepoint observations that are relevant to research | |
| projects (e.g. date of IACUC approval, date of IRB approval, date of embargo | |
| end, etc.) | |
| @@ -25580,12 +24820,11 @@ | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - ICDC:Study.date_of_iacuc_approval | |
| domain: ResearchProject | |
| range: TimePoint | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| ResearchSubject: | |
| name: ResearchSubject | |
| description: "A research subject is the entity of interest in a research study,\ | |
| @@ -25598,6 +24837,9 @@ | |
| attributes: | |
| id: | |
| name: id | |
| + exact_mappings: | |
| + - GDC:Case.id | |
| + - ICDC:Case.case_id | |
| description: The 'logical' identifier of the entity within the system of record. The | |
| simple value of this attribute stands for an identifier of this data object | |
| within the system, it can be used as a reference from other objects within | |
| @@ -25623,15 +24865,15 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Case.id | |
| - - ICDC:Case.case_id | |
| domain: ResearchSubject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| identifier: | |
| name: identifier | |
| + close_mappings: | |
| + - GDC:Case.submitter_id | |
| + - PDC:Case.case_submitter_id | |
| description: A 'business' identifier or accession number for the entity, typically | |
| as provided by an external system or authority, that are globally unique | |
| and persist across implementing systems. Also, since these identifiers are | |
| @@ -25651,13 +24893,11 @@ | |
| the identifier itself, along with metadata about its source. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Case.submitter_id | |
| - - PDC:Case.case_submitter_id | |
| domain: ResearchSubject | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| description: | |
| name: description | |
| description: A free text field to capture additional info/explanation about | |
| @@ -25667,41 +24907,44 @@ | |
| examples: | |
| - value: '' | |
| domain: ResearchSubject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| member_of_research_project: | |
| name: member_of_research_project | |
| + exact_mappings: | |
| + - GDC:Case.member_of | |
| + - GDC:Case.project_id | |
| + - PDC:Case.Project | |
| + - ICDC:Case.member_of | |
| description: A reference to the Study(s) of which this ResearchSubject is | |
| a member | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Case.member_of | |
| - - GDC:Case.project_id | |
| - - PDC:Case.Project | |
| - - ICDC:Case.member_of | |
| domain: ResearchSubject | |
| range: ResearchProject | |
| multivalued: false | |
| required: false | |
| age_at_enrollment: | |
| name: age_at_enrollment | |
| + close_mappings: | |
| + - ICDC:Demographic.patient_age_at_enrollment | |
| description: The age in days when the Subject enrolled on the ResearchProject | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - ICDC:Demographic.patient_age_at_enrollment | |
| domain: ResearchSubject | |
| range: Quantity | |
| multivalued: false | |
| required: false | |
| primary_diagnosis_condition: | |
| name: primary_diagnosis_condition | |
| + exact_mappings: | |
| + - GDC:Case.disease_type | |
| + - PDC:Case.disease_type | |
| description: The text term used to describe the type of malignant disease, | |
| as categorized by the World Health Organization's (WHO) International Classification | |
| of Diseases for Oncology (ICD-O). This attribute represents the disease | |
| @@ -25718,15 +24961,15 @@ | |
| - value: Adenomas and Adenocarcinomas | |
| - value: Adnexal and Skin Appendage Neoplasms | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Case.disease_type | |
| - - PDC:Case.disease_type | |
| domain: ResearchSubject | |
| - range: enum_CCDH_ResearchSubject_primary_diagnosis_condition | |
| + range: enum_CRDCH_ResearchSubject_primary_diagnosis_condition | |
| multivalued: false | |
| required: false | |
| primary_diagnosis_site: | |
| name: primary_diagnosis_site | |
| + close_mappings: | |
| + - GDC:Case.primary_site | |
| + - PDC:Case.primary_site | |
| description: The text term used to describe the primary site of disease, as | |
| categorized by the World Health Organization's (WHO) International Classification | |
| of Diseases for Oncology (ICD-O). This categorization groups cases into | |
| @@ -25744,9 +24987,6 @@ | |
| - value: Adrenal gland | |
| - value: Anus and anal canal | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Case.primary_site | |
| - - PDC:Case.primary_site | |
| domain: ResearchSubject | |
| range: BodySite | |
| multivalued: false | |
| @@ -25767,8 +25007,14 @@ | |
| range: Diagnosis | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| comorbid_diagnosis: | |
| name: comorbid_diagnosis | |
| + close_mappings: | |
| + - ICDC:Diagnosis.concurrent_disease | |
| + - ICDC:Diagnosis.concurrent_disease_type | |
| + - GDC:Diagnosis.synchronous_malignancy | |
| + - PDC:Diagnosis.synchronous_malignancy | |
| description: One or more diagnosis instance that are comorbid with the primary_diagnosis | |
| that qualified a subject for inclusion on a ResearchProject | |
| notes: | |
| @@ -25780,17 +25026,16 @@ | |
| here. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - ICDC:Diagnosis.concurrent_disease | |
| - - ICDC:Diagnosis.concurrent_disease_type | |
| - - GDC:Diagnosis.synchronous_malignancy | |
| - - PDC:Diagnosis.synchronous_malignancy | |
| domain: ResearchSubject | |
| range: Diagnosis | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| index_timepoint: | |
| name: index_timepoint | |
| + exact_mappings: | |
| + - GDC:Case.index_date | |
| + - PDC:Case.index_date | |
| description: The text term used to describe the reference or anchor date used | |
| for date obfuscation, where a single date is obscured by creating one or | |
| more date ranges in relation to this date. | |
| @@ -25801,22 +25046,19 @@ | |
| - value: First Patient Visit | |
| - value: First Treatment | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Case.index_date | |
| - - PDC:Case.index_date | |
| domain: ResearchSubject | |
| - range: enum_CCDH_ResearchSubject_index_timepoint | |
| + range: enum_CRDCH_ResearchSubject_index_timepoint | |
| multivalued: false | |
| required: false | |
| originating_site: | |
| name: originating_site | |
| + exact_mappings: | |
| + - PDC:Case.tissue_source_site_code | |
| description: The Organization at which a subject was enrolled on a ResearchProject. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - PDC:Case.tissue_source_site_code | |
| domain: ResearchSubject | |
| range: Organization | |
| multivalued: false | |
| @@ -25845,6 +25087,18 @@ | |
| attributes: | |
| id: | |
| name: id | |
| + exact_mappings: | |
| + - GDC:Aliquot.id | |
| + - GDC:Analyte.id | |
| + - GDC:Portion.id | |
| + - GDC:Sample.id | |
| + - GDC:Slide.id | |
| + - PDC:Aliquot.aliquot_id | |
| + - PDC:Analyte.analyte_id | |
| + - PDC:Portion.portion_id | |
| + - PDC:Sample.sample_id | |
| + - ICDC:Sample.sample_id | |
| + - HTAN:Biospecimen.HTANBiospecimenID | |
| description: The 'logical' identifier of the entity within the system of record. The | |
| simple value of this attribute stands for an identifier of this data object | |
| within the system, it can be used as a reference from other objects within | |
| @@ -25870,24 +25124,18 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Aliquot.id | |
| - - GDC:Analyte.id | |
| - - GDC:Portion.id | |
| - - GDC:Sample.id | |
| - - GDC:Slide.id | |
| - - PDC:Aliquot.aliquot_id | |
| - - PDC:Analyte.analyte_id | |
| - - PDC:Portion.portion_id | |
| - - PDC:Sample.sample_id | |
| - - ICDC:Sample.sample_id | |
| - - HTAN:Biospecimen.HTANBiospecimenID | |
| domain: Specimen | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| identifier: | |
| name: identifier | |
| + close_mappings: | |
| + - GDC:Sample.submitter_id | |
| + - GDC:Analyte.submitter_id | |
| + - GDC:Slide.submitter_id | |
| + - PDC:Sample.sample_submitter_id | |
| + - PDC:Analyte.analyte_submitter_id | |
| description: A 'business' identifier or accession number for the entity, typically | |
| as provided by an external system or authority, that are globally unique | |
| and persist across implementing systems. Also, since these identifiers are | |
| @@ -25907,32 +25155,41 @@ | |
| the identifier itself, along with metadata about its source. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Sample.submitter_id | |
| - - GDC:Analyte.submitter_id | |
| - - GDC:Slide.submitter_id | |
| - - PDC:Sample.sample_submitter_id | |
| - - PDC:Analyte.analyte_submitter_id | |
| domain: Specimen | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| description: | |
| name: description | |
| + exact_mappings: | |
| + - ICDC:Sample.comment | |
| description: A free text field to capture additional information or explanation | |
| about the specimen. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - ICDC:Sample.comment | |
| domain: Specimen | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| specimen_type: | |
| name: specimen_type | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.BiospecimenType | |
| + close_mappings: | |
| + - GDC:Sample | |
| + - GDC:Portion | |
| + - GDC:Analyte | |
| + - GDC:Aliquot | |
| + - GDC:Slide | |
| + - PDC:Sample | |
| + - PDC:Portion | |
| + - PDC:Analyte | |
| + - PDC:Aliquot | |
| + - PDC:Slide | |
| + - ICDC:Sample | |
| description: The high-level type of the specimen, based on its derivation | |
| provenance (i.e. how far removed it is from the original sample extracted | |
| from a source). | |
| @@ -25946,31 +25203,27 @@ | |
| values are meant to be mutually exclusive, such that only one can be applied | |
| to a given specimen. | |
| examples: | |
| - - value: Initial Sample | |
| + - value: Fresh Specimen | |
| - value: Portion | |
| - value: Aliquot | |
| - value: Analyte | |
| - value: Slide | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.BiospecimenType | |
| - close_mappings: | |
| - - GDC:Sample | |
| - - GDC:Portion | |
| - - GDC:Analyte | |
| - - GDC:Aliquot | |
| - - GDC:Slide | |
| - - PDC:Sample | |
| - - PDC:Portion | |
| - - PDC:Analyte | |
| - - PDC:Aliquot | |
| - - PDC:Slide | |
| - - ICDC:Sample | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_specimen_type | |
| + range: enum_CRDCH_Specimen_specimen_type | |
| multivalued: false | |
