diff --git a/docs/schema/include_access_model.yaml b/docs/schema/include_access_model.yaml deleted file mode 100644 index 36f3650..0000000 --- a/docs/schema/include_access_model.yaml +++ /dev/null @@ -1,2750 +0,0 @@ -name: include-access-model -description: LinkML Schema for the internal INCLUDE DCC Access Model -title: INCLUDE DCC Access Model -see_also: -- https://includedcc.github.io/include-access-model -id: https://includedcc.org/include-access-model -imports: -- linkml:types -license: MIT -prefixes: - includedcc: - prefix_prefix: includedcc - prefix_reference: https://includedcc.org/include-access-model/ - linkml: - prefix_prefix: linkml - prefix_reference: https://w3id.org/linkml/ - schema: - prefix_prefix: schema - prefix_reference: http://schema.org/ - cdc_race_eth: - prefix_prefix: cdc_race_eth - prefix_reference: urn:oid:2.16.840.1.113883.6.238/ - hl7_null: - prefix_prefix: hl7_null - prefix_reference: http://terminology.hl7.org/CodeSystem/v3-NullFlavor/ - ig_dob_method: - prefix_prefix: ig_dob_method - prefix_reference: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/ - igcondtype: - prefix_prefix: igcondtype - prefix_reference: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/ - ig2dac: - prefix_prefix: ig2dac - prefix_reference: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code/ - ig2dat: - prefix_prefix: ig2dat - prefix_reference: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type/ - ig2_biospecimen_availability: - prefix_prefix: ig2_biospecimen_availability - prefix_reference: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/biospecimen-availability/ - snomed_ct: - prefix_prefix: snomed_ct - prefix_reference: http://snomed.info/id/ - MONDO: - prefix_prefix: MONDO - prefix_reference: http://purl.obolibrary.org/obo/MONDO_ - HP: - prefix_prefix: HP - prefix_reference: http://purl.obolibrary.org/obo/HP_ - mesh: - prefix_prefix: mesh - prefix_reference: http://id.nlm.nih.gov/mesh/ - NCIT: - prefix_prefix: NCIT - prefix_reference: http://purl.obolibrary.org/obo/NCIT_ - PATO: - prefix_prefix: PATO - prefix_reference: http://purl.obolibrary.org/obo/PATO_ -default_prefix: includedcc -default_range: string -types: - string: - name: string - definition_uri: https://w3id.org/linkml/String - description: A character string - notes: - - In RDF serializations, a slot with range of string is treated as a literal or - type xsd:string. If you are authoring schemas in LinkML YAML, the type is - referenced with the lower case "string". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Text - base: str - uri: xsd:string - integer: - name: integer - definition_uri: https://w3id.org/linkml/Integer - description: An integer - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "integer". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Integer - base: int - uri: xsd:integer - boolean: - name: boolean - definition_uri: https://w3id.org/linkml/Boolean - description: A binary (true or false) value - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "boolean". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Boolean - base: Bool - uri: xsd:boolean - repr: bool - float: - name: float - definition_uri: https://w3id.org/linkml/Float - description: A real number that conforms to the xsd:float specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "float". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Float - base: float - uri: xsd:float - double: - name: double - definition_uri: https://w3id.org/linkml/Double - description: A real number that conforms to the xsd:double specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "double". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - close_mappings: - - schema:Float - base: float - uri: xsd:double - decimal: - name: decimal - definition_uri: https://w3id.org/linkml/Decimal - description: A real number with arbitrary precision that conforms to the xsd:decimal - specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "decimal". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - broad_mappings: - - schema:Number - base: Decimal - uri: xsd:decimal - time: - name: time - definition_uri: https://w3id.org/linkml/Time - description: A time object represents a (local) time of day, independent of any - particular day - notes: - - URI is dateTime because OWL reasoners do not work with straight date or time - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "time". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Time - base: XSDTime - uri: xsd:time - repr: str - date: - name: date - definition_uri: https://w3id.org/linkml/Date - description: a date (year, month and day) in an idealized calendar - notes: - - URI is dateTime because OWL reasoners don't work with straight date or time - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "date". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Date - base: XSDDate - uri: xsd:date - repr: str - datetime: - name: datetime - definition_uri: https://w3id.org/linkml/Datetime - description: The combination of a date and time - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "datetime". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:DateTime - base: XSDDateTime - uri: xsd:dateTime - repr: str - date_or_datetime: - name: date_or_datetime - definition_uri: https://w3id.org/linkml/DateOrDatetime - description: Either a date or a datetime - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "date_or_datetime". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: linkml:DateOrDatetime - repr: str - uriorcurie: - name: uriorcurie - definition_uri: https://w3id.org/linkml/Uriorcurie - description: a URI or a CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uriorcurie". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: URIorCURIE - uri: xsd:anyURI - repr: str - curie: - name: curie - definition_uri: https://w3id.org/linkml/Curie - conforms_to: https://www.w3.org/TR/curie/ - description: a compact URI - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "curie". - comments: - - in RDF serializations this MUST be expanded to a URI - - in non-RDF serializations MAY be serialized as the compact representation - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: Curie - uri: xsd:string - repr: str - uri: - name: uri - definition_uri: https://w3id.org/linkml/Uri - conforms_to: https://www.ietf.org/rfc/rfc3987.txt - description: a complete URI - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uri". - comments: - - in RDF serializations a slot with range of uri is treated as a literal or type - xsd:anyURI unless it is an identifier or a reference to an identifier, in which - case it is translated directly to a node - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - close_mappings: - - schema:URL - base: URI - uri: xsd:anyURI - repr: str - ncname: - name: ncname - definition_uri: https://w3id.org/linkml/Ncname - description: Prefix part of CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "ncname". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: NCName - uri: xsd:string - repr: str - objectidentifier: - name: objectidentifier - definition_uri: https://w3id.org/linkml/Objectidentifier - description: A URI or CURIE that represents an object in the model. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "objectidentifier". - comments: - - Used for inheritance and type checking - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: ElementIdentifier - uri: shex:iri - repr: str - nodeidentifier: - name: nodeidentifier - definition_uri: https://w3id.org/linkml/Nodeidentifier - description: A URI, CURIE or BNODE that represents a node in a model. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "nodeidentifier". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: NodeIdentifier - uri: shex:nonLiteral - repr: str - jsonpointer: - name: jsonpointer - definition_uri: https://w3id.org/linkml/Jsonpointer - conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 - description: A string encoding a JSON Pointer. The value of the string MUST conform - to JSON Point syntax and SHOULD dereference to a valid object within the current - instance document when encoded in tree form. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "jsonpointer". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: xsd:string - repr: str - jsonpath: - name: jsonpath - definition_uri: https://w3id.org/linkml/Jsonpath - conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html - description: A string encoding a JSON Path. The value of the string MUST conform - to JSON Point syntax and SHOULD dereference to zero or more valid objects within - the current instance document when encoded in tree form. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "jsonpath". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: xsd:string - repr: str - sparqlpath: - name: sparqlpath - definition_uri: https://w3id.org/linkml/Sparqlpath - conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths - description: A string encoding a SPARQL Property Path. The value of the string - MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects - within the current instance document when encoded as RDF. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "sparqlpath". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: xsd:string - repr: str -enums: - EnumProgram: - name: EnumProgram - definition_uri: https://includedcc.org/include-access-model/EnumProgram - description: Funding programs relevant to inform operations. - title: Funding Programs - from_schema: https://includedcc.org/include-access-model - permissible_values: - include: - text: include - title: INCLUDE - kf: - text: kf - title: KF - other: - text: other - title: Other - EnumResearchDomain: - name: EnumResearchDomain - definition_uri: https://includedcc.org/include-access-model/EnumResearchDomain - description: Domains of Research used to find studies. - title: Research Domain - from_schema: https://includedcc.org/include-access-model - permissible_values: - behavior_and_behavior_mechanisms: - text: behavior_and_behavior_mechanisms - meaning: mesh:D001520 - title: Behavior and Behavior Mechanisms - congenital_heart_defects: - text: congenital_heart_defects - meaning: mesh:D006330 - title: Congenital Heart Defects - immune_system_diseases: - text: immune_system_diseases - meaning: mesh:D007154 - title: Immune System Diseases - hematologic_diseases: - text: hematologic_diseases - meaning: mesh:D006402 - title: Hematologic Diseases - neurodevelopment: - text: neurodevelopment - meaning: mesh:D065886 - title: Neurodevelopment - sleep_wake_disorders: - text: sleep_wake_disorders - meaning: mesh:D012893 - title: Sleep Wake Disorders - all_co_occurring_conditions: - text: all_co_occurring_conditions - meaning: mesh:D013568 - title: All Co-occurring Conditions - physical_fitness: - text: physical_fitness - meaning: mesh:D010809 - title: Physical Fitness - other: - text: other - title: Other - EnumParticipantLifespanStage: - name: EnumParticipantLifespanStage - definition_uri: https://includedcc.org/include-access-model/EnumParticipantLifespanStage - description: Stages of life during which participants may be recruited. - title: Participant Lifespan Stage - from_schema: https://includedcc.org/include-access-model - permissible_values: - fetal: - text: fetal - description: Before birth - title: Fetal - neonatal: - text: neonatal - description: 0-28 days old - title: Neonatal - pediatric: - text: pediatric - description: Birth-17 years old - title: Pediatric - adult: - text: adult - description: 18+ years old - title: Adult - EnumStudyDesign: - name: EnumStudyDesign - definition_uri: https://includedcc.org/include-access-model/EnumStudyDesign - description: Approaches for collecting data, investigating interventions, and/or - analyzing data. - title: Study Design - from_schema: https://includedcc.org/include-access-model - permissible_values: - case_control: - text: case_control - title: Case-Control - case_set: - text: case_set - title: Case Set - control_set: - text: control_set - title: Control Set - clinical_trial: - text: clinical_trial - title: Clinical Trial - cross_sectional: - text: cross_sectional - title: Cross-Sectional - family_twins_trios: - text: family_twins_trios - title: Family/Twins/Trios - interventional: - text: interventional - title: Interventional - longitudinal: - text: longitudinal - title: Longitudinal - trial_readiness_study: - text: trial_readiness_study - title: Trial Readiness Study - tumor_vs_matched_normal: - text: tumor_vs_matched_normal - title: Tumor vs Matched Normal - EnumClinicalDataSourceType: - name: EnumClinicalDataSourceType - definition_uri: https://includedcc.org/include-access-model/EnumClinicalDataSourceType - description: Approaches to ascertain clinical information about a participant. - title: Clinical Data Source Type - from_schema: https://includedcc.org/include-access-model - permissible_values: - medical_record: - text: medical_record - description: Data obtained directly from medical record - title: Medical Record - investigator_assessment: - text: investigator_assessment - description: Data obtained by examination, interview, etc. with investigator - title: Investigator Assessment - participant_or_caregiver_report: - text: participant_or_caregiver_report - description: Data obtained from survey, questionnaire, etc. filled out by - participant or caregiver - title: Participant or Caregiver Report - other: - text: other - description: Data obtained from other source, such as tissue bank - title: Other - unknown: - text: unknown - title: Unknown - EnumDataCategory: - name: EnumDataCategory - definition_uri: https://includedcc.org/include-access-model/EnumDataCategory - description: Categories of data which may be collected about participants. - title: Data Category - from_schema: https://includedcc.org/include-access-model - permissible_values: - unharmonized_demographic_clinical_data: - text: unharmonized_demographic_clinical_data - title: Unharmonized Demographic/Clinical Data - harmonized_demographic_clinical_data: - text: harmonized_demographic_clinical_data - title: Harmonized Demographic/Clinical Data - genomics: - text: genomics - title: Genomics - transcriptomics: - text: transcriptomics - title: Transcriptomics - epigenomics: - text: epigenomics - title: Epigenomics - proteomics: - text: proteomics - title: Proteomics - metabolomics: - text: metabolomics - title: Metabolomics - cognitive_behavioral: - text: cognitive_behavioral - title: Cognitive/Behavioral - immune_profiling: - text: immune_profiling - title: Immune Profiling - imaging: - text: imaging - title: Imaging - microbiome: - text: microbiome - title: Microbiome - fitness: - text: fitness - title: Fitness - physical_activity: - text: physical_activity - title: Physical Activity - other: - text: other - title: Other - sleep_study: - text: sleep_study - title: Sleep Study - EnumSubjectType: - name: EnumSubjectType - definition_uri: https://includedcc.org/include-access-model/EnumSubjectType - description: Types of Subject entities - from_schema: https://includedcc.org/include-access-model - permissible_values: - participant: - text: participant - description: Study participant with consent, assent, or waiver of consent. - non_participant: - text: non_participant - description: An individual associated with a study who was not explictly consented, - eg, the subject of a reported family history. - cell_line: - text: cell_line - description: Cell Line - animal_model: - text: animal_model - description: Animal model - group: - text: group - description: A group of individuals or entities. - other: - text: other - description: A different entity type- ideally this will be resolved! - EnumDownSyndromeStatus: - name: EnumDownSyndromeStatus - definition_uri: https://includedcc.org/include-access-model/EnumDownSyndromeStatus - description: Down syndrome / chromosome 21 status - from_schema: https://includedcc.org/include-access-model - permissible_values: - d21: - text: d21 - description: Disomy 21 (euploid) - meaning: PATO:0001393 - title: D21 - t21: - text: t21 - description: Trisomy 21 (Down syndrome) - meaning: MONDO:0008608 - title: T21 - EnumSex: - name: EnumSex - definition_uri: https://includedcc.org/include-access-model/EnumSex - description: Subject Sex - from_schema: https://includedcc.org/include-access-model - permissible_values: - female: - text: female - meaning: NCIT:C16576 - title: Female - male: - text: male - meaning: NCIT:C20197 - title: Male - other: - text: other - meaning: NCIT:C17649 - title: Other - unknown: - text: unknown - meaning: NCIT:C17998 - title: Unknown - EnumRace: - name: EnumRace - definition_uri: https://includedcc.org/include-access-model/EnumRace - description: Participant Race - from_schema: https://includedcc.org/include-access-model - permissible_values: - american_indian_or_alaska_native: - text: american_indian_or_alaska_native - meaning: NCIT:C41259 - title: American Indian or Alaska Native - asian: - text: asian - meaning: NCIT:C41260 - title: Asian - black_or_african_american: - text: black_or_african_american - meaning: NCIT:C16352 - title: Black or African American - more_than_one_race: - text: more_than_one_race - meaning: NCIT:C67109 - title: More than one race - native_hawaiian_or_other_pacific_islander: - text: native_hawaiian_or_other_pacific_islander - meaning: NCIT:C41219 - title: Native Hawaiian or Other Pacific Islander - other: - text: other - meaning: NCIT:C17649 - title: Other - white: - text: white - meaning: NCIT:C41261 - title: White - prefer_not_to_answer: - text: prefer_not_to_answer - meaning: NCIT:C132222 - title: Prefer not to answer - unknown: - text: unknown - meaning: NCIT:C17998 - title: Unknown - east_asian: - text: east_asian - description: UK only; do not use for US data - meaning: NCIT:C161419 - title: East Asian - latin_american: - text: latin_american - description: UK only; do not use for US data - meaning: NCIT:C126531 - title: Latin American - middle_eastern_or_north_african: - text: middle_eastern_or_north_african - description: UK only; do not use for US data - meaning: NCIT:C43866 - title: Middle Eastern or North African - south_asian: - text: south_asian - description: UK only; do not use for US data - meaning: NCIT:C41263 - title: South Asian - EnumEthnicity: - name: EnumEthnicity - definition_uri: https://includedcc.org/include-access-model/EnumEthnicity - description: Participant ethnicity, specific to Hispanic or Latino. - from_schema: https://includedcc.org/include-access-model - permissible_values: - hispanic_or_latino: - text: hispanic_or_latino - meaning: NCIT:C17459 - title: Hispanic or Latino - not_hispanic_or_latino: - text: not_hispanic_or_latino - meaning: NCIT:C41222 - title: Not Hispanic or Latino - prefer_not_to_answer: - text: prefer_not_to_answer - meaning: NCIT:C132222 - title: Prefer not to answer - unknown: - text: unknown - meaning: NCIT:C17998 - title: Unknown - EnumVitalStatus: - name: EnumVitalStatus - definition_uri: https://includedcc.org/include-access-model/EnumVitalStatus - description: Descriptions of a Subject's vital status - from_schema: https://includedcc.org/include-access-model - is_a: EnumNull - permissible_values: - dead: - text: dead - meaning: NCIT:C28554 - title: Dead - alive: - text: alive - meaning: NCIT:C37987 - title: Alive - EnumNull: - name: EnumNull - definition_uri: https://includedcc.org/include-access-model/EnumNull - description: Base enumeration providing null options. - from_schema: https://includedcc.org/include-access-model - permissible_values: - unknown: - text: unknown - meaning: NCIT:C17998 - title: Unknown - EnumAssertionProvenance: - name: EnumAssertionProvenance - definition_uri: https://includedcc.org/include-access-model/EnumAssertionProvenance - description: Possible data sources for assertions. - from_schema: https://includedcc.org/include-access-model - is_a: EnumNull - permissible_values: - medical_record: - text: medical_record - description: Data obtained from a medical record - title: Medical Record - investigator_assessment: - text: investigator_assessment - description: Data obtained by examination, interview, etc. with investigator - title: Investigator Assessment - participant_or_caregiver_report: - text: participant_or_caregiver_report - description: Data obtained from survey, questionnaire, etc. filled out by - participant or caregiver - title: Participant or Caregiver Report - other: - text: other - description: Data obtained from other source, such as tissue bank - title: Other - EnumAvailabilityStatus: - name: EnumAvailabilityStatus - definition_uri: https://includedcc.org/include-access-model/EnumAvailabilityStatus - description: Is the biospecimen available for use? - from_schema: https://includedcc.org/include-access-model - permissible_values: - available: - text: available - description: Biospecimen is Available - meaning: ig2_biospecimen_availability:available - title: Available - unavailable: - text: unavailable - description: Biospecimen is Unavailable - meaning: ig2_biospecimen_availability:unavailable - title: Unavailable - EnumSampleCollectionMethod: - name: EnumSampleCollectionMethod - definition_uri: https://includedcc.org/include-access-model/EnumSampleCollectionMethod - description: The approach used to collect the biospecimen. [LOINC](https://loinc.org) - is recommended. - from_schema: https://includedcc.org/include-access-model - EnumSite: - name: EnumSite - definition_uri: https://includedcc.org/include-access-model/EnumSite - description: The location of the specimen collection. [SNOMED Body Site](https://hl7.org/fhir/R4B/valueset-body-site.html) - is recommended. - from_schema: https://includedcc.org/include-access-model - EnumSpatialQualifiers: - name: EnumSpatialQualifiers - definition_uri: https://includedcc.org/include-access-model/EnumSpatialQualifiers - description: Any spatial/location qualifiers. - from_schema: https://includedcc.org/include-access-model - enum_uri: http://hl7.org/fhir/us/mcode/ValueSet/mcode-body-location-qualifier-vs - reachable_from: - source_ontology: bioregistry:snomedct - source_nodes: - - snomedct:106233006 - - snomedct:272424004 - - snomedct:51440002 - - snomedct:399488007 - - snomedct:24028007 - - snomedct:7771000 - relationship_types: - - rdfs:subClassOf - is_direct: false - EnumLaterality: - name: EnumLaterality - definition_uri: https://includedcc.org/include-access-model/EnumLaterality - description: Laterality information for the site - from_schema: https://includedcc.org/include-access-model - EnumEDAMFormats: - name: EnumEDAMFormats - definition_uri: https://includedcc.org/include-access-model/EnumEDAMFormats - description: Data formats from the EDAM ontology. - from_schema: https://includedcc.org/include-access-model - reachable_from: - source_ontology: bioregistry:edam - source_nodes: - - edam:format_1915 - relationship_types: - - rdfs:subClassOf - is_direct: false - include_self: false - EnumEDAMDataTypes: - name: EnumEDAMDataTypes - definition_uri: https://includedcc.org/include-access-model/EnumEDAMDataTypes - description: Data types from the EDAM ontology. - from_schema: https://includedcc.org/include-access-model - reachable_from: - source_ontology: bioregistry:edam - source_nodes: - - edam:data_0006 - relationship_types: - - rdfs:subClassOf - is_direct: false - include_self: false - EnumFileHashType: - name: EnumFileHashType - definition_uri: https://includedcc.org/include-access-model/EnumFileHashType - description: Types of file hashes supported. - from_schema: https://includedcc.org/include-access-model - permissible_values: - md5: - text: md5 - title: MD5 - etag: - text: etag - title: ETag - sha1: - text: sha1 - title: SHA-1 -slots: - study_id: - name: study_id - definition_uri: https://includedcc.org/include-access-model/study_id - description: INCLUDE Global ID for the study - title: Study ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:study_id - owner: StudyMetadata - domain_of: - - Study - - StudyMetadata - range: Study - multivalued: false - do_id: - name: do_id - definition_uri: https://includedcc.org/include-access-model/do_id - description: Digital Object Identifier (DOI) for this Record. - title: DOI - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:do_id - owner: Dataset - domain_of: - - Study - - DOI - - Dataset - range: DOI - multivalued: false - subject_id: - name: subject_id - definition_uri: https://includedcc.org/include-access-model/subject_id - description: INCLUDE Global ID for the Subject - title: Study ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:subject_id - owner: File - domain_of: - - Subject - - Demographics - - SubjectAssertion - - Encounter - - File - range: Subject - multivalued: false - assertion_id: - name: assertion_id - definition_uri: https://includedcc.org/include-access-model/assertion_id - description: INCLUDE Global ID for the Assertion - title: Assertion ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:assertion_id - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: SubjectAssertion - multivalued: false - external_id: - name: external_id - definition_uri: https://includedcc.org/include-access-model/external_id - description: Other identifiers for this entity, eg, from the submitting study - or in systems like dbGaP - title: External Identifiers - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:external_id - owner: Record - domain_of: - - Record - range: uriorcurie - required: false - multivalued: true - parent_study: - name: parent_study - definition_uri: https://includedcc.org/include-access-model/parent_study - description: The parent study for this study, if it is a nested study. - title: Parent Study - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:parent_study - owner: Study - domain_of: - - Study - range: Study - required: false - multivalued: false - funding_source: - name: funding_source - definition_uri: https://includedcc.org/include-access-model/funding_source - description: The funding source(s) of the study. - title: Funding Source - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:funding_source - owner: Study - domain_of: - - Study - range: string - required: false - multivalued: true - principal_investigator: - name: principal_investigator - definition_uri: https://includedcc.org/include-access-model/principal_investigator - description: The Principal Investigator(s) responsible for the study. - title: Principal Investigator - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:principal_investigator - owner: Study - domain_of: - - Study - range: Investigator - required: true - multivalued: true - inlined: true - inlined_as_list: true - study_title: - name: study_title - definition_uri: https://includedcc.org/include-access-model/study_title - description: Full Study Title - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:study_title - owner: Study - domain_of: - - Study - range: string - required: true - multivalued: false - study_code: - name: study_code - definition_uri: https://includedcc.org/include-access-model/study_code - description: Unique identifier for the study (generally a short acronym) - title: Study Code - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:study_code - owner: Study - domain_of: - - Study - range: string - required: true - study_short_name: - name: study_short_name - definition_uri: https://includedcc.org/include-access-model/study_short_name - description: Short name for the study - title: Study Code - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:study_short_name - owner: Study - domain_of: - - Study - range: string - required: false - investigator_title: - name: investigator_title - definition_uri: https://includedcc.org/include-access-model/investigator_title - description: The title of the Investigator, eg, "Assistant Professor" - title: Investigator Title - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:investigator_title - owner: Investigator - domain_of: - - Investigator - range: string - required: false - name: - name: name - definition_uri: https://includedcc.org/include-access-model/name - description: Name of the entity. - title: Name - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:name - owner: Dataset - domain_of: - - VirtualBiorepository - - Investigator - - EncounterDefinition - - ActivityDefinition - - Dataset - range: string - required: false - email: - name: email - definition_uri: https://includedcc.org/include-access-model/email - description: An email address to reach the entity. - title: Email Address - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:email - owner: Investigator - domain_of: - - Investigator - range: string - required: false - institution: - name: institution - definition_uri: https://includedcc.org/include-access-model/institution - description: Name of the institution this record is associated with. - title: Institution - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:institution - owner: Investigator - domain_of: - - VirtualBiorepository - - Investigator - range: string - required: false - program: - name: program - definition_uri: https://includedcc.org/include-access-model/program - description: Funding source(s) for the study - title: Program - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:program - owner: Study - domain_of: - - Study - range: EnumProgram - required: true - multivalued: true - study_description: - name: study_description - definition_uri: https://includedcc.org/include-access-model/study_description - description: Brief description of the study (2-4 sentences) - title: Study Description - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:study_description - owner: Study - domain_of: - - Study - range: string - required: true - website: - name: website - definition_uri: https://includedcc.org/include-access-model/website - description: Website for the Record. - title: Website - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:website - owner: Publication - domain_of: - - Study - - VirtualBiorepository - - Publication - range: uri - contact: - name: contact - definition_uri: https://includedcc.org/include-access-model/contact - description: The individual to contact with questions about this record. - title: Contact Person - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:contact - owner: VirtualBiorepository - domain_of: - - Study - - VirtualBiorepository - range: Investigator - required: true - multivalued: true - inlined: true - inlined_as_list: true - vbr: - name: vbr - definition_uri: https://includedcc.org/include-access-model/vbr - description: Information about the study's Virtual Biorepository, if participating - title: Virtual Biorepository - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:vbr - owner: StudyMetadata - domain_of: - - StudyMetadata - range: VirtualBiorepository - required: false - inlined: true - inlined_as_list: true - vbr_readme: - name: vbr_readme - definition_uri: https://includedcc.org/include-access-model/vbr_readme - description: Instructions for contacting or requesting samples from Virtual Biorepository, - if participating - title: VBR Readme - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:vbr_readme - owner: VirtualBiorepository - domain_of: - - VirtualBiorepository - range: string - research_domain: - name: research_domain - definition_uri: https://includedcc.org/include-access-model/research_domain - description: Main research domain(s) of the study, other than Down syndrome - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:research_domain - owner: StudyMetadata - domain_of: - - StudyMetadata - range: EnumResearchDomain - required: true - multivalued: true - participant_lifespan_stage: - name: participant_lifespan_stage - definition_uri: https://includedcc.org/include-access-model/participant_lifespan_stage - description: Focus age group(s) of the study population - title: Participant Lifespan Stage - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:participant_lifespan_stage - owner: StudyMetadata - domain_of: - - StudyMetadata - range: EnumParticipantLifespanStage - required: true - multivalued: true - selection_criteria: - name: selection_criteria - definition_uri: https://includedcc.org/include-access-model/selection_criteria - description: Brief description of inclusion and/or exclusion criteria for the - study - title: Selection Criteria - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:selection_criteria - owner: StudyMetadata - domain_of: - - StudyMetadata - range: string - study_design: - name: study_design - definition_uri: https://includedcc.org/include-access-model/study_design - description: Overall design of study, including whether it is longitudinal and - whether family members/unrelated controls are also enrolled - title: Study Design - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:study_design - owner: StudyMetadata - domain_of: - - StudyMetadata - range: EnumStudyDesign - required: true - multivalued: true - data_category: - name: data_category - definition_uri: https://includedcc.org/include-access-model/data_category - description: General category of data in this Record (e.g. Clinical, Genomics, - etc) - title: Data Category - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:data_category - owner: File - domain_of: - - StudyMetadata - - File - range: EnumDataCategory - clinical_data_source_type: - name: clinical_data_source_type - definition_uri: https://includedcc.org/include-access-model/clinical_data_source_type - description: Source(s) of data collected from study participants - title: Clinical Data Source Type - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:clinical_data_source_type - owner: StudyMetadata - domain_of: - - StudyMetadata - range: EnumClinicalDataSourceType - required: true - multivalued: true - publication: - name: publication - definition_uri: https://includedcc.org/include-access-model/publication - description: Publications associated with this Record. - title: Publication - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:publication - owner: Dataset - domain_of: - - Study - - Dataset - range: Publication - multivalued: true - inlined: true - inlined_as_list: true - expected_number_of_participants: - name: expected_number_of_participants - definition_uri: https://includedcc.org/include-access-model/expected_number_of_participants - description: Total expected number of participants to be recruited. - title: Expected Number of Participants - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:expected_number_of_participants - owner: StudyMetadata - domain_of: - - StudyMetadata - range: integer - required: true - actual_number_of_participants: - name: actual_number_of_participants - definition_uri: https://includedcc.org/include-access-model/actual_number_of_participants - description: Total participants included at this time. - title: Actual Number of Participants - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:actual_number_of_participants - owner: StudyMetadata - domain_of: - - StudyMetadata - range: integer - required: true - acknowledgments: - name: acknowledgments - definition_uri: https://includedcc.org/include-access-model/acknowledgments - description: Funding statement and acknowledgments for this study - title: Acknowledgments - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:acknowledgments - owner: Study - domain_of: - - Study - range: string - citation_statement: - name: citation_statement - definition_uri: https://includedcc.org/include-access-model/citation_statement - description: Statement that secondary data users should use to acknowledge use - of this study or dataset. E.g., "The results analyzed and - here are based in whole or in part upon data generated by the INCLUDE (INvestigation - of Co-occurring conditions across the Lifespan to Understand Down syndromE) - Project , and were accessed - from the INCLUDE Data Hub and ." - title: Citation Statement - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:citation_statement - owner: Study - domain_of: - - Study - range: string - bibliographic_reference: - name: bibliographic_reference - definition_uri: https://includedcc.org/include-access-model/bibliographic_reference - description: Text use to reference this Record. - title: Bibiliographic Reference - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:bibliographic_reference - owner: Publication - domain_of: - - DOI - - Publication - range: string - organism_type: - name: organism_type - definition_uri: https://includedcc.org/include-access-model/organism_type - description: Organism Type - title: Organism Type - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:organism_type - owner: Subject - domain_of: - - Subject - range: uriorcurie - required: false - subject_type: - name: subject_type - definition_uri: https://includedcc.org/include-access-model/subject_type - description: Type of entity this record represents - title: Subject Type - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:subject_type - owner: Subject - domain_of: - - Subject - range: EnumSubjectType - required: true - sex: - name: sex - definition_uri: https://includedcc.org/include-access-model/sex - description: Sex of Participant - title: Sex - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:sex - owner: Demographics - domain_of: - - Demographics - range: EnumSex - required: true - race: - name: race - definition_uri: https://includedcc.org/include-access-model/race - description: Race of Participant - title: Race - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:race - owner: Demographics - domain_of: - - Demographics - range: EnumRace - required: true - multivalued: true - ethnicity: - name: ethnicity - definition_uri: https://includedcc.org/include-access-model/ethnicity - description: Ethnicity of Participant - title: Ethnicity - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:ethnicity - owner: Demographics - domain_of: - - Demographics - range: EnumEthnicity - required: true - down_syndrome_status: - name: down_syndrome_status - definition_uri: https://includedcc.org/include-access-model/down_syndrome_status - description: Down Syndrome status of participant - title: Down Syndrome Status - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:down_syndrome_status - owner: Demographics - domain_of: - - Demographics - range: EnumDownSyndromeStatus - required: true - age_at_first_engagement: - name: age_at_first_engagement - definition_uri: https://includedcc.org/include-access-model/age_at_first_engagement - description: Age in days of Participant at first recorded study event (enrollment, - visit, observation, sample collection, survey completion, etc.). Age at enrollment - is preferred, if available. - title: Age at First Participant Engagement - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:age_at_first_engagement - owner: Demographics - domain_of: - - Demographics - range: integer - minimum_value: -365 - maximum_value: 32507 - unit: - ucum_code: d - vital_status: - name: vital_status - definition_uri: https://includedcc.org/include-access-model/vital_status - description: Whether participant is alive or dead - title: Vital Status - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:vital_status - owner: Demographics - domain_of: - - Demographics - range: EnumVitalStatus - age_at_last_vital_status: - name: age_at_last_vital_status - definition_uri: https://includedcc.org/include-access-model/age_at_last_vital_status - description: Age in days when participant's vital status was last recorded - title: Age at Last Vital Status - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:age_at_last_vital_status - owner: Demographics - domain_of: - - Demographics - range: integer - minimum_value: -365 - maximum_value: 32507 - unit: - ucum_code: d - assertion_provenance: - name: assertion_provenance - definition_uri: https://includedcc.org/include-access-model/assertion_provenance - description: The original source of this assertion - title: Assertion Provenance - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:assertion_provenance - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: EnumAssertionProvenance - age_at_assertion: - name: age_at_assertion - definition_uri: https://includedcc.org/include-access-model/age_at_assertion - description: The age in days of the Subject when the assertion was made. - title: Age at assertion - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:age_at_assertion - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: integer - unit: - ucum_code: d - age_at_event: - name: age_at_event - definition_uri: https://includedcc.org/include-access-model/age_at_event - description: The age in days of the Subject at the time point which the assertion - describes, eg, age of onset or when a measurement was performed. - title: Age at event - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:age_at_event - owner: Encounter - domain_of: - - SubjectAssertion - - Encounter - range: integer - unit: - ucum_code: d - age_at_resolution: - name: age_at_resolution - definition_uri: https://includedcc.org/include-access-model/age_at_resolution - description: The age in days of the Subject when the asserted state was resolved. - title: Age at resolution - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:age_at_resolution - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: integer - unit: - ucum_code: d - concept: - name: concept - definition_uri: https://includedcc.org/include-access-model/concept - description: The structured term defining the meaning of the assertion. - title: Concept - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:concept - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: Concept - multivalued: true - concept_curie: - name: concept_curie - definition_uri: https://includedcc.org/include-access-model/concept_curie - description: The standardized curie for the term. - title: Concept Curie - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:concept_curie - owner: Concept - domain_of: - - Concept - range: uriorcurie - display: - name: display - definition_uri: https://includedcc.org/include-access-model/display - description: The friendly display string of the coded term. - title: Display String - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:display - owner: Concept - domain_of: - - Concept - range: string - concept_source: - name: concept_source - definition_uri: https://includedcc.org/include-access-model/concept_source - description: The source text yielding the standardized concept. - title: Concept Source Text - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:concept_source - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: string - value_concept: - name: value_concept - definition_uri: https://includedcc.org/include-access-model/value_concept - description: The structured term defining the value of the assertion. - title: Value concept - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:value_concept - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: Concept - multivalued: true - value_number: - name: value_number - definition_uri: https://includedcc.org/include-access-model/value_number - description: The numeric value of the assertion. - title: Value Number - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:value_number - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: float - value_source: - name: value_source - definition_uri: https://includedcc.org/include-access-model/value_source - description: The source text yielding the value. - title: Value Source Text - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:value_source - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: string - value_unit: - name: value_unit - definition_uri: https://includedcc.org/include-access-model/value_unit - description: The structured term defining the units of the value. - title: Value Units - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:value_unit - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: Concept - value_unit_source: - name: value_unit_source - definition_uri: https://includedcc.org/include-access-model/value_unit_source - description: The source text yielding the value's units. - title: Value Units Source Text - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:value_unit_source - owner: SubjectAssertion - domain_of: - - SubjectAssertion - range: string - sample_id: - name: sample_id - definition_uri: https://includedcc.org/include-access-model/sample_id - description: The unique identifier for this Sample. - title: Sample ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:sample_id - owner: File - domain_of: - - Sample - - Aliquot - - File - range: Sample - parent_sample_id: - name: parent_sample_id - definition_uri: https://includedcc.org/include-access-model/parent_sample_id - description: Sample from which this sample is derived - title: Parent Sample ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:parent_sample_id - owner: Sample - domain_of: - - Sample - range: Sample - inlined: false - biospecimen_collection_id: - name: biospecimen_collection_id - definition_uri: https://includedcc.org/include-access-model/biospecimen_collection_id - description: Unique identifier for this Biospecimen Collection. - title: Biospecimen Collection ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:biospecimen_collection_id - owner: BiospecimenCollection - domain_of: - - Sample - - BiospecimenCollection - range: BiospecimenCollection - aliquot_id: - name: aliquot_id - definition_uri: https://includedcc.org/include-access-model/aliquot_id - description: Unique identifier for an Aliquot. - title: Aliquot ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:aliquot_id - owner: Aliquot - domain_of: - - Aliquot - range: Aliquot - sample_type: - name: sample_type - definition_uri: https://includedcc.org/include-access-model/sample_type - description: Type of material of which this Sample is comprised - title: Sample Type - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:sample_type - owner: Sample - domain_of: - - Sample - range: uriorcurie - required: true - processing: - name: processing - definition_uri: https://includedcc.org/include-access-model/processing - description: Processing that was applied to the Parent Sample or from the Biospecimen - Collection that yielded this distinct sample - title: Sample Processing - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:processing - owner: Sample - domain_of: - - Sample - range: uriorcurie - multivalued: true - availablity_status: - name: availablity_status - definition_uri: https://includedcc.org/include-access-model/availablity_status - description: Can this Sample be requested for further analysis? - title: Sample Availability - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:availablity_status - owner: Aliquot - domain_of: - - Sample - - Aliquot - range: EnumAvailabilityStatus - storage_method: - name: storage_method - definition_uri: https://includedcc.org/include-access-model/storage_method - description: Sample storage method, eg, Frozen or with additives - title: Sample Storage Method - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:storage_method - owner: Sample - domain_of: - - Sample - range: uriorcurie - multivalued: true - quantity_number: - name: quantity_number - definition_uri: https://includedcc.org/include-access-model/quantity_number - description: The total quantity of the specimen - title: Quantity - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:quantity_number - owner: Aliquot - domain_of: - - Sample - - Aliquot - range: float - quantity_unit: - name: quantity_unit - definition_uri: https://includedcc.org/include-access-model/quantity_unit - description: The structured term defining the units of the quantity. - title: Quantity Units - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:quantity_unit - owner: Aliquot - domain_of: - - Sample - - Aliquot - range: Concept - concentration_number: - name: concentration_number - definition_uri: https://includedcc.org/include-access-model/concentration_number - description: What is the concentration of the analyte in the Aliquot? - title: Concentration - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:concentration_number - owner: Aliquot - domain_of: - - Aliquot - range: float - concentration_unit: - name: concentration_unit - definition_uri: https://includedcc.org/include-access-model/concentration_unit - description: Units associated with the concentration of the analyte in the Aliquot. - title: Concentration Units - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:concentration_unit - owner: Aliquot - domain_of: - - Aliquot - range: Concept - age_at_collection: - name: age_at_collection - definition_uri: https://includedcc.org/include-access-model/age_at_collection - description: The age at which this biospecimen was collected in decimal years. - title: Age at Biospecimen Collection - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:age_at_collection - owner: BiospecimenCollection - domain_of: - - BiospecimenCollection - range: float - unit: - ucum_code: a - method: - name: method - definition_uri: https://includedcc.org/include-access-model/method - description: The approach used to collect the biospecimen. - title: Biospecimen Collection Method - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:method - owner: BiospecimenCollection - domain_of: - - BiospecimenCollection - range: EnumSampleCollectionMethod - site: - name: site - definition_uri: https://includedcc.org/include-access-model/site - description: The location of the specimen collection. - title: Biospecimen Collection Site - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:site - owner: BiospecimenCollection - domain_of: - - BiospecimenCollection - range: EnumSite - spatial_qualifier: - name: spatial_qualifier - definition_uri: https://includedcc.org/include-access-model/spatial_qualifier - description: Qualifier that further refine the specific location of biospecimen - collection - title: Spatial Qualifier - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:spatial_qualifier - owner: BiospecimenCollection - domain_of: - - BiospecimenCollection - range: EnumSpatialQualifiers - laterality: - name: laterality - definition_uri: https://includedcc.org/include-access-model/laterality - description: Laterality that further refine the specific location of biospecimen - collection - title: Location Laterality - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:laterality - owner: BiospecimenCollection - domain_of: - - BiospecimenCollection - range: EnumLaterality - encounter_id: - name: encounter_id - definition_uri: https://includedcc.org/include-access-model/encounter_id - description: Unique identifier for this Encounter. - title: Encounter ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:encounter_id - owner: Encounter - domain_of: - - SubjectAssertion - - BiospecimenCollection - - Encounter - range: Encounter - description: - name: description - definition_uri: https://includedcc.org/include-access-model/description - description: Description for this entity. - title: Description - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:description - owner: Dataset - domain_of: - - EncounterDefinition - - ActivityDefinition - - Dataset - range: string - encounter_definition_id: - name: encounter_definition_id - definition_uri: https://includedcc.org/include-access-model/encounter_definition_id - description: Unique identifier for this Encounter Definition. - title: Encounter Definition ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:encounter_definition_id - owner: EncounterDefinition - domain_of: - - Encounter - - EncounterDefinition - range: EncounterDefinition - activity_definition_id: - name: activity_definition_id - definition_uri: https://includedcc.org/include-access-model/activity_definition_id - description: Unique identifier for this Activity Definition. - title: Activity Definition ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:activity_definition_id - owner: ActivityDefinition - domain_of: - - EncounterDefinition - - ActivityDefinition - range: ActivityDefinition - file_id: - name: file_id - definition_uri: https://includedcc.org/include-access-model/file_id - description: Unique identifier for this File. - title: File ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:file_id - owner: Dataset - domain_of: - - File - - Dataset - range: File - filename: - name: filename - definition_uri: https://includedcc.org/include-access-model/filename - description: The name of the file. - title: Filename - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:filename - owner: File - domain_of: - - File - range: string - format: - name: format - definition_uri: https://includedcc.org/include-access-model/format - description: The format of the file. - title: File Format - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:format - owner: File - domain_of: - - File - range: EnumEDAMFormats - data_type: - name: data_type - definition_uri: https://includedcc.org/include-access-model/data_type - description: The type of data within this