| required: false | |
| analyte_type: | |
| name: analyte_type | |
| + exact_mappings: | |
| + - GDC:Aliquot.analyte_type | |
| + - GDC:Aliquot.analyte_type_id | |
| + - GDC:Analyte.analyte_type | |
| + - GDC:Analyte.analyte_type_id | |
| + - PDC:Aliquot.analyte_type | |
| + - PDC:Aliquot.analyte_type_id | |
| + - PDC:Analyte.analyte_type | |
| + - PDC:Analyte.analyte_type_id | |
| + - HTAN:Biospecimen.AnalyteBiospecimenType | |
| description: For specimens of type 'analyte' (or an 'aliquot' derived from | |
| an analyte), this is the category of chemcial the analyte of interest represents | |
| (e.g. DNA, RNA) | |
| @@ -25983,54 +25236,51 @@ | |
| - value: Repli-G (Qiagen) DNA | |
| - value: RNA | |
| - value: FFPE RNA | |
| - exact_mappings: | |
| - - GDC:Aliquot.analyte_type | |
| - - GDC:Aliquot.analyte_type_id | |
| - - GDC:Analyte.analyte_type | |
| - - GDC:Analyte.analyte_type_id | |
| - - PDC:Aliquot.analyte_type | |
| - - PDC:Aliquot.analyte_type_id | |
| - - PDC:Analyte.analyte_type | |
| - - PDC:Analyte.analyte_type_id | |
| - - HTAN:Biospecimen.AnalyteBiospecimenType | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_analyte_type | |
| + range: enum_CRDCH_Specimen_analyte_type | |
| multivalued: false | |
| required: false | |
| associated_project: | |
| name: associated_project | |
| - description: The Project associated with the specimen. | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - examples: | |
| - - value: '' | |
| exact_mappings: | |
| - GDC:Sample.project_id | |
| - GDC:Portion.project_id | |
| - GDC:Aliquot.project_id | |
| - GDC:Analyte.project_id | |
| - PDC:Sample.gdc_project_id | |
| + description: The Project associated with the specimen. | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + examples: | |
| + - value: '' | |
| domain: Specimen | |
| range: ResearchProject | |
| multivalued: false | |
| required: false | |
| data_provider: | |
| name: data_provider | |
| + close_mappings: | |
| + - GDC:Aliquot.source_center | |
| + - HTAN:Biospecimen.SiteDataSource | |
| description: The organization (e.g.a laboratory, processing center, or research | |
| site) that provided data associated with a specimen. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Aliquot.source_center | |
| - - HTAN:Biospecimen.SiteDataSource | |
| domain: Specimen | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| source_material_type: | |
| name: source_material_type | |
| + exact_mappings: | |
| + - GDC:Sample.sample_type | |
| + - GDC:Sample.sample_type_id | |
| + - PDC:Sample.sample_type | |
| + - PDC:Sample.sample_type_id | |
| + - ICDC:Sample.physical_sample_type | |
| + - HTAN:Biospecimen.BiospecimenType | |
| description: The general kind of material from which the specimen was derived. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -26039,33 +25289,19 @@ | |
| organ, body fluid, embryo, excretory substance, or experimental system from | |
| which a specimen was derived. | |
| examples: | |
| - - value: Tissue, Blood, Tumor Aspirate | |
| + - value: Tissue | |
| + - value: Blood | |
| + - value: Tumor Aspirate | |
| - value: Cell Line | |
| - value: Expanded Next Generation Cancer Model | |
| - value: Pleural Effusion | |
| - value: Xenograft Tissue | |
| - exact_mappings: | |
| - - GDC:Sample.sample_type | |
| - - GDC:Sample.sample_type_id | |
| - - PDC:Sample.sample_type | |
| - - PDC:Sample.sample_type_id | |
| - - ICDC:Sample.physical_sample_type | |
| - - HTAN:Biospecimen.BiospecimenType | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_source_material_type | |
| + range: enum_CRDCH_Specimen_source_material_type | |
| multivalued: false | |
| required: false | |
| parent_specimen: | |
| name: parent_specimen | |
| - description: An existing specimen from which the specimen of interest was | |
| - directly derived (i.e its immediate parent specimen). | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - comments: | |
| - - This property indicates only the direct parent specimen(s). Cardinality | |
| - is 0..m to account for specimens derived from pooling of multiple specimens. | |
| - examples: | |
| - - value: '' | |
| exact_mappings: | |
| - GDC:Sample.derived_from | |
| - GDC:Aliquot.derived_from | |
| @@ -26079,29 +25315,46 @@ | |
| - PDC:Analyte.Sample | |
| - PDC:Portion.Sample | |
| - HTAN:Biospecimen.HTANParentID | |
| + description: An existing specimen from which the specimen of interest was | |
| + directly derived (i.e its immediate parent specimen). | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + comments: | |
| + - This property indicates only the direct parent specimen(s). Cardinality | |
| + is 0..m to account for specimens derived from pooling of multiple specimens. | |
| + examples: | |
| + - value: '' | |
| domain: Specimen | |
| range: Specimen | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| source_subject: | |
| name: source_subject | |
| + exact_mappings: | |
| + - PDC:Sample.Case | |
| + - GDC:Sample.derived_from | |
| + - ICDC:Sample.of_case | |
| + - HTAN:Biospecimen.HTANParentID | |
| description: A specific Subject from which the specimen was directly or indirectly | |
| derived. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - PDC:Sample.Case | |
| - - GDC:Sample.derived_from | |
| - - ICDC:Sample.of_case | |
| - - HTAN:Biospecimen.HTANParentID | |
| domain: Specimen | |
| range: Subject | |
| multivalued: false | |
| required: false | |
| tumor_status_at_collection: | |
| name: tumor_status_at_collection | |
| + exact_mappings: | |
| + - GDC:Sample.tumor_descriptor | |
| + - PDC:Sample.tumor_descriptor | |
| + - HTAN:Biospecimen.TUMOR_TISSUE_TYPE | |
| + - ICDC:Sample.tumor_sample_origin | |
| + - GDC:Diagnosis.classification_of_tumor | |
| + - PDC:Diagnosis.classification_of_tumor | |
| description: The status of the tumor at the time the specimen was collected | |
| (e.g. if it was primary, recurrent, metastatic, etc). | |
| notes: | |
| @@ -26115,30 +25368,12 @@ | |
| - value: Primary | |
| - value: Recurrent | |
| - value: Xenograft | |
| - exact_mappings: | |
| - - GDC:Sample.tumor_descriptor | |
| - - PDC:Sample.tumor_descriptor | |
| - - HTAN:Biospecimen.TUMOR_TISSUE_TYPE | |
| - - ICDC:Sample.tumor_sample_origin | |
| - - GDC:Diagnosis.classification_of_tumor | |
| - - PDC:Diagnosis.classification_of_tumor | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_tumor_status_at_collection | |
| + range: enum_CRDCH_Specimen_tumor_status_at_collection | |
| multivalued: false | |
| required: false | |
| creation_activity: | |
| name: creation_activity | |
| - description: The activity through which a specimen was created, by removing | |
| - material from an biological subject, or deriving material from an existing | |
| - specimen. | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - comments: | |
| - - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, | |
| - but may be subject to many processing events that subsequently modify or | |
| - derive new specimens from it. | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Portion.creation_datetime | |
| - PDC:Portion.creation_datetime | |
| @@ -26172,23 +25407,23 @@ | |
| - ICDC:Sample.on_visit | |
| - ICDC:Sample.necropsy_sample | |
| - HTAN:Biospecimen.TimepointLabel | |
| + description: The activity through which a specimen was created, by removing | |
| + material from an biological subject, or deriving material from an existing | |
| + specimen. | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + comments: | |
| + - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, | |
| + but may be subject to many processing events that subsequently modify or | |
| + derive new specimens from it. | |
| + examples: | |
| + - value: '' | |
| domain: Specimen | |
| range: SpecimenCreationActivity | |
| multivalued: false | |
| required: false | |
| processing_activity: | |
| name: processing_activity | |
| - description: An activity that modifies the physical structure, composition, | |
| - or state of a specimen. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - comments: | |
| - - Note that a given specimen may undergo more than one distinct processing | |
| - activity, through application of different methodologies that modify its | |
| - physical state. However, if an activity generates a new specimen (e.g. via | |
| - portioning, slicing) it is considered a SpeciemnCreationActivity. | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - HTAN:Biospecimen.ProcessingDaysfromIndex | |
| - HTAN:Biospecimen.FIXATION_DURATION | |
| @@ -26207,12 +25442,26 @@ | |
| - HTAN:Biospecimen.PRESERVATION_METHOD | |
| - HTAN:Biospecimen.FixativeType | |
| - HTAN:Biospecimen.MountingMedium | |
| + description: An activity that modifies the physical structure, composition, | |
| + or state of a specimen. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + comments: | |
| + - Note that a given specimen may undergo more than one distinct processing | |
| + activity, through application of different methodologies that modify its | |
| + physical state. However, if an activity generates a new specimen (e.g. via | |
| + portioning, slicing) it is considered a SpeciemnCreationActivity. | |
| + examples: | |
| + - value: '' | |
| domain: Specimen | |
| range: SpecimenProcessingActivity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| storage_activity: | |
| name: storage_activity | |
| + close_mappings: | |
| + - HTAN:Biospecimen.StorageMethod | |
| description: An activity that results in the storage or maintenance of a specimen | |
| in a particular location, container, or state. | |
| notes: | |
| @@ -26223,14 +25472,16 @@ | |
| under different conditions ' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - HTAN:Biospecimen.StorageMethod | |
| domain: Specimen | |
| range: SpecimenStorageActivity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| transport_activity: | |
| name: transport_activity | |
| + close_mappings: | |
| + - GDC:Portion.shipped_to | |
| + - GDC:Aliquot.shipped_to | |
| description: An activity through which the specimen is transported between | |
| locations. | |
| notes: | |
| @@ -26240,15 +25491,18 @@ | |
| may undergo many separate transport processes at different periods of time. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Portion.shipped_to | |
| - - GDC:Aliquot.shipped_to | |
| domain: Specimen | |
| range: SpecimenTransportActivity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| contained_in: | |
| name: contained_in | |
| + close_mappings: | |
| + - GDC:Analyte.well_number | |
| + - PDC:Analyte.well_number | |
| + - HTAN:Biospecimen.CollectionMedia | |
| + - GDC:Slide.charge_type | |
| description: A physical container in which a specimen is presently held or | |
| attached - as storage for future use, a substrate for growth (e.g. a cell | |
| culture dish), or a vessel to enable analysis (e.g. a microscope slide or | |
| @@ -26261,28 +25515,12 @@ | |
| the ''parent_container'' attribute of the Container entity. ' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Analyte.well_number | |
| - - PDC:Analyte.well_number | |
| - - HTAN:Biospecimen.CollectionMedia | |
| - - GDC:Slide.charge_type | |
| domain: Specimen | |
| range: SpecimenContainer | |
| multivalued: false | |
| required: false | |
| dimensional_measures: | |
| name: dimensional_measures | |
| - description: A set of one or more observations about the current physical | |
| - dimensions of an object (e.g. length, width, area). | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - comments: | |
| - - Observations are flexible containers for capturing a specific type of observation/measurement | |
| - data about an object, along with metadata about how it was generated. The | |
| - specific type of observation made is captured as data in the Observation | |
| - object. | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Sample.longest_dimension | |
| - GDC:Sample.shortest_dimension | |
| @@ -26293,16 +25531,10 @@ | |
| - ICDC:Sample.length_of_tumor | |
| - ICDC:Sample.width_of_tumor | |
| - ICDC:Sample.total_tissue_area | |
| - domain: Specimen | |
| - range: DimensionalObservationSet | |
| - multivalued: false | |
| - required: false | |
| - quantity_measure: | |
| - name: quantity_measure | |
| - description: An observation related to the present quantity of a specimen | |
| - - e.g. its weight, volume, or analyte concentration. | |
| + description: Observations about the current physical dimensions of an object | |
| + (e.g. length, width, area). | |
| notes: | |
| - - 'Cardinality: 0..m' | |
| + - 'Cardinality: 0..1' | |
| comments: | |
| - Observations are flexible containers for capturing a specific type of observation/measurement | |
| data about an object, along with metadata about how it was generated. The | |
| @@ -26310,6 +25542,12 @@ | |
| object. | |
| examples: | |
| - value: '' | |
| + domain: Specimen | |
| + range: DimensionalObservationSet | |
| + multivalued: false | |
| + required: false | |
| + quantity_measure: | |
| + name: quantity_measure | |
| close_mappings: | |
| - GDC:Sample.current_weight | |
| - GDC:Aliquot.amount | |
| @@ -26337,12 +25575,29 @@ | |
| - PDC:Analyte.concentration | |
| - GDC:Analyte.spectrophotometer_method | |
| - PDC:Analyte.spectrophotometer_method | |
| + description: An observation related to the present quantity of a specimen | |
| + - e.g. its weight, volume, or analyte concentration. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + comments: | |
| + - Observations are flexible containers for capturing a specific type of observation/measurement | |
| + data about an object, along with metadata about how it was generated. The | |
| + specific type of observation made is captured as data in the Observation | |
| + object. | |
| + examples: | |
| + - value: '' | |
| domain: Specimen | |
| range: SpecimenQuantityObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| quality_measure: | |
| name: quality_measure | |
| + close_mappings: | |
| + - GDC:Analyte.a260_a280_ratio | |
| + - GDC:Analyte.ribosomal_rna_28s_16s_ratio | |
| + - PDC:Analyte.a260_a280_ratio | |
| + - PDC:Analyte.ribosomal_rna_28s_16s_ratio | |
| description: An observation about characteristics of a specimen that are indicative | |
| of its quality or suitability for use. | |
| notes: | |
| @@ -26354,17 +25609,16 @@ | |
| object. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Analyte.a260_a280_ratio | |
| - - GDC:Analyte.ribosomal_rna_28s_16s_ratio | |
| - - PDC:Analyte.a260_a280_ratio | |
| - - PDC:Analyte.ribosomal_rna_28s_16s_ratio | |
| domain: Specimen | |
| range: SpecimenQualityObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| cellular_composition_type: | |
| name: cellular_composition_type | |
| + exact_mappings: | |
| + - GDC:Sample.composition | |
| + - PDC:Sample.composition | |
| description: A term describing the type of cell or cellular material comprising | |
| a specimen. | |
| notes: | |
| @@ -26380,28 +25634,12 @@ | |
| - value: Pleural Effusion | |
| - value: Human Original Cells | |
| - value: Liquid Suspension Cell Line | |
| - exact_mappings: | |
| - - GDC:Sample.composition | |
| - - PDC:Sample.composition | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_cellular_composition_type | |
| + range: enum_CRDCH_Specimen_cellular_composition_type | |
| multivalued: false | |
| required: false | |
| histological_composition_measures: | |
| name: histological_composition_measures | |
| - description: A set of one or more observations that quantify the relative | |
| - or absolute composition of a specimen at cellular level - e.g. how many | |
| - cells in the specimen are of a given type, or exhibit a particular cellular | |
| - phenotype. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - comments: | |
| - - Observations are flexible containers for capturing a specific type of observation/measurement | |
| - data about an object, along with metadata about how it was generated. The | |
| - specific type of observation made is captured as data in the Observation | |
| - object. | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Slide.number_proliferating_cells | |
| - GDC:Slide.percent_eosinophil_infiltration | |
| @@ -26439,12 +25677,30 @@ | |
| - ICDC:Sample.analysis_area_percentage_tumor | |
| - ICDC:Sample.analysis_area_percentage_glass | |
| - ICDC:Sample.analysis_area_percentage_pigmented_tumor | |
| + description: A set of one or more observations that quantify the relative | |
| + or absolute composition of a specimen at cellular level - e.g. how many | |
| + cells in the specimen are of a given type, or exhibit a particular cellular | |
| + phenotype. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + comments: | |
| + - Observations are flexible containers for capturing a specific type of observation/measurement | |
| + data about an object, along with metadata about how it was generated. The | |
| + specific type of observation made is captured as data in the Observation | |
| + object. | |
| + examples: | |
| + - value: '' | |
| domain: Specimen | |
| range: HistologicalCompositionObservationSet | |
| multivalued: true | |
| required: false | |
| - general_tissue_morphology: | |
| - name: general_tissue_morphology | |
| + inlined_as_list: true | |
| + general_tissue_pathology: | |
| + name: general_tissue_pathology | |
| + exact_mappings: | |
| + - GDC:Sample.tissue_type | |
| + - PDC:Sample.tissue_type | |
| + - ICDC:Sample.general_sample_pathology | |
| description: The high-level kind of tissue collected when generating a specimen, | |
| based on its disease status or proximity to tumor tissue (e.g. is it normal, | |
| abnormal, tumor, tumor-adjacent). | |
| @@ -26456,16 +25712,19 @@ | |
| - value: Abnormal | |
| - value: Peritumoral | |
| - value: not applicable | |
| - exact_mappings: | |
| - - GDC:Sample.tissue_type | |
| - - PDC:Sample.tissue_type | |
| - - ICDC:Sample.general_sample_pathology | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_general_tissue_morphology | |
| + range: enum_CRDCH_Specimen_general_tissue_pathology | |
| multivalued: false | |
| required: false | |
| - specific_tissue_morphology: | |
| - name: specific_tissue_morphology | |
| + specific_tissue_pathology: | |
| + name: specific_tissue_pathology | |
| + exact_mappings: | |
| + - GDC:Sample.tumor_code | |
| + - GDC:Sample.tumor_code_id | |
| + - PDC:Sample.tumor_code | |
| + - PDC:Sample.tumor_code_id | |
| + - ICDC:Sample.specific_sample_pathology | |
| + - HTAN:Biospecimen.HistologicMorphologyCode | |
| description: A term describing the specific pathology exhibited by the tissue | |
| comprising a specimen. | |
| notes: | |
| @@ -26480,48 +25739,43 @@ | |
| - value: Melanocytic hyperplasia | |
| - value: Atypical melanocytic proliferation | |
| - value: Melanoma in situ, superficial spreading | |
| - exact_mappings: | |
| - - GDC:Sample.tumor_code | |
| - - GDC:Sample.tumor_code_id | |
| - - PDC:Sample.tumor_code | |
| - - PDC:Sample.tumor_code_id | |
| - - ICDC:Sample.specific_sample_pathology | |
| - - HTAN:Biospecimen.HistologicMorphologyCode | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_specific_tissue_morphology | |
| + range: enum_CRDCH_Specimen_specific_tissue_pathology | |
| multivalued: false | |
| required: false | |
| preinvasive_tissue_morphology: | |
| name: preinvasive_tissue_morphology | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.PreinvasiveMorphology | |
| description: A term describing the specific pathology exhibited by pre-invasive | |
| tissue comprising a specimen. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.PreinvasiveMorphology | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_preinvasive_tissue_morphology | |
| + range: enum_CRDCH_Specimen_preinvasive_tissue_morphology | |
| multivalued: false | |
| required: false | |
| morphology_pathologically_confirmed: | |
| name: morphology_pathologically_confirmed | |
| + exact_mappings: | |
| + - GDC:Sample.diagnosis_pathologically_confirmed | |
| + - PDC:Sample.diagnosis_pathologically_confirmed | |
| description: A flag indicating whether the histologic assessment of specific | |
| morphology was confirmed by pathologist review. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Sample.diagnosis_pathologically_confirmed | |
| - - PDC:Sample.diagnosis_pathologically_confirmed | |
| domain: Specimen | |
| - range: ccdh_boolean | |
| + range: crdch_boolean | |
| multivalued: false | |
| required: false | |
| morphology_assessor_role: | |
| name: morphology_assessor_role | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.HistologyAssessmentBy | |
| description: A term describing the role of the person who histologically assessed | |