file. - title: Data Type - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:data_type - owner: File - domain_of: - - File - range: EnumEDAMDataTypes - size: - name: size - definition_uri: https://includedcc.org/include-access-model/size - description: Size of the file, in Bytes. - title: File Size - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:size - owner: File - domain_of: - - File - range: integer - unit: - ucum_code: By - staging_url: - name: staging_url - definition_uri: https://includedcc.org/include-access-model/staging_url - description: URL for internal access to the data. May be temporary. - title: Staging Location - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:staging_url - owner: File - domain_of: - - File - range: uriorcurie - release_url: - name: release_url - definition_uri: https://includedcc.org/include-access-model/release_url - description: URL for controlled or open access to the data. - title: Release Location - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:release_url - owner: File - domain_of: - - File - range: uriorcurie - drs_uri: - name: drs_uri - definition_uri: https://includedcc.org/include-access-model/drs_uri - description: DRS location to access the data. - title: DRS URI - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:drs_uri - owner: File - domain_of: - - File - range: uriorcurie - hash: - name: hash - definition_uri: https://includedcc.org/include-access-model/hash - description: File hash information - title: File Hash - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:hash - owner: File - domain_of: - - File - range: FileHash - inlined: true - inlined_as_list: true - hash_type: - name: hash_type - definition_uri: https://includedcc.org/include-access-model/hash_type - description: The type of file hash, eg, md5 - title: File Hash Type - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:hash_type - owner: FileHash - domain_of: - - FileHash - range: EnumFileHashType - hash_value: - name: hash_value - definition_uri: https://includedcc.org/include-access-model/hash_value - description: The value of the file hash - title: File Hash Value - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:hash_value - owner: FileHash - domain_of: - - FileHash - range: string - dataset_id: - name: dataset_id - definition_uri: https://includedcc.org/include-access-model/dataset_id - description: Unique identifier for a Dataset. - title: Dataset ID - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:dataset_id - owner: Dataset - domain_of: - - Dataset - range: Dataset - data_collection_start: - name: data_collection_start - definition_uri: https://includedcc.org/include-access-model/data_collection_start - description: The date that data collection started. May include only a year. - title: Data Collection Start - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:data_collection_start - owner: Dataset - domain_of: - - Dataset - range: string - data_collection_end: - name: data_collection_end - definition_uri: https://includedcc.org/include-access-model/data_collection_end - description: The date that data collection started. May include only a year. - title: Data Collection End - from_schema: https://includedcc.org/include-access-model - slot_uri: includedcc:data_collection_end - owner: Dataset - domain_of: - - Dataset - range: string - Study_study_id: - name: Study_study_id - definition_uri: https://includedcc.org/include-access-model/study_id - description: INCLUDE Global ID for the study - title: Study ID - from_schema: https://includedcc.org/include-access-model - is_a: study_id - domain: Study - slot_uri: includedcc:study_id - identifier: true - alias: study_id - owner: Study - domain_of: - - Study - is_usage_slot: true - usage_slot_name: study_id - range: string - required: true - multivalued: false - StudyMetadata_study_id: - name: StudyMetadata_study_id - definition_uri: https://includedcc.org/include-access-model/study_id - description: INCLUDE Global ID for the study - title: Study ID - from_schema: https://includedcc.org/include-access-model - is_a: study_id - domain: StudyMetadata - slot_uri: includedcc:study_id - identifier: true - alias: study_id - owner: StudyMetadata - domain_of: - - StudyMetadata - is_usage_slot: true - usage_slot_name: study_id - range: Study - required: true - multivalued: false - StudyMetadata_data_category: - name: StudyMetadata_data_category - definition_uri: https://includedcc.org/include-access-model/data_category - description: General category of data in this Record (e.g. Clinical, Genomics, - etc) - title: Data Category - from_schema: https://includedcc.org/include-access-model - is_a: data_category - domain: StudyMetadata - slot_uri: includedcc:data_category - alias: data_category - owner: StudyMetadata - domain_of: - - StudyMetadata - is_usage_slot: true - usage_slot_name: data_category - range: EnumDataCategory - required: true - multivalued: true - DOI_do_id: - name: DOI_do_id - definition_uri: https://includedcc.org/include-access-model/do_id - description: Digital Object Identifier (DOI) for this Record. - title: DOI - from_schema: https://includedcc.org/include-access-model - is_a: do_id - domain: DOI - slot_uri: includedcc:do_id - identifier: true - alias: do_id - owner: DOI - domain_of: - - DOI - is_usage_slot: true - usage_slot_name: do_id - range: string - required: true - multivalued: false - Subject_subject_id: - name: Subject_subject_id - definition_uri: https://includedcc.org/include-access-model/subject_id - description: INCLUDE Global ID for the Subject - title: Study ID - from_schema: https://includedcc.org/include-access-model - is_a: subject_id - domain: Subject - slot_uri: includedcc:subject_id - identifier: true - alias: subject_id - owner: Subject - domain_of: - - Subject - is_usage_slot: true - usage_slot_name: subject_id - range: string - required: true - multivalued: false - Demographics_subject_id: - name: Demographics_subject_id - definition_uri: https://includedcc.org/include-access-model/subject_id - description: INCLUDE Global ID for the Subject - title: Study ID - from_schema: https://includedcc.org/include-access-model - is_a: subject_id - domain: Demographics - slot_uri: includedcc:subject_id - identifier: true - alias: subject_id - owner: Demographics - domain_of: - - Demographics - is_usage_slot: true - usage_slot_name: subject_id - range: Subject - required: true - multivalued: false - SubjectAssertion_assertion_id: - name: SubjectAssertion_assertion_id - definition_uri: https://includedcc.org/include-access-model/assertion_id - description: INCLUDE Global ID for the Assertion - title: Assertion ID - from_schema: https://includedcc.org/include-access-model - is_a: assertion_id - domain: SubjectAssertion - slot_uri: includedcc:assertion_id - identifier: true - alias: assertion_id - owner: SubjectAssertion - domain_of: - - SubjectAssertion - is_usage_slot: true - usage_slot_name: assertion_id - range: string - required: true - multivalued: false - Concept_concept_curie: - name: Concept_concept_curie - definition_uri: https://includedcc.org/include-access-model/concept_curie - description: The standardized curie for the term. - title: Concept Curie - from_schema: https://includedcc.org/include-access-model - is_a: concept_curie - domain: Concept - slot_uri: includedcc:concept_curie - identifier: true - alias: concept_curie - owner: Concept - domain_of: - - Concept - is_usage_slot: true - usage_slot_name: concept_curie - range: uriorcurie - required: true - Sample_sample_id: - name: Sample_sample_id - definition_uri: https://includedcc.org/include-access-model/sample_id - description: The unique identifier for this Sample. - title: Sample ID - from_schema: https://includedcc.org/include-access-model - is_a: sample_id - domain: Sample - slot_uri: includedcc:sample_id - identifier: true - alias: sample_id - owner: Sample - domain_of: - - Sample - is_usage_slot: true - usage_slot_name: sample_id - range: string - required: true - Sample_biospecimen_collection_id: - name: Sample_biospecimen_collection_id - definition_uri: https://includedcc.org/include-access-model/biospecimen_collection_id - description: Biospecimen Collection during which this sample was generated. - title: Biospecimen Collection ID - from_schema: https://includedcc.org/include-access-model - is_a: biospecimen_collection_id - domain: Sample - slot_uri: includedcc:biospecimen_collection_id - alias: biospecimen_collection_id - owner: Sample - domain_of: - - Sample - is_usage_slot: true - usage_slot_name: biospecimen_collection_id - range: BiospecimenCollection - BiospecimenCollection_biospecimen_collection_id: - name: BiospecimenCollection_biospecimen_collection_id - definition_uri: https://includedcc.org/include-access-model/biospecimen_collection_id - description: Unique identifier for this Biospecimen Collection. - title: Biospecimen Collection ID - from_schema: https://includedcc.org/include-access-model - is_a: biospecimen_collection_id - domain: BiospecimenCollection - slot_uri: includedcc:biospecimen_collection_id - identifier: true - alias: biospecimen_collection_id - owner: BiospecimenCollection - domain_of: - - BiospecimenCollection - is_usage_slot: true - usage_slot_name: biospecimen_collection_id - range: string - required: true - Aliquot_aliquot_id: - name: Aliquot_aliquot_id - definition_uri: https://includedcc.org/include-access-model/aliquot_id - description: Unique identifier for an Aliquot. - title: Aliquot ID - from_schema: https://includedcc.org/include-access-model - is_a: aliquot_id - domain: Aliquot - slot_uri: includedcc:aliquot_id - identifier: true - alias: aliquot_id - owner: Aliquot - domain_of: - - Aliquot - is_usage_slot: true - usage_slot_name: aliquot_id - range: string - required: true - Encounter_encounter_id: - name: Encounter_encounter_id - definition_uri: https://includedcc.org/include-access-model/encounter_id - description: Unique identifier for this Encounter. - title: Encounter ID - from_schema: https://includedcc.org/include-access-model - is_a: encounter_id - domain: Encounter - slot_uri: includedcc:encounter_id - identifier: true - alias: encounter_id - owner: Encounter - domain_of: - - Encounter - is_usage_slot: true - usage_slot_name: encounter_id - range: string - required: true - EncounterDefinition_encounter_definition_id: - name: EncounterDefinition_encounter_definition_id - definition_uri: https://includedcc.org/include-access-model/encounter_definition_id - description: Unique identifier for this Encounter Definition. - title: Encounter Definition ID - from_schema: https://includedcc.org/include-access-model - is_a: encounter_definition_id - domain: EncounterDefinition - slot_uri: includedcc:encounter_definition_id - identifier: true - alias: encounter_definition_id - owner: EncounterDefinition - domain_of: - - EncounterDefinition - is_usage_slot: true - usage_slot_name: encounter_definition_id - range: string - required: true - EncounterDefinition_activity_definition_id: - name: EncounterDefinition_activity_definition_id - definition_uri: https://includedcc.org/include-access-model/activity_definition_id - description: Unique identifier for this Activity Definition. - title: Activity Definition ID - from_schema: https://includedcc.org/include-access-model - is_a: activity_definition_id - domain: EncounterDefinition - slot_uri: includedcc:activity_definition_id - alias: activity_definition_id - owner: EncounterDefinition - domain_of: - - EncounterDefinition - is_usage_slot: true - usage_slot_name: activity_definition_id - range: ActivityDefinition - multivalued: true - ActivityDefinition_activity_definition_id: - name: ActivityDefinition_activity_definition_id - definition_uri: https://includedcc.org/include-access-model/activity_definition_id - description: Unique identifier for this Activity Definition. - title: Activity Definition ID - from_schema: https://includedcc.org/include-access-model - is_a: activity_definition_id - domain: ActivityDefinition - slot_uri: includedcc:activity_definition_id - identifier: true - alias: activity_definition_id - owner: ActivityDefinition - domain_of: - - ActivityDefinition - is_usage_slot: true - usage_slot_name: activity_definition_id - range: string - required: true - File_file_id: - name: File_file_id - definition_uri: https://includedcc.org/include-access-model/file_id - description: Unique identifier for this File. - title: File ID - from_schema: https://includedcc.org/include-access-model - is_a: file_id - domain: File - slot_uri: includedcc:file_id - identifier: true - alias: file_id - owner: File - domain_of: - - File - is_usage_slot: true - usage_slot_name: file_id - range: string - required: true - File_subject_id: - name: File_subject_id - definition_uri: https://includedcc.org/include-access-model/subject_id - description: INCLUDE Global ID for the Subject - title: Study ID - from_schema: https://includedcc.org/include-access-model - is_a: subject_id - domain: File - slot_uri: includedcc:subject_id - alias: subject_id - owner: File - domain_of: - - File - is_usage_slot: true - usage_slot_name: subject_id - range: Subject - multivalued: true - File_sample_id: - name: File_sample_id - definition_uri: https://includedcc.org/include-access-model/sample_id - description: The unique identifier for this Sample. - title: Sample ID - from_schema: https://includedcc.org/include-access-model - is_a: sample_id - domain: File - slot_uri: includedcc:sample_id - alias: sample_id - owner: File - domain_of: - - File - is_usage_slot: true - usage_slot_name: sample_id - range: Sample - multivalued: true - Dataset_dataset_id: - name: Dataset_dataset_id - definition_uri: https://includedcc.org/include-access-model/dataset_id - description: Unique identifier for a Dataset. - title: Dataset ID - from_schema: https://includedcc.org/include-access-model - is_a: dataset_id - domain: Dataset - slot_uri: includedcc:dataset_id - identifier: true - alias: dataset_id - owner: Dataset - domain_of: - - Dataset - is_usage_slot: true - usage_slot_name: dataset_id - range: string - required: true - Dataset_file_id: - name: Dataset_file_id - definition_uri: https://includedcc.org/include-access-model/file_id - description: The list of files comprising this dataset. - title: File ID - from_schema: https://includedcc.org/include-access-model - is_a: file_id - domain: Dataset - slot_uri: includedcc:file_id - alias: file_id - owner: Dataset - domain_of: - - Dataset - is_usage_slot: true - usage_slot_name: file_id - range: File - multivalued: true -classes: - Record: - name: Record - definition_uri: https://includedcc.org/include-access-model/Record - description: One row / entity within the database - title: Record - from_schema: https://includedcc.org/include-access-model - abstract: true - slots: - - external_id - class_uri: includedcc:Record - Study: - name: Study - definition_uri: https://includedcc.org/include-access-model/Study - description: Study Metadata - title: Research Study - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - Study_study_id - - parent_study - - study_title - - study_code - - study_short_name - - program - - funding_source - - principal_investigator - - contact - - study_description - - website - - publication - - acknowledgments - - citation_statement - - do_id - slot_usage: - study_id: - name: study_id - identifier: true - range: string - required: true - class_uri: includedcc:Study - StudyMetadata: - name: StudyMetadata - definition_uri: https://includedcc.org/include-access-model/StudyMetadata - description: Additional features about studies that may not apply to all studies - title: Study Metadata - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - StudyMetadata_study_id - - participant_lifespan_stage - - selection_criteria - - study_design - - clinical_data_source_type - - StudyMetadata_data_category - - vbr - - research_domain - - expected_number_of_participants - - actual_number_of_participants - slot_usage: - study_id: - name: study_id - identifier: true - required: true - data_category: - name: data_category - required: true - multivalued: true - class_uri: includedcc:StudyMetadata - VirtualBiorepository: - name: VirtualBiorepository - definition_uri: https://includedcc.org/include-access-model/VirtualBiorepository - description: An organization that can provide access to specimen for further analysis. - title: Virtual BioRepository (VBR) - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - name - - institution - - contact - - website - - vbr_readme - class_uri: includedcc:VirtualBiorepository - DOI: - name: DOI - definition_uri: https://includedcc.org/include-access-model/DOI - description: A DOI is a permanent reference with metadata about a digital object. - title: Digital Object Identifier (DOI) - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - DOI_do_id - - bibliographic_reference - slot_usage: - do_id: - name: do_id - identifier: true - range: string - required: true - class_uri: includedcc:DOI - Investigator: - name: Investigator - definition_uri: https://includedcc.org/include-access-model/Investigator - description: An individual who made contributions to the collection, analysis, - or sharing of data. - title: Investigator - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - name - - institution - - investigator_title - - email - class_uri: includedcc:Investigator - Publication: - name: Publication - definition_uri: https://includedcc.org/include-access-model/Publication - description: Information about a specific publication. - title: Publication - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - bibliographic_reference - - website - class_uri: includedcc:Publication - Subject: - name: Subject - definition_uri: https://includedcc.org/include-access-model/Subject - description: This entity is the subject about which data or references are recorded. - This includes the idea of a human participant in a study, a cell line, an animal - model, or any other similar entity. - title: Subject - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - Subject_subject_id - - subject_type - - organism_type - slot_usage: - subject_id: - name: subject_id - identifier: true - range: string - required: true - class_uri: includedcc:Subject - Demographics: - name: Demographics - definition_uri: https://includedcc.org/include-access-model/Demographics - description: Basic participant demographics summary - title: Demographics - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - Demographics_subject_id - - sex - - race - - ethnicity - - down_syndrome_status - - age_at_last_vital_status - - vital_status - - age_at_first_engagement - slot_usage: - subject_id: - name: subject_id - identifier: true - required: true - class_uri: includedcc:Demographics - SubjectAssertion: - name: SubjectAssertion - definition_uri: https://includedcc.org/include-access-model/SubjectAssertion - description: Assertion about a particular Subject. May include Conditions, Measurements, - etc. - title: Subject Assertion - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - SubjectAssertion_assertion_id - - subject_id - - encounter_id - - assertion_provenance - - age_at_assertion - - age_at_event - - age_at_resolution - - concept - - concept_source - - value_concept - - value_number - - value_source - - value_unit - - value_unit_source - slot_usage: - assertion_id: - name: assertion_id - identifier: true - range: string - required: true - class_uri: includedcc:SubjectAssertion - Concept: - name: Concept - definition_uri: https://includedcc.org/include-access-model/Concept - description: A standardized concept with display information. - title: Concept - from_schema: https://includedcc.org/include-access-model - slots: - - Concept_concept_curie - - display - slot_usage: - concept_curie: - name: concept_curie - identifier: true - required: true - class_uri: includedcc:Concept - Sample: - name: Sample - definition_uri: https://includedcc.org/include-access-model/Sample - description: A functionally equivalent specimen taken from a participant or processed - from such a sample. - title: Sample - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - Sample_sample_id - - Sample_biospecimen_collection_id - - parent_sample_id - - sample_type - - processing - - availablity_status - - storage_method - - quantity_number - - quantity_unit - slot_usage: - sample_id: - name: sample_id - identifier: true - range: string - required: true - biospecimen_collection_id: - name: biospecimen_collection_id - description: Biospecimen Collection during which this sample was generated. - class_uri: includedcc:Sample - BiospecimenCollection: - name: BiospecimenCollection - definition_uri: https://includedcc.org/include-access-model/BiospecimenCollection - description: A biospecimen collection event which yields one or more Samples. - title: BiospecimenCollection - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - BiospecimenCollection_biospecimen_collection_id - - age_at_collection - - method - - site - - spatial_qualifier - - laterality - - encounter_id - slot_usage: - biospecimen_collection_id: - name: biospecimen_collection_id - identifier: true - range: string - required: true - class_uri: includedcc:BiospecimenCollection - Aliquot: - name: Aliquot - definition_uri: https://includedcc.org/include-access-model/Aliquot - description: A specific tube or amount of a biospecimen associated with a Sample. - title: Aliquot - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - Aliquot_aliquot_id - - sample_id - - availablity_status - - quantity_number - - quantity_unit - - concentration_number - - concentration_unit - slot_usage: - aliquot_id: - name: aliquot_id - identifier: true - range: string - required: true - class_uri: includedcc:Aliquot - Encounter: - name: Encounter - definition_uri: https://includedcc.org/include-access-model/Encounter - description: An event at which data was collected about a participant, an intervention - was made, or information about a participant was recorded. - title: Participant Encounter - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - Encounter_encounter_id - - subject_id - - encounter_definition_id - - age_at_event - slot_usage: - encounter_id: - name: encounter_id - identifier: true - range: string - required: true - class_uri: includedcc:Encounter - EncounterDefinition: - name: EncounterDefinition - definition_uri: https://includedcc.org/include-access-model/EncounterDefinition - description: A definition of an encounter type in this study, ie, an event at - which data was collected about a participant, an intervention was made, or information - about a participant was recorded. This may be something planned by a study or - a type of data collection. - title: Encounter Definition - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - EncounterDefinition_encounter_definition_id - - name - - description - - EncounterDefinition_activity_definition_id - slot_usage: - encounter_definition_id: - name: encounter_definition_id - identifier: true - range: string - required: true - activity_definition_id: - name: activity_definition_id - multivalued: true - class_uri: includedcc:EncounterDefinition - ActivityDefinition: - name: ActivityDefinition - definition_uri: https://includedcc.org/include-access-model/ActivityDefinition - description: A definition of an activity in this study, eg, a biospecimen collection, - intervention, survey, or assessment. - title: Activity Definition - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - ActivityDefinition_activity_definition_id - - name - - description - slot_usage: - activity_definition_id: - name: activity_definition_id - identifier: true - range: string - required: true - class_uri: includedcc:ActivityDefinition - File: - name: File - definition_uri: https://includedcc.org/include-access-model/File - description: File - title: File - from_schema: https://includedcc.org/include-access-model - is_a: Record - slots: - - external_id - - File_file_id - - File_subject_id - - File_sample_id - - filename - - format - - data_category - - data_type - - format - - size - - staging_url - - release_url - - drs_uri - - hash - slot_usage: - file_id: - name: file_id - identifier: true - range: string - required: true - subject_id: - name: subject_id - multivalued: true - sample_id: - name: sample_id - multivalued: true - class_uri: includedcc:File - FileHash: - name: FileHash - definition_uri: https://includedcc.org/include-access-model/FileHash - description: Type and value of a file content hash. - title: File Hash - from_schema: https://includedcc.org/include-access-model - slots: - - hash_type - - hash_value - class_uri: includedcc:FileHash - Dataset: - name: Dataset - definition_uri: https://includedcc.org/include-access-model/Dataset - description: Set of files grouped together for release. - title: Dataset - from_schema: https://includedcc.org/include-access-model - slots: - - Dataset_dataset_id - - name - - description - - do_id - - Dataset_file_id - - publication - - data_collection_start - - data_collection_end - slot_usage: - dataset_id: - name: dataset_id - identifier: true - range: string - required: true - file_id: - name: file_id - description: The list of files comprising this dataset. - multivalued: true - class_uri: includedcc:Dataset -metamodel_version: 1.7.0 -source_file: include_access_model.yaml -source_file_date: '2026-03-12T11:06:57' -source_file_size: 36149 -generation_date: '2026-03-12T11:07:27' - diff --git a/src/include_access_model/datamodel/include_access_model.py b/src/include_access_model/datamodel/include_access_model.py deleted file mode 100644 index a1be426..0000000 --- a/src/include_access_model/datamodel/include_access_model.py +++ /dev/null @@ -1,1922 +0,0 @@ -# Auto generated from include_access_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2026-03-12T11:07:16 -# Schema: include-access-model -# -# id: https://includedcc.org/include-access-model -# description: LinkML Schema for the internal INCLUDE DCC Access Model -# license: MIT - -import dataclasses -import re -from dataclasses import dataclass -from datetime import ( - date, - datetime, - time -) -from typing import ( - Any, - ClassVar, - Dict, - List, - Optional, - Union -) - -from jsonasobj2 import ( - JsonObj, - as_dict -) -from linkml_runtime.linkml_model.meta import ( - EnumDefinition, - PermissibleValue, - PvFormulaOptions -) -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from linkml_runtime.utils.formatutils import ( - camelcase, - sfx, - underscore -) -from linkml_runtime.utils.metamodelcore import ( - bnode, - empty_dict, - empty_list -) -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.yamlutils import ( - YAMLRoot, - extended_float, - extended_int, - extended_str -) -from rdflib import ( - Namespace, - URIRef -) - -from linkml_runtime.linkml_model.types import Float, Integer, String, Uri, Uriorcurie -from linkml_runtime.utils.metamodelcore import URI, URIorCURIE - -metamodel_version = "1.7.0" -version = None - -# Namespaces -HP = CurieNamespace('HP', 'http://purl.obolibrary.org/obo/HP_') -MONDO = CurieNamespace('MONDO', 'http://purl.obolibrary.org/obo/MONDO_') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -PATO = CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_') -CDC_RACE_ETH = CurieNamespace('cdc_race_eth', 'urn:oid:2.16.840.1.113883.6.238/') -HL7_NULL = CurieNamespace('hl7_null', 'http://terminology.hl7.org/CodeSystem/v3-NullFlavor/') -IG2_BIOSPECIMEN_AVAILABILITY = CurieNamespace('ig2_biospecimen_availability', 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/biospecimen-availability/') -IG2DAC = CurieNamespace('ig2dac', 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code/') -IG2DAT = CurieNamespace('ig2dat', 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type/') -IG_DOB_METHOD = CurieNamespace('ig_dob_method', 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/') -IGCONDTYPE = CurieNamespace('igcondtype', 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/') -INCLUDEDCC = CurieNamespace('includedcc', 'https://includedcc.org/include-access-model/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -MESH = CurieNamespace('mesh', 'http://id.nlm.nih.gov/mesh/') -SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SNOMED_CT = CurieNamespace('snomed_ct', 'http://snomed.info/id/') -DEFAULT_ = INCLUDEDCC - - -# Types - -# Class references -class StudyStudyId(extended_str): - pass - - -class StudyMetadataStudyId(StudyStudyId): - pass - - -class DOIDoId(extended_str): - pass - - -class SubjectSubjectId(extended_str): - pass - - -class DemographicsSubjectId(SubjectSubjectId): - pass - - -class SubjectAssertionAssertionId(extended_str): - pass - - -class ConceptConceptCurie(URIorCURIE): - pass - - -class SampleSampleId(extended_str): - pass - - -class BiospecimenCollectionBiospecimenCollectionId(extended_str): - pass - - -class AliquotAliquotId(extended_str): - pass - - -class EncounterEncounterId(extended_str): - pass - - -class EncounterDefinitionEncounterDefinitionId(extended_str): - pass - - -class ActivityDefinitionActivityDefinitionId(extended_str): - pass - - -class FileFileId(extended_str): - pass - - -class DatasetDatasetId(extended_str): - pass - - -@dataclass(repr=False) -class Record(YAMLRoot): - """ - One row / entity within the database - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Record"] - class_class_curie: ClassVar[str] = "includedcc:Record" - class_name: ClassVar[str] = "Record" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Record - - external_id: Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]] = empty_list() - - def __post_init__(self, *_: str, **kwargs: Any): - if not isinstance(self.external_id, list): - self.external_id = [self.external_id] if self.external_id is not None else [] - self.external_id = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.external_id] - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Study(Record): - """ - Study Metadata - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Study"] - class_class_curie: ClassVar[str] = "includedcc:Study" - class_name: ClassVar[str] = "Study" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Study - - study_id: Union[str, StudyStudyId] = None - study_title: str = None - study_code: str = None - program: Union[Union[str, "EnumProgram"], list[Union[str, "EnumProgram"]]] = None - principal_investigator: Union[Union[dict, "Investigator"], list[Union[dict, "Investigator"]]] = None - contact: Union[Union[dict, "Investigator"], list[Union[dict, "Investigator"]]] = None - study_description: str = None - parent_study: Optional[Union[str, StudyStudyId]] = None - study_short_name: Optional[str] = None - funding_source: Optional[Union[str, list[str]]] = empty_list() - website: Optional[Union[str, URI]] = None - publication: Optional[Union[Union[dict, "Publication"], list[Union[dict, "Publication"]]]] = empty_list() - acknowledgments: Optional[str] = None - citation_statement: Optional[str] = None - do_id: Optional[Union[str, DOIDoId]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.study_id): - self.MissingRequiredField("study_id") - if not isinstance(self.study_id, StudyStudyId): - self.study_id = StudyStudyId(self.study_id) - - if self._is_empty(self.study_title): - self.MissingRequiredField("study_title") - if not isinstance(self.study_title, str): - self.study_title = str(self.study_title) - - if self._is_empty(self.study_code): - self.MissingRequiredField("study_code") - if not isinstance(self.study_code, str): - self.study_code = str(self.study_code) - - if self._is_empty(self.program): - self.MissingRequiredField("program") - if not isinstance(self.program, list): - self.program = [self.program] if self.program is not None else [] - self.program = [v if isinstance(v, EnumProgram) else EnumProgram(v) for v in self.program] - - if self._is_empty(self.principal_investigator): - self.MissingRequiredField("principal_investigator") - if not isinstance(self.principal_investigator, list): - self.principal_investigator = [self.principal_investigator] if self.principal_investigator is not None else [] - self.principal_investigator = [v if isinstance(v, Investigator) else Investigator(**as_dict(v)) for v in self.principal_investigator] - - if self._is_empty(self.contact): - self.MissingRequiredField("contact") - if not isinstance(self.contact, list): - self.contact = [self.contact] if self.contact is not None else [] - self.contact = [v if isinstance(v, Investigator) else Investigator(**as_dict(v)) for v in self.contact] - - if self._is_empty(self.study_description): - self.MissingRequiredField("study_description") - if not isinstance(self.study_description, str): - self.study_description = str(self.study_description) - - if self.parent_study is not None and not isinstance(self.parent_study, StudyStudyId): - self.parent_study = StudyStudyId(self.parent_study) - - if self.study_short_name is not None and not isinstance(self.study_short_name, str): - self.study_short_name = str(self.study_short_name) - - if not isinstance(self.funding_source, list): - self.funding_source = [self.funding_source] if self.funding_source is not None else [] - self.funding_source = [v if isinstance(v, str) else str(v) for v in self.funding_source] - - if self.website is not None and not isinstance(self.website, URI): - self.website = URI(self.website) - - if not isinstance(self.publication, list): - self.publication = [self.publication] if self.publication is not None else [] - self.publication = [v if isinstance(v, Publication) else Publication(**as_dict(v)) for v in self.publication] - - if self.acknowledgments is not None and not isinstance(self.acknowledgments, str): - self.acknowledgments = str(self.acknowledgments) - - if self.citation_statement is not None and not isinstance(self.citation_statement, str): - self.citation_statement = str(self.citation_statement) - - if self.do_id is not None and not isinstance(self.do_id, DOIDoId): - self.do_id = DOIDoId(self.do_id) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class StudyMetadata(Record): - """ - Additional features about studies that may not apply to all studies - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["StudyMetadata"] - class_class_curie: ClassVar[str] = "includedcc:StudyMetadata" - class_name: ClassVar[str] = "StudyMetadata" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.StudyMetadata - - study_id: Union[str, StudyMetadataStudyId] = None - participant_lifespan_stage: Union[Union[str, "EnumParticipantLifespanStage"], list[Union[str, "EnumParticipantLifespanStage"]]] = None - study_design: Union[Union[str, "EnumStudyDesign"], list[Union[str, "EnumStudyDesign"]]] = None - clinical_data_source_type: Union[Union[str, "EnumClinicalDataSourceType"], list[Union[str, "EnumClinicalDataSourceType"]]] = None - data_category: Union[Union[str, "EnumDataCategory"], list[Union[str, "EnumDataCategory"]]] = None - research_domain: Union[Union[str, "EnumResearchDomain"], list[Union[str, "EnumResearchDomain"]]] = None - expected_number_of_participants: int = None - actual_number_of_participants: int = None - selection_criteria: Optional[str] = None - vbr: Optional[Union[dict, "VirtualBiorepository"]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.study_id): - self.MissingRequiredField("study_id") - if not isinstance(self.study_id, StudyMetadataStudyId): - self.study_id = StudyMetadataStudyId(self.study_id) - - if