| the specific tissue morphology of a specimen | |
| notes: | |
| @@ -26531,14 +25785,14 @@ | |
| - value: Research Scientist | |
| - value: Other | |
| - value: Unknown | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.HistologyAssessmentBy | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_morphology_assessor_role | |
| + range: enum_CRDCH_Specimen_morphology_assessor_role | |
| multivalued: false | |
| required: false | |
| - morphlogy_assessment_method: | |
| - name: morphlogy_assessment_method | |
| + morphology_assessment_method: | |
| + name: morphology_assessment_method | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.HistologyAssessmentMedium | |
| description: The general method used to assess a specimens specific tissue | |
| morphology | |
| notes: | |
| @@ -26548,14 +25802,14 @@ | |
| - value: Microscopy | |
| - value: Other | |
| - value: Unknown | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.HistologyAssessmentMedium | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_morphlogy_assessment_method | |
| + range: enum_CRDCH_Specimen_morphology_assessment_method | |
| multivalued: false | |
| required: false | |
| degree_of_dysplasia: | |
| name: degree_of_dysplasia | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.DegreeofDysplasia | |
| description: A term describing the nature/extent of abnormal cells that are | |
| not cancer, as observed upon microscopic assessment of a specimen. Records | |
| the degree of dysplasia for the cyst or lesion under consideration. | |
| @@ -26568,28 +25822,30 @@ | |
| - value: Severe dysplasia | |
| - value: Carcinoma in Situ | |
| - value: Unknown | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.DegreeofDysplasia | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_degree_of_dysplasia | |
| + range: enum_CRDCH_Specimen_degree_of_dysplasia | |
| multivalued: false | |
| required: false | |
| dysplasia_fraction: | |
| name: dysplasia_fraction | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.DysplasiaFraction | |
| description: Resulting value to represent the number of pieces of dysplasia | |
| divided by the total number of pieces. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.DysplasiaFraction | |
| domain: Specimen | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| related_document: | |
| name: related_document | |
| + close_mappings: | |
| + - GDC:Sample.pathology_report_uuid | |
| + - PDC:Sample.pathology_report_uuid | |
| + - HTAN:Biospecimen.ProtocolLink | |
| description: A reference to an external document that is about or related | |
| to the specimen (e.g. a publication related to the study it is a part of, | |
| pathology report containing additional details about it, protocol describing | |
| @@ -26598,16 +25854,15 @@ | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Sample.pathology_report_uuid | |
| - - PDC:Sample.pathology_report_uuid | |
| - - HTAN:Biospecimen.ProtocolLink | |
| domain: Specimen | |
| range: Document | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| section_location: | |
| name: section_location | |
| + exact_mappings: | |
| + - GDC:Slide.section_location | |
| description: The location in a parent specimen from which a section/portion | |
| was excised (e.g. top, middle, bottom) | |
| notes: | |
| @@ -26618,31 +25873,33 @@ | |
| - value: Top | |
| - value: Bottom | |
| - value: Unknown | |
| - exact_mappings: | |
| - - GDC:Slide.section_location | |
| domain: Specimen | |
| - range: enum_CCDH_Specimen_section_location | |
| + range: enum_CRDCH_Specimen_section_location | |
| multivalued: false | |
| required: false | |
| derived_product: | |
| name: derived_product | |
| + close_mappings: | |
| + - GDC:Sample.passage_count | |
| + - GDC:Sample.growth_rate | |
| + - PDC:Sample.passage_count | |
| + - PDC:Sample.growth_rate | |
| description: A 'living' biologically active product that was derived from | |
| the specimen (e.g. a cell culture, tissue culture, or organoid) | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Sample.passage_count | |
| - - GDC:Sample.growth_rate | |
| - - PDC:Sample.passage_count | |
| - - PDC:Sample.growth_rate | |
| domain: Specimen | |
| range: BiologicProduct | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| distance_from_paired_specimen: | |
| name: distance_from_paired_specimen | |
| + close_mappings: | |
| + - GDC:Sample.distance_normal_to_tumor | |
| + - PDC:Sample.distance_normal_to_tumor | |
| description: The observed distance in the body of the specimen from a 'paired | |
| specimen' at the time of collection. (e.g. the distance between the in vivo | |
| location of a tumor tissue specimen and its paired normal specimen) | |
| @@ -26650,9 +25907,6 @@ | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Sample.distance_normal_to_tumor | |
| - - PDC:Sample.distance_normal_to_tumor | |
| domain: Specimen | |
| range: Quantity | |
| multivalued: false | |
| @@ -26694,7 +25948,7 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenContainer | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| identifier: | |
| @@ -26722,6 +25976,7 @@ | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| container_type: | |
| name: container_type | |
| description: The kind of the container. | |
| @@ -26733,26 +25988,28 @@ | |
| - value: Cell culture flask | |
| - value: Glass slide | |
| domain: SpecimenContainer | |
| - range: enum_CCDH_SpecimenContainer_container_type | |
| + range: enum_CRDCH_SpecimenContainer_container_type | |
| multivalued: false | |
| required: false | |
| container_number: | |
| name: container_number | |
| + exact_mappings: | |
| + - GDC:Analyte.well_number | |
| + - PDC:Analyte.well_number | |
| description: Informal number by which the container is referenced or identified | |
| (e.g. a slide number, or a well number in a plate) | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Analyte.well_number | |
| - - PDC:Analyte.well_number | |
| domain: SpecimenContainer | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| additive: | |
| name: additive | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.CollectionMedia | |
| description: A material substance added to the container (typically to support | |
| the primary contained object - e.g. culture media to support cell growth) | |
| notes: | |
| @@ -26762,12 +26019,11 @@ | |
| - value: DMEM+Serum | |
| - value: RPMI | |
| - value: RPMI+Serum | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.CollectionMedia | |
| domain: SpecimenContainer | |
| range: Substance | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| parent_container: | |
| name: parent_container | |
| description: A larger container of which this container is a part (e.g. the | |
| @@ -26807,11 +26063,18 @@ | |
| - value: Collection from Source | |
| - value: Derivation from Specimen | |
| domain: SpecimenCreationActivity | |
| - range: enum_CCDH_SpecimenCreationActivity_activity_type | |
| + range: enum_CRDCH_SpecimenCreationActivity_activity_type | |
| multivalued: false | |
| required: false | |
| date_started: | |
| name: date_started | |
| + close_mappings: | |
| + - GDC:Sample.days_to_collection | |
| + - GDC:Portion.creation_datetime | |
| + - PDC:Portion.creation_datetime | |
| + - PDC:Sample.days_to_collection | |
| + - ICDC:Sample.date_of_sample_collection | |
| + - HTAN:Biospecimen.CollectionDaysfromIndex | |
| description: The date when the activity began (in this case, a specimen creation | |
| event). | |
| notes: | |
| @@ -26823,18 +26086,19 @@ | |
| date_ended. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Portion.creation_datetime | |
| - - PDC:Portion.creation_datetime | |
| - - PDC:Sample.days_to_collection | |
| - - ICDC:Sample.date_of_sample_collection | |
| - - HTAN:Biospecimen.CollectionDaysfromIndex | |
| domain: SpecimenCreationActivity | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| date_ended: | |
| name: date_ended | |
| + close_mappings: | |
| + - GDC:Sample.days_to_collection | |
| + - GDC:Portion.creation_datetime | |
| + - PDC:Portion.creation_datetime | |
| + - PDC:Sample.days_to_collection | |
| + - ICDC:Sample.date_of_sample_collection | |
| + - HTAN:Biospecimen.CollectionDaysfromIndex | |
| description: The date when the activity ended (in this case, a specimen creation | |
| event). | |
| notes: | |
| @@ -26846,12 +26110,6 @@ | |
| date_ended. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Portion.creation_datetime | |
| - - PDC:Portion.creation_datetime | |
| - - PDC:Sample.days_to_collection | |
| - - ICDC:Sample.date_of_sample_collection | |
| - - HTAN:Biospecimen.CollectionDaysfromIndex | |
| domain: SpecimenCreationActivity | |
| range: TimePoint | |
| multivalued: false | |
| @@ -26869,6 +26127,12 @@ | |
| required: false | |
| collection_method_type: | |
| name: collection_method_type | |
| + exact_mappings: | |
| + - GDC:Sample.method_of_sample_procurement | |
| + - PDC:Sample.method_of_sample_procurement | |
| + - PDC:Sample.pool | |
| + - PDC:Aliquot.pool | |
| + - HTAN:Biospecimen.AcquisitionMethodType | |
| description: The type of method applied in collecting a sample from its original | |
| source. | |
| notes: | |
| @@ -26880,18 +26144,15 @@ | |
| - value: Ascites Drainage | |
| - value: Excisional Biopsy | |
| - value: Specimen Pooling | |
| - exact_mappings: | |
| - - GDC:Sample.method_of_sample_procurement | |
| - - PDC:Sample.method_of_sample_procurement | |
| - - PDC:Sample.pool | |
| - - PDC:Aliquot.pool | |
| - - HTAN:Biospecimen.AcquisitionMethodType | |
| domain: SpecimenCreationActivity | |
| - range: enum_CCDH_SpecimenCreationActivity_collection_method_type | |
| + range: enum_CRDCH_SpecimenCreationActivity_collection_method_type | |
| multivalued: false | |
| required: false | |
| derivation_method_type: | |
| name: derivation_method_type | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.SlicingMethod | |
| + - HTAN:Biospecimen.MethodofNucleicAcidIsolation | |
| description: The type of method applied to derive a new specimen from an existing | |
| one. | |
| notes: | |
| @@ -26908,29 +26169,34 @@ | |
| - value: Other | |
| - value: Unknown | |
| - value: NotReported | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.SlicingMethod | |
| - - HTAN:Biospecimen.MethodofNucleicAcidIsolation | |
| domain: SpecimenCreationActivity | |
| - range: enum_CCDH_SpecimenCreationActivity_derivation_method_type | |
| + range: enum_CRDCH_SpecimenCreationActivity_derivation_method_type | |
| multivalued: false | |
| required: false | |
| additive: | |
| name: additive | |
| + close_mappings: | |
| + - HTAN:Biospecimen.LysisBuffer | |
| description: A type of material or reagent used applied as input when creating | |
| a specimen. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - HTAN:Biospecimen.LysisBuffer | |
| domain: SpecimenCreationActivity | |
| range: Substance | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| collection_site: | |
| name: collection_site | |
| + close_mappings: | |
| + - GDC:Sample.biospecimen_anatomic_site | |
| + - GDC:Sample.biospecimen_laterality | |
| + - PDC:Sample.biospecimen_anatomic_site | |
| + - PDC:Sample.biospecimen_laterality | |
| + - ICDC:Sample.sample_site | |
| + - HTAN:Biospecimen.SiteofResectionorBiopsy | |
| description: The anatomic site from which a specimen was collected. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -26941,19 +26207,15 @@ | |
| - value: Abdomen | |
| - value: Abdominal Wall | |
| - value: Acetabulum | |
| - close_mappings: | |
| - - GDC:Sample.biospecimen_anatomic_site | |
| - - GDC:Sample.biospecimen_laterality | |
| - - PDC:Sample.biospecimen_anatomic_site | |
| - - PDC:Sample.biospecimen_laterality | |
| - - ICDC:Sample.sample_site | |
| - - HTAN:Biospecimen.SiteofResectionorBiopsy | |
| domain: SpecimenCreationActivity | |
| range: BodySite | |
| multivalued: false | |
| required: false | |
| quantity_collected: | |
| name: quantity_collected | |
| + close_mappings: | |
| + - GDC:Sample.initial_weight | |
| + - PDC:Sample.initial_weight | |
| description: The quantity of material in the specimen as originally collected | |
| from its original source material (prior to downstream portioning or processing) | |
| notes: | |
| @@ -26962,47 +26224,49 @@ | |
| - This attribute applies only when Specimen.category='initial sample'. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Sample.initial_weight | |
| - - PDC:Sample.initial_weight | |
| domain: SpecimenCreationActivity | |
| range: Quantity | |
| multivalued: false | |
| required: false | |
| execution_time_observation: | |
| name: execution_time_observation | |
| + close_mappings: | |
| + - GDC:Sample.time_between_excision_and_freezing | |
| + - GDC:Sample.time_between_clamping_and_freezing | |
| + - PDC:Sample.time_between_excision_and_freezing | |
| + - PDC:Sample.time_between_clamping_and_freezing | |
| description: Information describing how long certain parts on an activity | |
| took to complete. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Sample.time_between_excision_and_freezing | |
| - - GDC:Sample.time_between_clamping_and_freezing | |
| - - PDC:Sample.time_between_excision_and_freezing | |
| - - PDC:Sample.time_between_clamping_and_freezing | |
| domain: SpecimenCreationActivity | |
| range: ExecutionTimeObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| execution_condition_observation: | |
| name: execution_condition_observation | |
| + close_mappings: | |
| + - HTAN:Biospecimen.ISCHEMIC_TEMPERATURE | |
| + - HTAN:Biospecimen.ISCHEMIC_TIME | |
| description: Information describing the environmental conditions in which | |
| an activity, or a specific part of an activity, was performed. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - HTAN:Biospecimen.ISCHEMIC_TEMPERATURE | |
| - - HTAN:Biospecimen.ISCHEMIC_TIME | |
| domain: SpecimenCreationActivity | |
| range: ExecutionConditionObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| specimen_order: | |
| name: specimen_order | |
| + exact_mappings: | |
| + - GDC:Portion.portion_number | |
| + - PDC:Portion.portion_number | |
| description: A numeric value that represents the sequential order of this | |
| creation activity relative to those producing other specimens from the same | |
| source material or parent specimen. | |
| @@ -27010,11 +26274,8 @@ | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Portion.portion_number | |
| - - PDC:Portion.portion_number | |
| domain: SpecimenCreationActivity | |
| - range: ccdh_integer | |
| + range: crdch_integer | |
| multivalued: false | |
| required: false | |
| SpecimenQualityObservation: | |
| @@ -27054,7 +26315,7 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenQualityObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -27067,7 +26328,7 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenQualityObservation | |
| - range: enum_CCDH_SpecimenQualityObservation_category | |
| + range: enum_CRDCH_SpecimenQualityObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -27082,7 +26343,7 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenQualityObservation | |
| - range: enum_CCDH_SpecimenQualityObservation_observation_type | |
| + range: enum_CRDCH_SpecimenQualityObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -27100,7 +26361,7 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenQualityObservation | |
| - range: enum_CCDH_SpecimenQualityObservation_method_type | |
| + range: enum_CRDCH_SpecimenQualityObservation_method_type | |
| multivalued: true | |
| required: false | |
| focus: | |
| @@ -27121,6 +26382,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -27146,8 +26408,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueQuantity: | |
| - name: valueQuantity | |
| + value_quantity: | |
| + name: value_quantity | |
| description: The result of the observation, encoded as a free-text Quantity. | |
| notes: | |
| - 'Cardinality: 1..1' | |
| @@ -27201,7 +26463,7 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenQuantityObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -27214,7 +26476,7 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenQuantityObservation | |
| - range: enum_CCDH_SpecimenQuantityObservation_category | |
| + range: enum_CRDCH_SpecimenQuantityObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -27229,11 +26491,14 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenQuantityObservation | |
| - range: enum_CCDH_SpecimenQuantityObservation_observation_type | |
| + range: enum_CRDCH_SpecimenQuantityObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| name: method_type | |
| + exact_mappings: | |
| + - GDC:Analyte.spectrophotometer_method | |
| + - PDC:Analyte.spectrophotometer_method | |
| description: A type of method used in generating the Observation result. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| @@ -27246,11 +26511,8 @@ | |
| as that provided by the ACMG). | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Analyte.spectrophotometer_method | |
| - - PDC:Analyte.spectrophotometer_method | |
| domain: SpecimenQuantityObservation | |
| - range: enum_CCDH_SpecimenQuantityObservation_method_type | |
| + range: enum_CRDCH_SpecimenQuantityObservation_method_type | |
| multivalued: true | |
| required: false | |
| focus: | |
| @@ -27271,6 +26533,7 @@ | |
| range: Entity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| subject: | |
| name: subject | |
| description: The patient that the observation is about (if not the direct | |
| @@ -27296,8 +26559,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueQuantity: | |
| - name: valueQuantity | |
| + value_quantity: | |
| + name: value_quantity | |
| description: The result of the observation, encoded as a free-text Quantity. | |
| notes: | |
| - 'Cardinality: 1..1' | |
| @@ -27336,11 +26599,14 @@ | |
| - value: Mounting | |
| - value: Preservation | |
| domain: SpecimenProcessingActivity | |
| - range: enum_CCDH_SpecimenProcessingActivity_activity_type | |
| + range: enum_CRDCH_SpecimenProcessingActivity_activity_type | |
| multivalued: false | |
| required: false | |
| date_started: | |
| name: date_started | |
| + close_mappings: | |
| + - HTAN:Biospecimen.ProcessingDaysfromIndex | |
| + - HTAN:Biospecimen.SectioningDaysfromIndex | |
| description: The date when the activity began (in this case, a specimen processing | |
| event). | |
| notes: | |
| @@ -27352,15 +26618,14 @@ | |
| date_ended. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - HTAN:Biospecimen.ProcessingDaysfromIndex | |
| - - HTAN:Biospecimen.SectioningDaysfromIndex | |
| domain: SpecimenProcessingActivity | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| date_ended: | |
| name: date_ended | |
| + close_mappings: | |
| + - HTAN:Biospecimen.ProcessingDaysfromIndex | |
| description: The date when the activity began (in this case, a specimen processing | |
| event). | |
| notes: | |
| @@ -27372,51 +26637,38 @@ | |
| date_ended. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - HTAN:Biospecimen.ProcessingDaysfromIndex | |
| domain: SpecimenProcessingActivity | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| duration: | |
| name: duration | |
| + close_mappings: | |
| + - HTAN:Biospecimen.FIXATION_DURATION | |
| description: The length of time over which the activity was performed. | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - HTAN:Biospecimen.FIXATION_DURATION | |
| domain: SpecimenProcessingActivity | |
| range: Quantity | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| performed_by: | |
| name: performed_by | |
| + exact_mappings: | |
| + - GDC:Sample.processed_at | |
| + - HTAN:Biospecimen.ProcessingLocation | |
| description: The organization or group that performed the activity. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Sample.processed_at | |
| - - HTAN:Biospecimen.ProcessingLocation | |
| domain: SpecimenProcessingActivity | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| method_type: | |
| name: method_type | |
| - description: A specific type of method or procedure performed to process the | |
| - specimen | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - examples: | |
| - - value: Snap Freezing | |
| - - value: Cryopreservation in liquid nitrogen (dead tissue) | |
| - - value: Cryopreservation in dry ice (dead tissue) | |
| - - value: Formalin fixed paraffin embedded (FFPE) | |
| - - value: Formalin fixed-unbuffered | |
| - - value: Formalin fixed-buffered | |
| - - value: OCT | |
| exact_mappings: | |
| - GDC:Sample.freezing_method | |
| - GDC:Sample.preservation_method | |
| @@ -27429,25 +26681,39 @@ | |
| - GDC:Portion.is_ffpe | |
| - PDC:Sample.oct_embedded | |
| - HTAN:Biospecimen.PRESERVATION_METHOD | |
| + - ICDC:Sample.sample_preservation | |
| + description: A specific type of method or procedure performed to process the | |
| + specimen | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + examples: | |
| + - value: Snap Freezing | |
| + - value: Cryopreservation in liquid nitrogen (dead tissue) | |
| + - value: Cryopreservation in dry ice (dead tissue) | |
| + - value: Formalin fixed paraffin embedded (FFPE) | |
| + - value: Formalin fixed-unbuffered | |
| + - value: Formalin fixed-buffered | |
| + - value: OCT | |
| domain: SpecimenProcessingActivity | |
| - range: enum_CCDH_SpecimenProcessingActivity_method_type | |
| + range: enum_CRDCH_SpecimenProcessingActivity_method_type | |
| multivalued: false | |
| required: false | |
| additive: | |
| name: additive | |
| + close_mappings: | |
| + - HTAN:Biospecimen.FixativeType | |
| + - HTAN:Biospecimen.MountingMedium | |
| description: A type of material or reagent used as input when processing the | |
| specimen | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: Formalin | |
| - close_mappings: | |
| - - HTAN:Biospecimen.FixativeType | |
| - - HTAN:Biospecimen.MountingMedium | |
| domain: SpecimenProcessingActivity | |
| range: Substance | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| execution_time_observation: | |
| name: execution_time_observation | |
| description: Information describing how long certain parts on an activity | |
| @@ -27460,6 +26726,7 @@ | |
| range: ExecutionTimeObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| execution_condition_observation: | |
| name: execution_condition_observation | |
| description: Information describing the environmental conditions in which | |
| @@ -27472,6 +26739,7 @@ | |
| range: ExecutionConditionObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| SpecimenStorageActivity: | |
| name: SpecimenStorageActivity | |
| description: "An activity in which a specimen is stored or maintained in a particular\ | |
| @@ -27543,6 +26811,8 @@ | |
| required: false | |
| method_type: | |
| name: method_type | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.StorageMethod | |
| description: A specific type of method or procedure performed to store the | |
| specimen | |
| notes: | |
| @@ -27557,10 +26827,8 @@ | |
| - value: frozen in vapor phase | |
| - value: paraffin block | |
| - value: RNAlater at 4C | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.StorageMethod | |
| domain: SpecimenStorageActivity | |
| - range: enum_CCDH_SpecimenStorageActivity_method_type | |
| + range: enum_CRDCH_SpecimenStorageActivity_method_type | |
| multivalued: false | |
| required: false | |
| container: | |
| @@ -27575,6 +26843,7 @@ | |
| range: SpecimenContainer | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| SpecimenTransportActivity: | |
| name: SpecimenTransportActivity | |
| description: An activity through which a specimen is transported between locations | |
| @@ -27625,9 +26894,10 @@ | |
| examples: | |
| - value: '' | |
| domain: SpecimenTransportActivity | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| performed_by: | |
| name: performed_by | |
| description: The organization or group that performed the activity. | |
| @@ -27653,21 +26923,23 @@ | |
| required: false | |
| transport_destination: | |
| name: transport_destination | |
| + exact_mappings: | |
| + - GDC:Portion.shipped_to | |
| + - GDC:Aliquot.shipped_to | |
| description: An organization (facility, site, lab, etc) to which the specimen | |
| is delivered as a result of the activity. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Portion.shipped_to | |
| - - GDC:Aliquot.shipped_to | |
| domain: SpecimenTransportActivity | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| execution_condition_observation: | |
| name: execution_condition_observation | |
| + close_mappings: | |
| + - HTAN:Biospecimen.SHIPPING_CONDITIONS | |
| description: Information describing the environmental conditions in which | |
| an activity, or a specific part of an activity, was performed. | |
| notes: | |
| @@ -27676,12 +26948,11 @@ | |
| - 'e.g. that a specimen was shipped with an ice pack, or at a specific temperature. ' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - HTAN:Biospecimen.SHIPPING_CONDITIONS | |
| domain: SpecimenTransportActivity | |
| range: ExecutionConditionObservation | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| Subject: | |
| name: Subject | |
| description: Demographics and other administrative information about an individual | |
| @@ -27718,11 +26989,13 @@ | |
| examples: | |
| - value: '' | |
| domain: Subject | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: true | |
| identifier: | |
| name: identifier | |
| + exact_mappings: | |
| + - ICDC:Case.patient_id | |
| description: A 'business' identifier or accession number for the entity, typically | |
| as provided by an external system or authority, that are globally unique | |
| and persist across implementing systems. Also, since these identifiers are | |
| @@ -27742,12 +27015,11 @@ | |
| the identifier itself, along with metadata about its source. | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - ICDC:Case.patient_id | |
| domain: Subject | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| species: | |
| name: species | |
| description: The scientific binomial name for the species of the subject (e.g. | |
| @@ -27759,11 +27031,13 @@ | |
| - value: Canis familiaris | |
| - value: Mus musculus | |
| domain: Subject | |
| - range: enum_CCDH_Subject_species | |
| + range: enum_CRDCH_Subject_species | |
| multivalued: false | |
| required: false | |
| breed: | |
| name: breed | |
| + exact_mappings: | |
| + - ICDC:Demographic.breed | |
| description: A label given to a group of animals homogeneous in appearance | |
| and other characteristics that distinguish it from other animals of the | |
| same species. | |
| @@ -27774,14 +27048,17 @@ | |
| - value: Afghan Hound | |
| - value: Airedale Terrier | |
| - value: Akita | |
| - exact_mappings: | |
| - - ICDC:Demographic.breed | |
| domain: Subject | |
| - range: enum_CCDH_Subject_breed | |
| + range: enum_CRDCH_Subject_breed | |
| multivalued: false | |
| required: false | |
| sex: | |
| name: sex | |
| + exact_mappings: | |
| + - ICDC:Demographic.sex | |
| + - GDC:Demographic.gender | |
| + - PDC:Demographic.gender | |
| + - HTAN:Demographics.Gender | |
| description: The biologic character or quality that distinguishes male and | |
| female from one another as expressed by analysis of the person's gonadal, | |
| morphologic (internal and external), chromosomal, and hormonal characteristics. | |
| @@ -27794,17 +27071,17 @@ | |
| - value: Not Reported | |
| - value: Unknown | |
| - value: Unspecified | |
| - exact_mappings: | |
| - - ICDC:Demographic.sex | |
| - - GDC:Demographic.gender | |
| - - PDC:Demographic.gender | |
| - - HTAN:Demographics.Gender | |
| domain: Subject | |
| - range: enum_CCDH_Subject_sex | |
| + range: enum_CRDCH_Subject_sex | |
| multivalued: false | |
| required: false | |
| ethnicity: | |
| name: ethnicity | |
| + exact_mappings: | |
| + - GDC:Clinical.ethnicity | |
| + - GDC:Demographic.ethnicity | |
| + - PDC:Demographic.ethnicity | |
| + - HTAN:Demographics.Ethnicity | |
| description: An individual's self-described social and cultural grouping, | |
| specifically whether an individual describes themselves as Hispanic or Latino. | |
| The provided values are based on the categories defined by the U.S. Office | |
| @@ -27819,17 +27096,17 @@ | |
| - value: Not Hispanic or Latino | |
| - value: Not Reported | |
| - value: Unknown | |
| - exact_mappings: | |
| - - GDC:Clinical.ethnicity | |
| - - GDC:Demographic.ethnicity | |
| - - PDC:Demographic.ethnicity | |
| - - HTAN:Demographics.Ethnicity | |
| domain: Subject | |
| - range: enum_CCDH_Subject_ethnicity | |
| + range: enum_CRDCH_Subject_ethnicity | |
| multivalued: false | |
| required: false | |
| race: | |
| name: race | |
| + exact_mappings: | |
| + - GDC:Clinical.race | |
| + - GDC:Demographic.race | |
| + - PDC:Demographic.race | |
| + - HTAN:Demographics.Race | |
| description: An arbitrary classification of a taxonomic group that is a division | |
| of a species. It usually arises as a consequence of geographical isolation | |
| within a species and is characterized by shared heredity, physical attributes | |
| @@ -27848,17 +27125,17 @@ | |
| - value: Not Reported | |
| - value: Unknown | |
| - value: White | |
| - exact_mappings: | |
| - - GDC:Clinical.race | |
| - - GDC:Demographic.race | |
| - - PDC:Demographic.race | |
| - - HTAN:Demographics.Race | |
| domain: Subject | |
| - range: enum_CCDH_Subject_race | |
| + range: enum_CRDCH_Subject_race | |
| multivalued: true | |
| required: false | |
| year_of_birth: | |
| name: year_of_birth | |
| + exact_mappings: | |
| + - GDC:Demographic.year_of_birth | |
| + - PDC:Demographic.year_of_birth | |
| + - ICDC:Demographic.date_of_birth | |
| + - HTAN:Demographics.YearOfBirth | |
| description: Numeric value to represent the calendar year in which an individual | |
| was born. | |
| notes: | |
| @@ -27867,17 +27144,16 @@ | |
| - Applicable only when Subject.species is Homo Sapiens | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Demographic.year_of_birth | |
| - - PDC:Demographic.year_of_birth | |
| - - ICDC:Demographic.date_of_birth | |
| - - HTAN:Demographics.YearOfBirth | |
| domain: Subject | |
| - range: ccdh_integer | |
| + range: crdch_integer | |
| multivalued: false | |
| required: false | |
| vital_status: | |
| name: vital_status | |
| + exact_mappings: | |
| + - GDC:Demographic.vital_status | |
| + - PDC:Demographic.vital_status | |
| + - HTAN:Demographics.VitalStatus | |
| description: Coded value indicating the state or condition of being living | |
| or deceased; also includes the case where the vital status is unknown. | |
| notes: | |
| @@ -27887,46 +27163,45 @@ | |
| - value: Dead | |
| - value: Unknown | |
| - value: Not Reported | |
| - exact_mappings: | |
| - - GDC:Demographic.vital_status | |
| - - PDC:Demographic.vital_status | |
| - - HTAN:Demographics.VitalStatus | |
| domain: Subject | |
| - range: enum_CCDH_Subject_vital_status | |
| + range: enum_CRDCH_Subject_vital_status | |
| multivalued: false | |
| required: false | |
| age_at_death: | |
| name: age_at_death | |
| + close_mappings: | |
| + - GDC:Demographic.days_to_death | |
| + - PDC:Demographic.days_to_death | |
| description: The age of an individual at the time of death, expressed in days | |
| since birth | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Demographic.days_to_death | |
| - - PDC:Demographic.days_to_death | |
| domain: Subject | |
| range: Quantity | |
| multivalued: false | |
| required: false | |
| year_of_death: | |
| name: year_of_death | |
| + exact_mappings: | |
| + - GDC:Demographic.year_of_death | |
| + - PDC:Demographic.year_of_death | |
| description: Numeric value to represent the calendar year in which an individual | |
| died. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Demographic.year_of_death | |
| - - PDC:Demographic.year_of_death | |
| domain: Subject | |
| - range: ccdh_integer | |
| + range: crdch_integer | |
| multivalued: false | |
| required: false | |
| cause_of_death: | |
| name: cause_of_death | |
| + exact_mappings: | |
| + - GDC:Demographic.cause_of_death | |
| + - PDC:Demographic.cause_of_death | |
| description: Coded value indicating the circumstance or condition that results | |
| in the death of the subject. | |
| notes: | |
| @@ -27936,11 +27211,8 @@ | |
| - value: Cardiovascular Disorder, NOS | |
| - value: End-stage Renal Disease | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Demographic.cause_of_death | |
| - - PDC:Demographic.cause_of_death | |
| domain: Subject | |
| - range: enum_CCDH_Subject_cause_of_death | |
| + range: enum_CRDCH_Subject_cause_of_death | |
| multivalued: false | |
| required: false | |
| Substance: | |
| @@ -27954,6 +27226,13 @@ | |
| attributes: | |
| substance_type: | |
| name: substance_type | |
| + exact_mappings: | |
| + - HTAN:Biospecimen.LysisBuffer | |
| + - HTAN:Biospecimen.FixativeType | |
| + - HTAN:Biospecimen.MountingMedium | |
| + - HTAN:Biospecimen.CollectionMedia | |
| + - GDC:Treatment.therapeutic_agents | |
| + - PDC:Treatment.therapeutic_agents | |
| description: The specific type of the substance - at as granular a level as | |
| possible. May be a specific chemical compound, or the name of a formulation/preparation | |
| made up of many compounds. | |
| @@ -27963,15 +27242,8 @@ | |
| - value: toluene | |
| - value: formalin | |
| - value: DMEM | |
| - exact_mappings: | |
| - - HTAN:Biospecimen.LysisBuffer | |
| - - HTAN:Biospecimen.FixativeType | |
| - - HTAN:Biospecimen.MountingMedium | |
| - - HTAN:Biospecimen.CollectionMedia | |
| - - GDC:Treatment.therapeutic_agents | |
| - - PDC:Treatment.therapeutic_agents | |
| domain: Substance | |
| - range: enum_CCDH_Substance_substance_type | |
| + range: enum_CRDCH_Substance_substance_type | |
| multivalued: false | |
| required: false | |
| role: | |
| @@ -27987,19 +27259,19 @@ | |
| - value: mounting medium | |
| - value: collection media | |
| domain: Substance | |
| - range: enum_CCDH_Substance_role | |
| + range: enum_CRDCH_Substance_role | |
| multivalued: true | |
| required: false | |
| substance_quantity: | |
| name: substance_quantity | |
| + exact_mappings: | |
| + - GDC:Treatment.treatment_dose | |
| + - GDC:Treatment.treatment_dose_unit | |
| description: The quantity of substance this instance stands for. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Treatment.treatment_dose | |
| - - GDC:Treatment.treatment_dose_unit | |
| domain: Substance | |
| range: Quantity | |
| multivalued: false | |
| @@ -28007,10 +27279,18 @@ | |
| TimePoint: | |
| name: TimePoint | |
| description: A structured representation of a single point in time that allows | |
| - direct/explicit declaration as a dateTime, or specification in terms of offset | |
| - from a defined index. | |
| + direct/explicit declaration as a dateTime, specification in terms of offset | |
| + from a defined index, or description of an event type as a proxy for the time | |
| + point when it occurred. | |
| notes: | |
| - Derived from [TimePoint in sheet TimePoint](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=300932847) | |
| + comments: | |
| + - 'The TimePoint object supports three ways to specify a point in time. The date_time | |
| + field is the most direct - capturing an explicit date (e.g. 2021-05-05). The | |
| + paired fields index_time_point and offset_from_index allows specification of | |
| + a point in time as an offset from a related fixed time point. Finally, the | |
| + event_type field uses type of event as a proxy for the time point when the event | |
| + occurred. ' | |
| is_a: Entity | |
| attributes: | |
| id: | |
| @@ -28041,11 +27321,18 @@ | |
| examples: | |
| - value: '' | |
| domain: TimePoint | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| - dateTime: | |
| - name: dateTime | |
| + date_time: | |
| + name: date_time | |
| + exact_mappings: | |
| + - GDC:Portion.creation_datetime | |
| + - PDC:Portion.creation_datetime | |
| + - ICDC:Sample.date_of_sample_collection | |
| + - ICDC:Study.date_of_iacuc_approval | |
| + - GDC:Diagnosis.year_of_diagnosis | |
| + - PDC:Diagnosis.year_of_diagnosis | |
| description: An explicitly specified timepoint described in terms of a date | |
| and optionally a time on that date. | |
| notes: | |
| @@ -28054,17 +27341,12 @@ | |
| - 'Use when the TimePeriod is just a single instant / point in time. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Portion.creation_datetime | |
| - - PDC:Portion.creation_datetime | |
| - - ICDC:Sample.date_of_sample_collection | |
| - - ICDC:Study.date_of_iacuc_approval | |
| domain: TimePoint | |
| - range: ccdh_dateTime | |
| + range: crdch_dateTime | |
| multivalued: false | |
| required: false | |
| - indexTimePoint: | |
| - name: indexTimePoint | |
| + index_time_point: | |
| + name: index_time_point | |
| description: Another TimePoint from which this point is offset. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -28074,16 +27356,8 @@ | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| - offsetFromIndex: | |
| - name: offsetFromIndex | |
| - description: A quantity of time that, together with the index date or event, | |
| - can be used to derive a specific timepoint. | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - comments: | |
| - - Quantity.unit MUST be a unit of time, and SHOULD be set to 'days'. | |
| - examples: | |
| - - value: '' | |
| + offset_from_index: | |
| + name: offset_from_index | |
| close_mappings: | |
| - HTAN:Biospecimen.CollectionDaysfromIndex | |
| - HTAN:Biospecimen.ProcessingDaysfromIndex | |
| @@ -28093,12 +27367,22 @@ | |
| - PDC:Treatment.days_to_treatment_end | |
| - GDC:Treatment.days_to_treatment_start | |
| - PDC:Treatment.days_to_treatment_start | |
| + - GDC:Diagnosis.days_to_diagnosis | |
| + - PDC:Diagnosis.days_to_diagnosis | |
| + description: A quantity of time that, together with the index date or event, | |
| + can be used to derive a specific timepoint. | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + comments: | |
| + - Quantity.unit MUST be a unit of time, and SHOULD be set to 'days'. | |
| + examples: | |
| + - value: '' | |
| domain: TimePoint | |
| range: Quantity | |
| multivalued: false | |
| required: false | |
| - eventType: | |
| - name: eventType | |
| + event_type: | |
| + name: event_type | |
| description: An event that occurred at the point in time specified by this | |
| TimePoint. | |
| notes: | |
| @@ -28109,7 +27393,7 @@ | |
| examples: | |
| - value: '' | |
| domain: TimePoint | |
| - range: enum_CCDH_TimePoint_eventType | |
| + range: enum_CRDCH_TimePoint_event_type | |
| multivalued: true | |
| required: false | |
| TimePeriod: | |
| @@ -28119,10 +27403,10 @@ | |
| - Derived from [TimePeriod in sheet TimePeriod](https://docs.google.com/spreadsheets/d/1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4/edit#gid=1590126992) | |
| is_a: Entity | |
| attributes: | |
| - ? 'periodStart | |
| + ? 'period_start | |
| start' | |
| - : name: 'periodStart | |
| + : name: 'period_start | |
| start' | |
| description: When a period of time started. | |
| @@ -28134,10 +27418,10 @@ | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| - ? 'periodEnd | |
| + ? 'period_end | |
| end' | |
| - : name: 'periodEnd | |
| + : name: 'period_end | |
| end' | |
| description: When a period of time ended. | |
| @@ -28186,7 +27470,7 @@ | |
| examples: | |
| - value: '' | |
| domain: TobaccoExposureObservation | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| category: | |
| @@ -28197,7 +27481,7 @@ | |
| examples: | |
| - value: '' | |
| domain: TobaccoExposureObservation | |
| - range: enum_CCDH_TobaccoExposureObservation_category | |
| + range: enum_CRDCH_TobaccoExposureObservation_category | |
| multivalued: false | |
| required: false | |
| observation_type: | |
| @@ -28221,7 +27505,7 @@ | |
| - value: type_of_tobacco_used | |
| - value: years_smoked | |
| domain: TobaccoExposureObservation | |
| - range: enum_CCDH_TobaccoExposureObservation_observation_type | |
| + range: enum_CRDCH_TobaccoExposureObservation_observation_type | |
| multivalued: false | |
| required: true | |
| method_type: | |
| @@ -28239,7 +27523,7 @@ | |
| examples: | |
| - value: '' | |
| domain: TobaccoExposureObservation | |
| - range: enum_CCDH_TobaccoExposureObservation_method_type | |
| + range: enum_CRDCH_TobaccoExposureObservation_method_type | |
| multivalued: false | |
| required: false | |
| focus: | |
| @@ -28285,15 +27569,8 @@ | |
| range: Organization | |
| multivalued: false | |
| required: false | |
| - valueInteger: | |
| - name: valueInteger | |
| - description: The result of the observation, encoded as an integer. | |
| - notes: | |
| - - 'Cardinality: 0..1' | |
| - comments: | |
| - - One and only one of the value(x) fields must be populated. | |
| - examples: | |
| - - value: '' | |
| + value_integer: | |
| + name: value_integer | |
| exact_mappings: | |
| - GDC:Exposure.cigarettes_per_day | |
| - PDC:Exposure.cigarettes_per_day | |
| @@ -28305,19 +27582,19 @@ | |
| - PDC:Exposure.tobacco_smoking_quit_year | |
| - GDC:Exposure.years_smoked | |
| - PDC:Exposure.years_smoked | |
| - domain: TobaccoExposureObservation | |
| - range: ccdh_integer | |
| - multivalued: false | |
| - required: false | |
| - valueCodeableConcept: | |
| - name: valueCodeableConcept | |
| - description: The result of the observation, encoded as a CodeableConcept. | |
| + description: The result of the observation, encoded as an integer. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| comments: | |
| - One and only one of the value(x) fields must be populated. | |
| examples: | |
| - value: '' | |
| + domain: TobaccoExposureObservation | |
| + range: crdch_integer | |
| + multivalued: false | |
| + required: false | |
| + value_enum: | |
| + name: value_enum | |
| exact_mappings: | |
| - GDC:Exposure.environmental_tobacco_smoke_exposure | |
| - PDC:Exposure.environmental_tobacco_smoke_exposure | |
| @@ -28329,8 +27606,15 @@ | |
| - PDC:Exposure.tobacco_smoking_status | |
| - GDC:Exposure.type_of_tobacco_used | |
| - PDC:Exposure.type_of_tobacco_used | |
| + description: The result of the observation, encoded as a CodeableConcept. | |
| + notes: | |
| + - 'Cardinality: 0..1' | |
| + comments: | |
| + - One and only one of the value(x) fields must be populated. | |
| + examples: | |
| + - value: '' | |
| domain: TobaccoExposureObservation | |
| - range: enum_CCDH_TobaccoExposureObservation_valueCodeableConcept | |
| + range: enum_CRDCH_TobaccoExposureObservation_value_enum | |
| multivalued: false | |
| required: false | |
| Treatment: | |
| @@ -28352,6 +27636,9 @@ | |
| attributes: | |
| id: | |
| name: id | |
| + exact_mappings: | |
| + - GDC:Treatment.id | |
| + - PDC:Treatment.id | |
| description: The 'logical' identifier of the entity within the system of record. The | |
| simple value of this attribute stands for an identifier of this data object | |
| within the system, it can be used as a reference from other objects within | |
| @@ -28377,11 +27664,8 @@ | |
| to be an embeddable entity that can not stand on its own. ' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Treatment.id | |
| - - PDC:Treatment.id | |
| domain: Treatment | |
| - range: ccdh_string | |
| + range: crdch_string | |
| multivalued: false | |
| required: false | |
| identifier: | |
| @@ -28409,37 +27693,43 @@ | |
| range: Identifier | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| treatment_for_diagnosis: | |
| name: treatment_for_diagnosis | |
| - description: The diagnosis for which this treatment is intended. | |
| - notes: | |
| - - 'Cardinality: 0..m' | |
| - examples: | |
| - - value: '' | |
| close_mappings: | |
| - GDC:Treatment.diagnosis | |
| - PDC:Treatment.Diagnosis | |
| - GDC:Treatment.initial_disease_status | |
| - PDC:Treatment.initial_disease_status | |
| + description: The diagnosis for which this treatment is intended. | |
| + notes: | |
| + - 'Cardinality: 0..m' | |
| + examples: | |
| + - value: '' | |
| domain: Treatment | |
| range: Diagnosis | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| concurrent_treatment: | |
| name: concurrent_treatment | |
| + close_mappings: | |
| + - GDC:Treatment.chemo_concurrent_to_radiation | |
| description: Treatment instance(s) that are concurrent with this treatment. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Treatment.chemo_concurrent_to_radiation | |
| domain: Treatment | |
| range: Treatment | |
| multivalued: true | |
| required: false | |
| + inlined_as_list: true | |
| treatment_type: | |
| name: treatment_type | |
| + exact_mappings: | |
| + - GDC:Treatment.treatment_type | |
| + - PDC:Treatment.treatment_type | |
| description: The type of treatment administered, which may include medication/therapeutics | |
| or other procedures. | |
| notes: | |
| @@ -28451,11 +27741,8 @@ | |
| - value: Ablation, Cryo Ablation | |
| - value: Ethanol Injection Ablation | |
| - value: Microwave Ablation | |
| - exact_mappings: | |
| - - GDC:Treatment.treatment_type | |
| - - PDC:Treatment.treatment_type | |
| domain: Treatment | |
| - range: enum_CCDH_Treatment_treatment_type | |
| + range: enum_CRDCH_Treatment_treatment_type | |
| multivalued: false | |
| required: false | |
| subject: | |
| @@ -28472,34 +27759,36 @@ | |
| required: false | |
| date_started: | |
| name: date_started | |
| + close_mappings: | |
| + - GDC:Treatment.days_to_treatment_start | |
| + - PDC:Treatment.days_to_treatment_start | |
| description: The timepoint at which the treatment started. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Treatment.days_to_treatment_start | |
| - - PDC:Treatment.days_to_treatment_start | |
| domain: Treatment | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| date_ended: | |
| name: date_ended | |
| + close_mappings: | |
| + - GDC:Treatment.days_to_treatment_end | |
| + - PDC:Treatment.days_to_treatment_end | |
| description: The timepoint at which the treatment ended. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Treatment.days_to_treatment_end | |
| - - PDC:Treatment.days_to_treatment_end | |
| domain: Treatment | |
| range: TimePoint | |
| multivalued: false | |
| required: false | |
| treatment_end_reason: | |
| name: treatment_end_reason | |
| + exact_mappings: | |
| + - GDC:Treatment.reason_treatment_ended | |
| description: The reason the treatment ended. | |
| notes: | |
| - 'Cardinality: 0..m' | |
| @@ -28508,58 +27797,58 @@ | |
| - value: Death | |
| - value: Disease Progression | |
| - value: Other | |
| - exact_mappings: | |
| - - GDC:Treatment.reason_treatment_ended | |
| domain: Treatment | |
| - range: enum_CCDH_Treatment_treatment_end_reason | |
| + range: enum_CRDCH_Treatment_treatment_end_reason | |
| multivalued: true | |
| required: false | |
| regimen: | |
| name: regimen | |
| + exact_mappings: | |
| + - GDC:Treatment.regimen_or_line_of_therapy | |
| + - PDC:Treatment.regimen_or_line_of_therapy | |
| description: The regimen or line of therapy | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Treatment.regimen_or_line_of_therapy | |
| - - PDC:Treatment.regimen_or_line_of_therapy | |
| domain: Treatment | |
| - range: enum_CCDH_Treatment_regimen | |
| + range: enum_CRDCH_Treatment_regimen | |
| multivalued: false | |
| required: false | |
| therapeutic_agent: | |
| name: therapeutic_agent | |
| + close_mappings: | |
| + - GDC:Treatment.therapeutic_agents | |
| + - PDC:Treatment.therapeutic_agents | |
| + - GDC:Treatment.treatment_dose | |
| + - GDC:Treatment.treatment_dose_unit | |
| description: One or more therapeutic agents that are administered as part | |
| of this treatment. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Treatment.therapeutic_agents | |
| - - PDC:Treatment.therapeutic_agents | |
| - - GDC:Treatment.treatment_dose | |
| - - GDC:Treatment.treatment_dose_unit | |
| domain: Treatment | |
| range: Substance | |
| multivalued: false | |
| required: false | |
| number_of_cycles: | |
| name: number_of_cycles | |
| + exact_mappings: | |
| + - GDC:Treatment.number_of_cycles | |
| description: The number of treatment cycles the subject received. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - exact_mappings: | |
| - - GDC:Treatment.number_of_cycles | |
| domain: Treatment | |
| - range: ccdh_integer | |
| + range: crdch_integer | |
| multivalued: false | |
| required: false | |
| treatment_frequency: | |
| name: treatment_frequency | |
| + exact_mappings: | |
| + - GDC:Treatment.treatment_frequency | |
| description: The frequency of using the substance described by this instance. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -28568,28 +27857,29 @@ | |
| - value: Five Times Daily | |
| - value: Four Times Daily | |
| - value: Three Times Daily | |
| - exact_mappings: | |
| - - GDC:Treatment.treatment_frequency | |
| domain: Treatment | |
| - range: enum_CCDH_Treatment_treatment_frequency | |
| + range: enum_CRDCH_Treatment_treatment_frequency | |
| multivalued: false | |
| required: false | |
| treatment_anatomic_site: | |
| name: treatment_anatomic_site | |
| + close_mappings: | |
| + - GDC:Treatment.treatment_anatomic_site | |
| + - PDC:Treatment.treatment_anatomic_site | |
| description: The anatomical site that the treatment targets. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: '' | |
| - close_mappings: | |
| - - GDC:Treatment.treatment_anatomic_site | |
| - - PDC:Treatment.treatment_anatomic_site | |
| domain: Treatment | |
| range: BodySite | |
| multivalued: false | |
| required: false | |
| treatment_intent: | |
| name: treatment_intent | |
| + exact_mappings: | |
| + - GDC:Treatment.treatment_intent_type | |
| + - PDC:Treatment.treatment_intent_type | |
| description: The medical intent of the treatment. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -28597,31 +27887,31 @@ | |
| - value: Adjuvant | |
| - value: Cure | |
| - value: Palliative | |
| - exact_mappings: | |
| - - GDC:Treatment.treatment_intent_type | |
| - - PDC:Treatment.treatment_intent_type | |
| domain: Treatment | |
| - range: enum_CCDH_Treatment_treatment_intent | |
| + range: enum_CRDCH_Treatment_treatment_intent | |
| multivalued: false | |
| required: false | |
| treatment_effect: | |
| name: treatment_effect | |
| + exact_mappings: | |
| + - GDC:Treatment.treatment_effect | |
| + - PDC:Treatment.treatment_effect | |
| + - GDC:Treatment.treatment_effect_indicator | |
| description: The effect of a treatment on the diagnosis or tumor. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| examples: | |
| - value: Complete Necrosis (No Viable Tumor) | |
| - value: No Necrosis | |
| - exact_mappings: | |
| - - GDC:Treatment.treatment_effect | |
| - - PDC:Treatment.treatment_effect | |
| - - GDC:Treatment.treatment_effect_indicator | |
| domain: Treatment | |
| - range: enum_CCDH_Treatment_treatment_effect | |
| + range: enum_CRDCH_Treatment_treatment_effect | |
| multivalued: false | |
| required: false | |
| treatment_outcome: | |
| name: treatment_outcome | |
| + exact_mappings: | |
| + - GDC:Treatment.treatment_outcome | |
| + - PDC:Treatment.treatment_outcome | |
| description: The final outcome of the treatment. | |
| notes: | |
| - 'Cardinality: 0..1' | |
| @@ -28632,11 +27922,8 @@ | |
| - value: No Response | |
| - value: Partial Response | |
| - value: Persistent Disease | |
| - exact_mappings: | |
| - - GDC:Treatment.treatment_outcome | |
| - - PDC:Treatment.treatment_outcome | |
| domain: Treatment | |
| - range: enum_CCDH_Treatment_treatment_outcome | |
| + range: enum_CRDCH_Treatment_treatment_outcome | |
| multivalued: false | |
| required: false | |
| -generation_date: '2021-06-08T21:44:30.210349+00:00' | |
| +generation_date: '2021-09-16T18:42:18.402298+00:00' |
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