self._is_empty(self.participant_lifespan_stage): - self.MissingRequiredField("participant_lifespan_stage") - if not isinstance(self.participant_lifespan_stage, list): - self.participant_lifespan_stage = [self.participant_lifespan_stage] if self.participant_lifespan_stage is not None else [] - self.participant_lifespan_stage = [v if isinstance(v, EnumParticipantLifespanStage) else EnumParticipantLifespanStage(v) for v in self.participant_lifespan_stage] - - if self._is_empty(self.study_design): - self.MissingRequiredField("study_design") - if not isinstance(self.study_design, list): - self.study_design = [self.study_design] if self.study_design is not None else [] - self.study_design = [v if isinstance(v, EnumStudyDesign) else EnumStudyDesign(v) for v in self.study_design] - - if self._is_empty(self.clinical_data_source_type): - self.MissingRequiredField("clinical_data_source_type") - if not isinstance(self.clinical_data_source_type, list): - self.clinical_data_source_type = [self.clinical_data_source_type] if self.clinical_data_source_type is not None else [] - self.clinical_data_source_type = [v if isinstance(v, EnumClinicalDataSourceType) else EnumClinicalDataSourceType(v) for v in self.clinical_data_source_type] - - if self._is_empty(self.data_category): - self.MissingRequiredField("data_category") - if not isinstance(self.data_category, list): - self.data_category = [self.data_category] if self.data_category is not None else [] - self.data_category = [v if isinstance(v, EnumDataCategory) else EnumDataCategory(v) for v in self.data_category] - - if self._is_empty(self.research_domain): - self.MissingRequiredField("research_domain") - if not isinstance(self.research_domain, list): - self.research_domain = [self.research_domain] if self.research_domain is not None else [] - self.research_domain = [v if isinstance(v, EnumResearchDomain) else EnumResearchDomain(v) for v in self.research_domain] - - if self._is_empty(self.expected_number_of_participants): - self.MissingRequiredField("expected_number_of_participants") - if not isinstance(self.expected_number_of_participants, int): - self.expected_number_of_participants = int(self.expected_number_of_participants) - - if self._is_empty(self.actual_number_of_participants): - self.MissingRequiredField("actual_number_of_participants") - if not isinstance(self.actual_number_of_participants, int): - self.actual_number_of_participants = int(self.actual_number_of_participants) - - if self.selection_criteria is not None and not isinstance(self.selection_criteria, str): - self.selection_criteria = str(self.selection_criteria) - - if self.vbr is not None and not isinstance(self.vbr, VirtualBiorepository): - self.vbr = VirtualBiorepository(**as_dict(self.vbr)) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class VirtualBiorepository(Record): - """ - An organization that can provide access to specimen for further analysis. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["VirtualBiorepository"] - class_class_curie: ClassVar[str] = "includedcc:VirtualBiorepository" - class_name: ClassVar[str] = "VirtualBiorepository" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.VirtualBiorepository - - contact: Union[Union[dict, "Investigator"], list[Union[dict, "Investigator"]]] = None - name: Optional[str] = None - institution: Optional[str] = None - website: Optional[Union[str, URI]] = None - vbr_readme: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.contact): - self.MissingRequiredField("contact") - if not isinstance(self.contact, list): - self.contact = [self.contact] if self.contact is not None else [] - self.contact = [v if isinstance(v, Investigator) else Investigator(**as_dict(v)) for v in self.contact] - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.institution is not None and not isinstance(self.institution, str): - self.institution = str(self.institution) - - if self.website is not None and not isinstance(self.website, URI): - self.website = URI(self.website) - - if self.vbr_readme is not None and not isinstance(self.vbr_readme, str): - self.vbr_readme = str(self.vbr_readme) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class DOI(Record): - """ - A DOI is a permanent reference with metadata about a digital object. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["DOI"] - class_class_curie: ClassVar[str] = "includedcc:DOI" - class_name: ClassVar[str] = "DOI" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.DOI - - do_id: Union[str, DOIDoId] = None - bibliographic_reference: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.do_id): - self.MissingRequiredField("do_id") - if not isinstance(self.do_id, DOIDoId): - self.do_id = DOIDoId(self.do_id) - - if self.bibliographic_reference is not None and not isinstance(self.bibliographic_reference, str): - self.bibliographic_reference = str(self.bibliographic_reference) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Investigator(Record): - """ - An individual who made contributions to the collection, analysis, or sharing of data. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Investigator"] - class_class_curie: ClassVar[str] = "includedcc:Investigator" - class_name: ClassVar[str] = "Investigator" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Investigator - - name: Optional[str] = None - institution: Optional[str] = None - investigator_title: Optional[str] = None - email: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.institution is not None and not isinstance(self.institution, str): - self.institution = str(self.institution) - - if self.investigator_title is not None and not isinstance(self.investigator_title, str): - self.investigator_title = str(self.investigator_title) - - if self.email is not None and not isinstance(self.email, str): - self.email = str(self.email) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Publication(Record): - """ - Information about a specific publication. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Publication"] - class_class_curie: ClassVar[str] = "includedcc:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Publication - - bibliographic_reference: Optional[str] = None - website: Optional[Union[str, URI]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self.bibliographic_reference is not None and not isinstance(self.bibliographic_reference, str): - self.bibliographic_reference = str(self.bibliographic_reference) - - if self.website is not None and not isinstance(self.website, URI): - self.website = URI(self.website) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Subject(Record): - """ - This entity is the subject about which data or references are recorded. This includes the idea of a human - participant in a study, a cell line, an animal model, or any other similar entity. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Subject"] - class_class_curie: ClassVar[str] = "includedcc:Subject" - class_name: ClassVar[str] = "Subject" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Subject - - subject_id: Union[str, SubjectSubjectId] = None - subject_type: Union[str, "EnumSubjectType"] = None - organism_type: Optional[Union[str, URIorCURIE]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.subject_id): - self.MissingRequiredField("subject_id") - if not isinstance(self.subject_id, SubjectSubjectId): - self.subject_id = SubjectSubjectId(self.subject_id) - - if self._is_empty(self.subject_type): - self.MissingRequiredField("subject_type") - if not isinstance(self.subject_type, EnumSubjectType): - self.subject_type = EnumSubjectType(self.subject_type) - - if self.organism_type is not None and not isinstance(self.organism_type, URIorCURIE): - self.organism_type = URIorCURIE(self.organism_type) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Demographics(Record): - """ - Basic participant demographics summary - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Demographics"] - class_class_curie: ClassVar[str] = "includedcc:Demographics" - class_name: ClassVar[str] = "Demographics" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Demographics - - subject_id: Union[str, DemographicsSubjectId] = None - sex: Union[str, "EnumSex"] = None - race: Union[Union[str, "EnumRace"], list[Union[str, "EnumRace"]]] = None - ethnicity: Union[str, "EnumEthnicity"] = None - down_syndrome_status: Union[str, "EnumDownSyndromeStatus"] = None - age_at_last_vital_status: Optional[int] = None - vital_status: Optional[Union[str, "EnumVitalStatus"]] = None - age_at_first_engagement: Optional[int] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.subject_id): - self.MissingRequiredField("subject_id") - if not isinstance(self.subject_id, DemographicsSubjectId): - self.subject_id = DemographicsSubjectId(self.subject_id) - - if self._is_empty(self.sex): - self.MissingRequiredField("sex") - if not isinstance(self.sex, EnumSex): - self.sex = EnumSex(self.sex) - - if self._is_empty(self.race): - self.MissingRequiredField("race") - if not isinstance(self.race, list): - self.race = [self.race] if self.race is not None else [] - self.race = [v if isinstance(v, EnumRace) else EnumRace(v) for v in self.race] - - if self._is_empty(self.ethnicity): - self.MissingRequiredField("ethnicity") - if not isinstance(self.ethnicity, EnumEthnicity): - self.ethnicity = EnumEthnicity(self.ethnicity) - - if self._is_empty(self.down_syndrome_status): - self.MissingRequiredField("down_syndrome_status") - if not isinstance(self.down_syndrome_status, EnumDownSyndromeStatus): - self.down_syndrome_status = EnumDownSyndromeStatus(self.down_syndrome_status) - - if self.age_at_last_vital_status is not None and not isinstance(self.age_at_last_vital_status, int): - self.age_at_last_vital_status = int(self.age_at_last_vital_status) - - if self.vital_status is not None and not isinstance(self.vital_status, EnumVitalStatus): - self.vital_status = EnumVitalStatus(self.vital_status) - - if self.age_at_first_engagement is not None and not isinstance(self.age_at_first_engagement, int): - self.age_at_first_engagement = int(self.age_at_first_engagement) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class SubjectAssertion(Record): - """ - Assertion about a particular Subject. May include Conditions, Measurements, etc. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["SubjectAssertion"] - class_class_curie: ClassVar[str] = "includedcc:SubjectAssertion" - class_name: ClassVar[str] = "SubjectAssertion" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.SubjectAssertion - - assertion_id: Union[str, SubjectAssertionAssertionId] = None - subject_id: Optional[Union[str, SubjectSubjectId]] = None - encounter_id: Optional[Union[str, EncounterEncounterId]] = None - assertion_provenance: Optional[Union[str, "EnumAssertionProvenance"]] = None - age_at_assertion: Optional[int] = None - age_at_event: Optional[int] = None - age_at_resolution: Optional[int] = None - concept: Optional[Union[Union[str, ConceptConceptCurie], list[Union[str, ConceptConceptCurie]]]] = empty_list() - concept_source: Optional[str] = None - value_concept: Optional[Union[Union[str, ConceptConceptCurie], list[Union[str, ConceptConceptCurie]]]] = empty_list() - value_number: Optional[float] = None - value_source: Optional[str] = None - value_unit: Optional[Union[str, ConceptConceptCurie]] = None - value_unit_source: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.assertion_id): - self.MissingRequiredField("assertion_id") - if not isinstance(self.assertion_id, SubjectAssertionAssertionId): - self.assertion_id = SubjectAssertionAssertionId(self.assertion_id) - - if self.subject_id is not None and not isinstance(self.subject_id, SubjectSubjectId): - self.subject_id = SubjectSubjectId(self.subject_id) - - if self.encounter_id is not None and not isinstance(self.encounter_id, EncounterEncounterId): - self.encounter_id = EncounterEncounterId(self.encounter_id) - - if self.assertion_provenance is not None and not isinstance(self.assertion_provenance, EnumAssertionProvenance): - self.assertion_provenance = EnumAssertionProvenance(self.assertion_provenance) - - if self.age_at_assertion is not None and not isinstance(self.age_at_assertion, int): - self.age_at_assertion = int(self.age_at_assertion) - - if self.age_at_event is not None and not isinstance(self.age_at_event, int): - self.age_at_event = int(self.age_at_event) - - if self.age_at_resolution is not None and not isinstance(self.age_at_resolution, int): - self.age_at_resolution = int(self.age_at_resolution) - - if not isinstance(self.concept, list): - self.concept = [self.concept] if self.concept is not None else [] - self.concept = [v if isinstance(v, ConceptConceptCurie) else ConceptConceptCurie(v) for v in self.concept] - - if self.concept_source is not None and not isinstance(self.concept_source, str): - self.concept_source = str(self.concept_source) - - if not isinstance(self.value_concept, list): - self.value_concept = [self.value_concept] if self.value_concept is not None else [] - self.value_concept = [v if isinstance(v, ConceptConceptCurie) else ConceptConceptCurie(v) for v in self.value_concept] - - if self.value_number is not None and not isinstance(self.value_number, float): - self.value_number = float(self.value_number) - - if self.value_source is not None and not isinstance(self.value_source, str): - self.value_source = str(self.value_source) - - if self.value_unit is not None and not isinstance(self.value_unit, ConceptConceptCurie): - self.value_unit = ConceptConceptCurie(self.value_unit) - - if self.value_unit_source is not None and not isinstance(self.value_unit_source, str): - self.value_unit_source = str(self.value_unit_source) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Concept(YAMLRoot): - """ - A standardized concept with display information. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Concept"] - class_class_curie: ClassVar[str] = "includedcc:Concept" - class_name: ClassVar[str] = "Concept" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Concept - - concept_curie: Union[str, ConceptConceptCurie] = None - display: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.concept_curie): - self.MissingRequiredField("concept_curie") - if not isinstance(self.concept_curie, ConceptConceptCurie): - self.concept_curie = ConceptConceptCurie(self.concept_curie) - - if self.display is not None and not isinstance(self.display, str): - self.display = str(self.display) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Sample(Record): - """ - A functionally equivalent specimen taken from a participant or processed from such a sample. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Sample"] - class_class_curie: ClassVar[str] = "includedcc:Sample" - class_name: ClassVar[str] = "Sample" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Sample - - sample_id: Union[str, SampleSampleId] = None - sample_type: Union[str, URIorCURIE] = None - biospecimen_collection_id: Optional[Union[str, BiospecimenCollectionBiospecimenCollectionId]] = None - parent_sample_id: Optional[Union[str, SampleSampleId]] = None - processing: Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]] = empty_list() - availablity_status: Optional[Union[str, "EnumAvailabilityStatus"]] = None - storage_method: Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]] = empty_list() - quantity_number: Optional[float] = None - quantity_unit: Optional[Union[str, ConceptConceptCurie]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.sample_id): - self.MissingRequiredField("sample_id") - if not isinstance(self.sample_id, SampleSampleId): - self.sample_id = SampleSampleId(self.sample_id) - - if self._is_empty(self.sample_type): - self.MissingRequiredField("sample_type") - if not isinstance(self.sample_type, URIorCURIE): - self.sample_type = URIorCURIE(self.sample_type) - - if self.biospecimen_collection_id is not None and not isinstance(self.biospecimen_collection_id, BiospecimenCollectionBiospecimenCollectionId): - self.biospecimen_collection_id = BiospecimenCollectionBiospecimenCollectionId(self.biospecimen_collection_id) - - if self.parent_sample_id is not None and not isinstance(self.parent_sample_id, SampleSampleId): - self.parent_sample_id = SampleSampleId(self.parent_sample_id) - - if not isinstance(self.processing, list): - self.processing = [self.processing] if self.processing is not None else [] - self.processing = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.processing] - - if self.availablity_status is not None and not isinstance(self.availablity_status, EnumAvailabilityStatus): - self.availablity_status = EnumAvailabilityStatus(self.availablity_status) - - if not isinstance(self.storage_method, list): - self.storage_method = [self.storage_method] if self.storage_method is not None else [] - self.storage_method = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.storage_method] - - if self.quantity_number is not None and not isinstance(self.quantity_number, float): - self.quantity_number = float(self.quantity_number) - - if self.quantity_unit is not None and not isinstance(self.quantity_unit, ConceptConceptCurie): - self.quantity_unit = ConceptConceptCurie(self.quantity_unit) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class BiospecimenCollection(Record): - """ - A biospecimen collection event which yields one or more Samples. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["BiospecimenCollection"] - class_class_curie: ClassVar[str] = "includedcc:BiospecimenCollection" - class_name: ClassVar[str] = "BiospecimenCollection" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.BiospecimenCollection - - biospecimen_collection_id: Union[str, BiospecimenCollectionBiospecimenCollectionId] = None - age_at_collection: Optional[float] = None - method: Optional[Union[str, "EnumSampleCollectionMethod"]] = None - site: Optional[Union[str, "EnumSite"]] = None - spatial_qualifier: Optional[Union[str, "EnumSpatialQualifiers"]] = None - laterality: Optional[Union[str, "EnumLaterality"]] = None - encounter_id: Optional[Union[str, EncounterEncounterId]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.biospecimen_collection_id): - self.MissingRequiredField("biospecimen_collection_id") - if not isinstance(self.biospecimen_collection_id, BiospecimenCollectionBiospecimenCollectionId): - self.biospecimen_collection_id = BiospecimenCollectionBiospecimenCollectionId(self.biospecimen_collection_id) - - if self.age_at_collection is not None and not isinstance(self.age_at_collection, float): - self.age_at_collection = float(self.age_at_collection) - - if self.encounter_id is not None and not isinstance(self.encounter_id, EncounterEncounterId): - self.encounter_id = EncounterEncounterId(self.encounter_id) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Aliquot(Record): - """ - A specific tube or amount of a biospecimen associated with a Sample. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Aliquot"] - class_class_curie: ClassVar[str] = "includedcc:Aliquot" - class_name: ClassVar[str] = "Aliquot" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Aliquot - - aliquot_id: Union[str, AliquotAliquotId] = None - sample_id: Optional[Union[str, SampleSampleId]] = None - availablity_status: Optional[Union[str, "EnumAvailabilityStatus"]] = None - quantity_number: Optional[float] = None - quantity_unit: Optional[Union[str, ConceptConceptCurie]] = None - concentration_number: Optional[float] = None - concentration_unit: Optional[Union[str, ConceptConceptCurie]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.aliquot_id): - self.MissingRequiredField("aliquot_id") - if not isinstance(self.aliquot_id, AliquotAliquotId): - self.aliquot_id = AliquotAliquotId(self.aliquot_id) - - if self.sample_id is not None and not isinstance(self.sample_id, SampleSampleId): - self.sample_id = SampleSampleId(self.sample_id) - - if self.availablity_status is not None and not isinstance(self.availablity_status, EnumAvailabilityStatus): - self.availablity_status = EnumAvailabilityStatus(self.availablity_status) - - if self.quantity_number is not None and not isinstance(self.quantity_number, float): - self.quantity_number = float(self.quantity_number) - - if self.quantity_unit is not None and not isinstance(self.quantity_unit, ConceptConceptCurie): - self.quantity_unit = ConceptConceptCurie(self.quantity_unit) - - if self.concentration_number is not None and not isinstance(self.concentration_number, float): - self.concentration_number = float(self.concentration_number) - - if self.concentration_unit is not None and not isinstance(self.concentration_unit, ConceptConceptCurie): - self.concentration_unit = ConceptConceptCurie(self.concentration_unit) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Encounter(Record): - """ - An event at which data was collected about a participant, an intervention was made, or information about a - participant was recorded. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Encounter"] - class_class_curie: ClassVar[str] = "includedcc:Encounter" - class_name: ClassVar[str] = "Encounter" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Encounter - - encounter_id: Union[str, EncounterEncounterId] = None - subject_id: Optional[Union[str, SubjectSubjectId]] = None - encounter_definition_id: Optional[Union[str, EncounterDefinitionEncounterDefinitionId]] = None - age_at_event: Optional[int] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.encounter_id): - self.MissingRequiredField("encounter_id") - if not isinstance(self.encounter_id, EncounterEncounterId): - self.encounter_id = EncounterEncounterId(self.encounter_id) - - if self.subject_id is not None and not isinstance(self.subject_id, SubjectSubjectId): - self.subject_id = SubjectSubjectId(self.subject_id) - - if self.encounter_definition_id is not None and not isinstance(self.encounter_definition_id, EncounterDefinitionEncounterDefinitionId): - self.encounter_definition_id = EncounterDefinitionEncounterDefinitionId(self.encounter_definition_id) - - if self.age_at_event is not None and not isinstance(self.age_at_event, int): - self.age_at_event = int(self.age_at_event) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class EncounterDefinition(Record): - """ - A definition of an encounter type in this study, ie, an event at which data was collected about a participant, an - intervention was made, or information about a participant was recorded. This may be something planned by a study - or a type of data collection. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["EncounterDefinition"] - class_class_curie: ClassVar[str] = "includedcc:EncounterDefinition" - class_name: ClassVar[str] = "EncounterDefinition" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.EncounterDefinition - - encounter_definition_id: Union[str, EncounterDefinitionEncounterDefinitionId] = None - name: Optional[str] = None - description: Optional[str] = None - activity_definition_id: Optional[Union[Union[str, ActivityDefinitionActivityDefinitionId], list[Union[str, ActivityDefinitionActivityDefinitionId]]]] = empty_list() - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.encounter_definition_id): - self.MissingRequiredField("encounter_definition_id") - if not isinstance(self.encounter_definition_id, EncounterDefinitionEncounterDefinitionId): - self.encounter_definition_id = EncounterDefinitionEncounterDefinitionId(self.encounter_definition_id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.activity_definition_id, list): - self.activity_definition_id = [self.activity_definition_id] if self.activity_definition_id is not None else [] - self.activity_definition_id = [v if isinstance(v, ActivityDefinitionActivityDefinitionId) else ActivityDefinitionActivityDefinitionId(v) for v in self.activity_definition_id] - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class ActivityDefinition(Record): - """ - A definition of an activity in this study, eg, a biospecimen collection, intervention, survey, or assessment. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["ActivityDefinition"] - class_class_curie: ClassVar[str] = "includedcc:ActivityDefinition" - class_name: ClassVar[str] = "ActivityDefinition" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.ActivityDefinition - - activity_definition_id: Union[str, ActivityDefinitionActivityDefinitionId] = None - name: Optional[str] = None - description: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.activity_definition_id): - self.MissingRequiredField("activity_definition_id") - if not isinstance(self.activity_definition_id, ActivityDefinitionActivityDefinitionId): - self.activity_definition_id = ActivityDefinitionActivityDefinitionId(self.activity_definition_id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class File(Record): - """ - File - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["File"] - class_class_curie: ClassVar[str] = "includedcc:File" - class_name: ClassVar[str] = "File" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.File - - file_id: Union[str, FileFileId] = None - subject_id: Optional[Union[Union[str, SubjectSubjectId], list[Union[str, SubjectSubjectId]]]] = empty_list() - sample_id: Optional[Union[Union[str, SampleSampleId], list[Union[str, SampleSampleId]]]] = empty_list() - filename: Optional[str] = None - format: Optional[Union[str, "EnumEDAMFormats"]] = None - data_category: Optional[Union[str, "EnumDataCategory"]] = None - data_type: Optional[Union[str, "EnumEDAMDataTypes"]] = None - size: Optional[int] = None - staging_url: Optional[Union[str, URIorCURIE]] = None - release_url: Optional[Union[str, URIorCURIE]] = None - drs_uri: Optional[Union[str, URIorCURIE]] = None - hash: Optional[Union[dict, "FileHash"]] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.file_id): - self.MissingRequiredField("file_id") - if not isinstance(self.file_id, FileFileId): - self.file_id = FileFileId(self.file_id) - - if not isinstance(self.subject_id, list): - self.subject_id = [self.subject_id] if self.subject_id is not None else [] - self.subject_id = [v if isinstance(v, SubjectSubjectId) else SubjectSubjectId(v) for v in self.subject_id] - - if not isinstance(self.sample_id, list): - self.sample_id = [self.sample_id] if self.sample_id is not None else [] - self.sample_id = [v if isinstance(v, SampleSampleId) else SampleSampleId(v) for v in self.sample_id] - - if self.filename is not None and not isinstance(self.filename, str): - self.filename = str(self.filename) - - if self.data_category is not None and not isinstance(self.data_category, EnumDataCategory): - self.data_category = EnumDataCategory(self.data_category) - - if self.size is not None and not isinstance(self.size, int): - self.size = int(self.size) - - if self.staging_url is not None and not isinstance(self.staging_url, URIorCURIE): - self.staging_url = URIorCURIE(self.staging_url) - - if self.release_url is not None and not isinstance(self.release_url, URIorCURIE): - self.release_url = URIorCURIE(self.release_url) - - if self.drs_uri is not None and not isinstance(self.drs_uri, URIorCURIE): - self.drs_uri = URIorCURIE(self.drs_uri) - - if self.hash is not None and not isinstance(self.hash, FileHash): - self.hash = FileHash(**as_dict(self.hash)) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class FileHash(YAMLRoot): - """ - Type and value of a file content hash. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["FileHash"] - class_class_curie: ClassVar[str] = "includedcc:FileHash" - class_name: ClassVar[str] = "FileHash" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.FileHash - - hash_type: Optional[Union[str, "EnumFileHashType"]] = None - hash_value: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self.hash_type is not None and not isinstance(self.hash_type, EnumFileHashType): - self.hash_type = EnumFileHashType(self.hash_type) - - if self.hash_value is not None and not isinstance(self.hash_value, str): - self.hash_value = str(self.hash_value) - - super().__post_init__(**kwargs) - - -@dataclass(repr=False) -class Dataset(YAMLRoot): - """ - Set of files grouped together for release. - """ - _inherited_slots: ClassVar[list[str]] = [] - - class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Dataset"] - class_class_curie: ClassVar[str] = "includedcc:Dataset" - class_name: ClassVar[str] = "Dataset" - class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Dataset - - dataset_id: Union[str, DatasetDatasetId] = None - name: Optional[str] = None - description: Optional[str] = None - do_id: Optional[Union[str, DOIDoId]] = None - file_id: Optional[Union[Union[str, FileFileId], list[Union[str, FileFileId]]]] = empty_list() - publication: Optional[Union[Union[dict, Publication], list[Union[dict, Publication]]]] = empty_list() - data_collection_start: Optional[str] = None - data_collection_end: Optional[str] = None - - def __post_init__(self, *_: str, **kwargs: Any): - if self._is_empty(self.dataset_id): - self.MissingRequiredField("dataset_id") - if not isinstance(self.dataset_id, DatasetDatasetId): - self.dataset_id = DatasetDatasetId(self.dataset_id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.do_id is not None and not isinstance(self.do_id, DOIDoId): - self.do_id = DOIDoId(self.do_id) - - if not isinstance(self.file_id, list): - self.file_id = [self.file_id] if self.file_id is not None else [] - self.file_id = [v if isinstance(v, FileFileId) else FileFileId(v) for v in self.file_id] - - if not isinstance(self.publication, list): - self.publication = [self.publication] if self.publication is not None else [] - self.publication = [v if isinstance(v, Publication) else Publication(**as_dict(v)) for v in self.publication] - - if self.data_collection_start is not None and not isinstance(self.data_collection_start, str): - self.data_collection_start = str(self.data_collection_start) - - if self.data_collection_end is not None and not isinstance(self.data_collection_end, str): - self.data_collection_end = str(self.data_collection_end) - - super().__post_init__(**kwargs) - - -# Enumerations -class EnumProgram(EnumDefinitionImpl): - """ - Funding programs relevant to inform operations. - """ - include = PermissibleValue( - text="include", - title="INCLUDE") - kf = PermissibleValue( - text="kf", - title="KF") - other = PermissibleValue( - text="other", - title="Other") - - _defn = EnumDefinition( - name="EnumProgram", - description="Funding programs relevant to inform operations.", - ) - -class EnumResearchDomain(EnumDefinitionImpl): - """ - Domains of Research used to find studies. - """ - behavior_and_behavior_mechanisms = PermissibleValue( - text="behavior_and_behavior_mechanisms", - title="Behavior and Behavior Mechanisms", - meaning=MESH["D001520"]) - congenital_heart_defects = PermissibleValue( - text="congenital_heart_defects", - title="Congenital Heart Defects", - meaning=MESH["D006330"]) - immune_system_diseases = PermissibleValue( - text="immune_system_diseases", - title="Immune System Diseases", - meaning=MESH["D007154"]) - hematologic_diseases = PermissibleValue( - text="hematologic_diseases", - title="Hematologic Diseases", - meaning=MESH["D006402"]) - neurodevelopment = PermissibleValue( - text="neurodevelopment", - title="Neurodevelopment", - meaning=MESH["D065886"]) - sleep_wake_disorders = PermissibleValue( - text="sleep_wake_disorders", - title="Sleep Wake Disorders", - meaning=MESH["D012893"]) - all_co_occurring_conditions = PermissibleValue( - text="all_co_occurring_conditions", - title="All Co-occurring Conditions", - meaning=MESH["D013568"]) - physical_fitness = PermissibleValue( - text="physical_fitness", - title="Physical Fitness", - meaning=MESH["D010809"]) - other = PermissibleValue( - text="other", - title="Other") - - _defn = EnumDefinition( - name="EnumResearchDomain", - description="Domains of Research used to find studies.", - ) - -class EnumParticipantLifespanStage(EnumDefinitionImpl): - """ - Stages of life during which participants may be recruited. - """ - fetal = PermissibleValue( - text="fetal", - title="Fetal", - description="Before birth") - neonatal = PermissibleValue( - text="neonatal", - title="Neonatal", - description="0-28 days old") - pediatric = PermissibleValue( - text="pediatric", - title="Pediatric", - description="Birth-17 years old") - adult = PermissibleValue( - text="adult", - title="Adult", - description="18+ years old") - - _defn = EnumDefinition( - name="EnumParticipantLifespanStage", - description="Stages of life during which participants may be recruited.", - ) - -class EnumStudyDesign(EnumDefinitionImpl): - """ - Approaches for collecting data, investigating interventions, and/or analyzing data. - """ - case_control = PermissibleValue( - text="case_control", - title="Case-Control") - case_set = PermissibleValue( - text="case_set", - title="Case Set") - control_set = PermissibleValue( - text="control_set", - title="Control Set") - clinical_trial = PermissibleValue( - text="clinical_trial", - title="Clinical Trial") - cross_sectional = PermissibleValue( - text="cross_sectional", - title="Cross-Sectional") - family_twins_trios = PermissibleValue( - text="family_twins_trios", - title="Family/Twins/Trios") - interventional = PermissibleValue( - text="interventional", - title="Interventional") - longitudinal = PermissibleValue( - text="longitudinal", - title="Longitudinal") - trial_readiness_study = PermissibleValue( - text="trial_readiness_study", - title="Trial Readiness Study") - tumor_vs_matched_normal = PermissibleValue( - text="tumor_vs_matched_normal", - title="Tumor vs Matched Normal") - - _defn = EnumDefinition( - name="EnumStudyDesign", - description="Approaches for collecting data, investigating interventions, and/or analyzing data.", - ) - -class EnumClinicalDataSourceType(EnumDefinitionImpl): - """ - Approaches to ascertain clinical information about a participant. - """ - medical_record = PermissibleValue( - text="medical_record", - title="Medical Record", - description="Data obtained directly from medical record") - investigator_assessment = PermissibleValue( - text="investigator_assessment", - title="Investigator Assessment", - description="Data obtained by examination, interview, etc. with investigator") - participant_or_caregiver_report = PermissibleValue( - text="participant_or_caregiver_report", - title="Participant or Caregiver Report", - description="Data obtained from survey, questionnaire, etc. filled out by participant or caregiver") - other = PermissibleValue( - text="other", - title="Other", - description="Data obtained from other source, such as tissue bank") - unknown = PermissibleValue( - text="unknown", - title="Unknown") - - _defn = EnumDefinition( - name="EnumClinicalDataSourceType", - description="Approaches to ascertain clinical information about a participant.", - ) - -class EnumDataCategory(EnumDefinitionImpl): - """ - Categories of data which may be collected about participants. - """ - unharmonized_demographic_clinical_data = PermissibleValue( - text="unharmonized_demographic_clinical_data", - title="Unharmonized Demographic/Clinical Data") - harmonized_demographic_clinical_data = PermissibleValue( - text="harmonized_demographic_clinical_data", - title="Harmonized Demographic/Clinical Data") - genomics = PermissibleValue( - text="genomics", - title="Genomics") - transcriptomics = PermissibleValue( - text="transcriptomics", - title="Transcriptomics") - epigenomics = PermissibleValue( - text="epigenomics", - title="Epigenomics") - proteomics = PermissibleValue( - text="proteomics", - title="Proteomics") - metabolomics = PermissibleValue( - text="metabolomics", - title="Metabolomics") - cognitive_behavioral = PermissibleValue( - text="cognitive_behavioral", - title="Cognitive/Behavioral") - immune_profiling = PermissibleValue( - text="immune_profiling", - title="Immune Profiling") - imaging = PermissibleValue( - text="imaging", - title="Imaging") - microbiome = PermissibleValue( - text="microbiome", - title="Microbiome") - fitness = PermissibleValue( - text="fitness", - title="Fitness") - physical_activity = PermissibleValue( - text="physical_activity", - title="Physical Activity") - other = PermissibleValue( - text="other", - title="Other") - sleep_study = PermissibleValue( - text="sleep_study", - title="Sleep Study") - - _defn = EnumDefinition( - name="EnumDataCategory", - description="Categories of data which may be collected about participants.", - ) - -class EnumSubjectType(EnumDefinitionImpl): - """ - Types of Subject entities - """ - participant = PermissibleValue( - text="participant", - description="Study participant with consent, assent, or waiver of consent.") - non_participant = PermissibleValue( - text="non_participant", - description="""An individual associated with a study who was not explictly consented, eg, the subject of a reported family history.""") - cell_line = PermissibleValue( - text="cell_line", - description="Cell Line") - animal_model = PermissibleValue( - text="animal_model", - description="Animal model") - group = PermissibleValue( - text="group", - description="A group of individuals or entities.") - other = PermissibleValue( - text="other", - description="A different entity type- ideally this will be resolved!") - - _defn = EnumDefinition( - name="EnumSubjectType", - description="Types of Subject entities", - ) - -class EnumDownSyndromeStatus(EnumDefinitionImpl): - """ - Down syndrome / chromosome 21 status - """ - d21 = PermissibleValue( - text="d21", - title="D21", - description="Disomy 21 (euploid)", - meaning=PATO["0001393"]) - t21 = PermissibleValue( - text="t21", - title="T21", - description="Trisomy 21 (Down syndrome)", - meaning=MONDO["0008608"]) - - _defn = EnumDefinition( - name="EnumDownSyndromeStatus", - description="Down syndrome / chromosome 21 status", - ) - -class EnumSex(EnumDefinitionImpl): - """ - Subject Sex - """ - female = PermissibleValue( - text="female", - title="Female", - meaning=NCIT["C16576"]) - male = PermissibleValue( - text="male", - title="Male", - meaning=NCIT["C20197"]) - other = PermissibleValue( - text="other", - title="Other", - meaning=NCIT["C17649"]) - unknown = PermissibleValue( - text="unknown", - title="Unknown", - meaning=NCIT["C17998"]) - - _defn = EnumDefinition( - name="EnumSex", - description="Subject Sex", - ) - -class EnumRace(EnumDefinitionImpl): - """ - Participant Race - """ - american_indian_or_alaska_native = PermissibleValue( - text="american_indian_or_alaska_native", - title="American Indian or Alaska Native", - meaning=NCIT["C41259"]) - asian = PermissibleValue( - text="asian", - title="Asian", - meaning=NCIT["C41260"]) - black_or_african_american = PermissibleValue( - text="black_or_african_american", - title="Black or African American", - meaning=NCIT["C16352"]) - more_than_one_race = PermissibleValue( - text="more_than_one_race", - title="More than one race", - meaning=NCIT["C67109"]) - native_hawaiian_or_other_pacific_islander = PermissibleValue( - text="native_hawaiian_or_other_pacific_islander", - title="Native Hawaiian or Other Pacific Islander", - meaning=NCIT["C41219"]) - other = PermissibleValue( - text="other", - title="Other", - meaning=NCIT["C17649"]) - white = PermissibleValue( - text="white", - title="White", - meaning=NCIT["C41261"]) - prefer_not_to_answer = PermissibleValue( - text="prefer_not_to_answer", - title="Prefer not to answer", - meaning=NCIT["C132222"]) - unknown = PermissibleValue( - text="unknown", - title="Unknown", - meaning=NCIT["C17998"]) - east_asian = PermissibleValue( - text="east_asian", - title="East Asian", - description="UK only; do not use for US data", - meaning=NCIT["C161419"]) - latin_american = PermissibleValue( - text="latin_american", - title="Latin American", - description="UK only; do not use for US data", - meaning=NCIT["C126531"]) - middle_eastern_or_north_african = PermissibleValue( - text="middle_eastern_or_north_african", - title="Middle Eastern or North African", - description="UK only; do not use for US data", - meaning=NCIT["C43866"]) - south_asian = PermissibleValue( - text="south_asian", - title="South Asian", - description="UK only; do not use for US data", - meaning=NCIT["C41263"]) - - _defn = EnumDefinition( - name="EnumRace", - description="Participant Race", - ) - -class EnumEthnicity(EnumDefinitionImpl): - """ - Participant ethnicity, specific to Hispanic or Latino. - """ - hispanic_or_latino = PermissibleValue( - text="hispanic_or_latino", - title="Hispanic or Latino", - meaning=NCIT["C17459"]) - not_hispanic_or_latino = PermissibleValue( - text="not_hispanic_or_latino", - title="Not Hispanic or Latino", - meaning=NCIT["C41222"]) - prefer_not_to_answer = PermissibleValue( - text="prefer_not_to_answer", - title="Prefer not to answer", - meaning=NCIT["C132222"]) - unknown = PermissibleValue( - text="unknown", - title="Unknown", - meaning=NCIT["C17998"]) - - _defn = EnumDefinition( - name="EnumEthnicity", - description="Participant ethnicity, specific to Hispanic or Latino.", - ) - -class EnumVitalStatus(EnumDefinitionImpl): - """ - Descriptions of a Subject's vital status - """ - dead = PermissibleValue( - text="dead", - title="Dead", - meaning=NCIT["C28554"]) - alive = PermissibleValue( - text="alive", - title="Alive", - meaning=NCIT["C37987"]) - - _defn = EnumDefinition( - name="EnumVitalStatus", - description="Descriptions of a Subject's vital status", - ) - -class EnumNull(EnumDefinitionImpl): - """ - Base enumeration providing null options. - """ - unknown = PermissibleValue( - text="unknown", - title="Unknown", - meaning=NCIT["C17998"]) - - _defn = EnumDefinition( - name="EnumNull", - description="Base enumeration providing null options.", - ) - -class EnumAssertionProvenance(EnumDefinitionImpl): - """ - Possible data sources for assertions. - """ - medical_record = PermissibleValue( - text="medical_record", - title="Medical Record", - description="Data obtained from a medical record") - investigator_assessment = PermissibleValue( - text="investigator_assessment", - title="Investigator Assessment", - description="Data obtained by examination, interview, etc. with investigator") - participant_or_caregiver_report = PermissibleValue( - text="participant_or_caregiver_report", - title="Participant or Caregiver Report", - description="Data obtained from survey, questionnaire, etc. filled out by participant or caregiver") - other = PermissibleValue( - text="other", - title="Other", - description="Data obtained from other source, such as tissue bank") - - _defn = EnumDefinition( - name="EnumAssertionProvenance", - description="Possible data sources for assertions.", - ) - -class EnumAvailabilityStatus(EnumDefinitionImpl): - """ - Is the biospecimen available for use? - """ - available = PermissibleValue( - text="available", - title="Available", - description="Biospecimen is Available", - meaning=IG2_BIOSPECIMEN_AVAILABILITY["available"]) - unavailable = PermissibleValue( - text="unavailable", - title="Unavailable", - description="Biospecimen is Unavailable", - meaning=IG2_BIOSPECIMEN_AVAILABILITY["unavailable"]) - - _defn = EnumDefinition( - name="EnumAvailabilityStatus", - description="Is the biospecimen available for use?", - ) - -class EnumSampleCollectionMethod(EnumDefinitionImpl): - """ - The approach used to collect the biospecimen. [LOINC](https://loinc.org) is recommended. - """ - _defn = EnumDefinition( - name="EnumSampleCollectionMethod", - description="The approach used to collect the biospecimen. [LOINC](https://loinc.org) is recommended.", - ) - -class EnumSite(EnumDefinitionImpl): - """ - The location of the specimen collection. [SNOMED Body Site](https://hl7.org/fhir/R4B/valueset-body-site.html) is - recommended. - """ - _defn = EnumDefinition( - name="EnumSite", - description="""The location of the specimen collection. [SNOMED Body Site](https://hl7.org/fhir/R4B/valueset-body-site.html) is recommended.""", - ) - -class EnumSpatialQualifiers(EnumDefinitionImpl): - """ - Any spatial/location qualifiers. - """ - _defn = EnumDefinition( - name="EnumSpatialQualifiers", - description="Any spatial/location qualifiers.", - ) - -class EnumLaterality(EnumDefinitionImpl): - """ - Laterality information for the site - """ - _defn = EnumDefinition( - name="EnumLaterality", - description="Laterality information for the site", - ) - -class EnumEDAMFormats(EnumDefinitionImpl): - """ - Data formats from the EDAM ontology. - """ - _defn = EnumDefinition( - name="EnumEDAMFormats", - description="Data formats from the EDAM ontology.", - ) - -class EnumEDAMDataTypes(EnumDefinitionImpl): - """ - Data types from the EDAM ontology. - """ - _defn = EnumDefinition( - name="EnumEDAMDataTypes", - description="Data types from the EDAM ontology.", - ) - -class EnumFileHashType(EnumDefinitionImpl): - """ - Types of file hashes supported. - """ - md5 = PermissibleValue( - text="md5", - title="MD5") - etag = PermissibleValue( - text="etag", - title="ETag") - sha1 = PermissibleValue( - text="sha1", - title="SHA-1") - - _defn = EnumDefinition( - name="EnumFileHashType", - description="Types of file hashes supported.", - ) - -# Slots -class slots: - pass - -slots.study_id = Slot(uri=INCLUDEDCC.study_id, name="study_id", curie=INCLUDEDCC.curie('study_id'), - model_uri=INCLUDEDCC.study_id, domain=None, range=Optional[Union[str, StudyStudyId]]) - -slots.do_id = Slot(uri=INCLUDEDCC.do_id, name="do_id", curie=INCLUDEDCC.curie('do_id'), - model_uri=INCLUDEDCC.do_id, domain=None, range=Optional[Union[str, DOIDoId]]) - -slots.subject_id = Slot(uri=INCLUDEDCC.subject_id, name="subject_id", curie=INCLUDEDCC.curie('subject_id'), - model_uri=INCLUDEDCC.subject_id, domain=None, range=Optional[Union[str, SubjectSubjectId]]) - -slots.assertion_id = Slot(uri=INCLUDEDCC.assertion_id, name="assertion_id", curie=INCLUDEDCC.curie('assertion_id'), - model_uri=INCLUDEDCC.assertion_id, domain=None, range=Optional[Union[str, SubjectAssertionAssertionId]]) - -slots.external_id = Slot(uri=INCLUDEDCC.external_id, name="external_id", curie=INCLUDEDCC.curie('external_id'), - model_uri=INCLUDEDCC.external_id, domain=None, range=Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]]) - -slots.parent_study = Slot(uri=INCLUDEDCC.parent_study, name="parent_study", curie=INCLUDEDCC.curie('parent_study'), - model_uri=INCLUDEDCC.parent_study, domain=None, range=Optional[Union[str, StudyStudyId]]) - -slots.funding_source = Slot(uri=INCLUDEDCC.funding_source, name="funding_source", curie=INCLUDEDCC.curie('funding_source'), - model_uri=INCLUDEDCC.funding_source, domain=None, range=Optional[Union[str, list[str]]]) - -slots.principal_investigator = Slot(uri=INCLUDEDCC.principal_investigator, name="principal_investigator", curie=INCLUDEDCC.curie('principal_investigator'), - model_uri=INCLUDEDCC.principal_investigator, domain=None, range=Union[Union[dict, Investigator], list[Union[dict, Investigator]]]) - -slots.study_title = Slot(uri=INCLUDEDCC.study_title, name="study_title", curie=INCLUDEDCC.curie('study_title'), - model_uri=INCLUDEDCC.study_title, domain=None, range=str) - -slots.study_code = Slot(uri=INCLUDEDCC.study_code, name="study_code", curie=INCLUDEDCC.curie('study_code'), - model_uri=INCLUDEDCC.study_code, domain=None, range=str) - -slots.study_short_name = Slot(uri=INCLUDEDCC.study_short_name, name="study_short_name", curie=INCLUDEDCC.curie('study_short_name'), - model_uri=INCLUDEDCC.study_short_name, domain=None, range=Optional[str]) - -slots.investigator_title = Slot(uri=INCLUDEDCC.investigator_title, name="investigator_title", curie=INCLUDEDCC.curie('investigator_title'), - model_uri=INCLUDEDCC.investigator_title, domain=None, range=Optional[str]) - -slots.name = Slot(uri=INCLUDEDCC.name, name="name", curie=INCLUDEDCC.curie('name'), - model_uri=INCLUDEDCC.name, domain=None, range=Optional[str]) - -slots.email = Slot(uri=INCLUDEDCC.email, name="email", curie=INCLUDEDCC.curie('email'), - model_uri=INCLUDEDCC.email, domain=None, range=Optional[str]) - -slots.institution = Slot(uri=INCLUDEDCC.institution, name="institution", curie=INCLUDEDCC.curie('institution'), - model_uri=INCLUDEDCC.institution, domain=None, range=Optional[str]) - -slots.program = Slot(uri=INCLUDEDCC.program, name="program", curie=INCLUDEDCC.curie('program'), - model_uri=INCLUDEDCC.program, domain=None, range=Union[Union[str, "EnumProgram"], list[Union[str, "EnumProgram"]]]) - -slots.study_description = Slot(uri=INCLUDEDCC.study_description, name="study_description", curie=INCLUDEDCC.curie('study_description'), - model_uri=INCLUDEDCC.study_description, domain=None, range=str) - -slots.website = Slot(uri=INCLUDEDCC.website, name="website", curie=INCLUDEDCC.curie('website'), - model_uri=INCLUDEDCC.website, domain=None, range=Optional[Union[str, URI]]) - -slots.contact = Slot(uri=INCLUDEDCC.contact, name="contact", curie=INCLUDEDCC.curie('contact'), - model_uri=INCLUDEDCC.contact, domain=None, range=Union[Union[dict, Investigator], list[Union[dict, Investigator]]]) - -slots.vbr = Slot(uri=INCLUDEDCC.vbr, name="vbr", curie=INCLUDEDCC.curie('vbr'), - model_uri=INCLUDEDCC.vbr, domain=None, range=Optional[Union[dict, VirtualBiorepository]]) - -slots.vbr_readme = Slot(uri=INCLUDEDCC.vbr_readme, name="vbr_readme", curie=INCLUDEDCC.curie('vbr_readme'), - model_uri=INCLUDEDCC.vbr_readme, domain=None, range=Optional[str]) - -slots.research_domain = Slot(uri=INCLUDEDCC.research_domain, name="research_domain", curie=INCLUDEDCC.curie('research_domain'), - model_uri=INCLUDEDCC.research_domain, domain=None, range=Union[Union[str, "EnumResearchDomain"], list[Union[str, "EnumResearchDomain"]]]) - -slots.participant_lifespan_stage = Slot(uri=INCLUDEDCC.participant_lifespan_stage, name="participant_lifespan_stage", curie=INCLUDEDCC.curie('participant_lifespan_stage'), - model_uri=INCLUDEDCC.participant_lifespan_stage, domain=None, range=Union[Union[str, "EnumParticipantLifespanStage"], list[Union[str, "EnumParticipantLifespanStage"]]]) - -slots.selection_criteria = Slot(uri=INCLUDEDCC.selection_criteria, name="selection_criteria", curie=INCLUDEDCC.curie('selection_criteria'), - model_uri=INCLUDEDCC.selection_criteria, domain=None, range=Optional[str]) - -slots.study_design = Slot(uri=INCLUDEDCC.study_design, name="study_design", curie=INCLUDEDCC.curie('study_design'), - model_uri=INCLUDEDCC.study_design, domain=None, range=Union[Union[str, "EnumStudyDesign"], list[Union[str, "EnumStudyDesign"]]]) - -slots.data_category = Slot(uri=INCLUDEDCC.data_category, name="data_category", curie=INCLUDEDCC.curie('data_category'), - model_uri=INCLUDEDCC.data_category, domain=None, range=Optional[Union[str, "EnumDataCategory"]]) - -slots.clinical_data_source_type = Slot(uri=INCLUDEDCC.clinical_data_source_type, name="clinical_data_source_type", curie=INCLUDEDCC.curie('clinical_data_source_type'), - model_uri=INCLUDEDCC.clinical_data_source_type, domain=None, range=Union[Union[str, "EnumClinicalDataSourceType"], list[Union[str, "EnumClinicalDataSourceType"]]]) - -slots.publication = Slot(uri=INCLUDEDCC.publication, name="publication", curie=INCLUDEDCC.curie('publication'), - model_uri=INCLUDEDCC.publication, domain=None, range=Optional[Union[Union[dict, Publication], list[Union[dict, Publication]]]]) - -slots.expected_number_of_participants = Slot(uri=INCLUDEDCC.expected_number_of_participants, name="expected_number_of_participants", curie=INCLUDEDCC.curie('expected_number_of_participants'), - model_uri=INCLUDEDCC.expected_number_of_participants, domain=None, range=int) - -slots.actual_number_of_participants = Slot(uri=INCLUDEDCC.actual_number_of_participants, name="actual_number_of_participants", curie=INCLUDEDCC.curie('actual_number_of_participants'), - model_uri=INCLUDEDCC.actual_number_of_participants, domain=None, range=int) - -slots.acknowledgments = Slot(uri=INCLUDEDCC.acknowledgments, name="acknowledgments", curie=INCLUDEDCC.curie('acknowledgments'), - model_uri=INCLUDEDCC.acknowledgments, domain=None, range=Optional[str]) - -slots.citation_statement = Slot(uri=INCLUDEDCC.citation_statement, name="citation_statement", curie=INCLUDEDCC.curie('citation_statement'), - model_uri=INCLUDEDCC.citation_statement, domain=None, range=Optional[str]) - -slots.bibliographic_reference = Slot(uri=INCLUDEDCC.bibliographic_reference, name="bibliographic_reference", curie=INCLUDEDCC.curie('bibliographic_reference'), - model_uri=INCLUDEDCC.bibliographic_reference, domain=None, range=Optional[str]) - -slots.organism_type = Slot(uri=INCLUDEDCC.organism_type, name="organism_type", curie=INCLUDEDCC.curie('organism_type'), - model_uri=INCLUDEDCC.organism_type, domain=None, range=Optional[Union[str, URIorCURIE]]) - -slots.subject_type = Slot(uri=INCLUDEDCC.subject_type, name="subject_type", curie=INCLUDEDCC.curie('subject_type'), - model_uri=INCLUDEDCC.subject_type, domain=None, range=Union[str, "EnumSubjectType"]) - -slots.sex = Slot(uri=INCLUDEDCC.sex, name="sex", curie=INCLUDEDCC.curie('sex'), - model_uri=INCLUDEDCC.sex, domain=None, range=Union[str, "EnumSex"]) - -slots.race = Slot(uri=INCLUDEDCC.race, name="race", curie=INCLUDEDCC.curie('race'), - model_uri=INCLUDEDCC.race, domain=None, range=Union[Union[str, "EnumRace"], list[Union[str, "EnumRace"]]]) - -slots.ethnicity = Slot(uri=INCLUDEDCC.ethnicity, name="ethnicity", curie=INCLUDEDCC.curie('ethnicity'), - model_uri=INCLUDEDCC.ethnicity, domain=None, range=Union[str, "EnumEthnicity"]) - -slots.down_syndrome_status = Slot(uri=INCLUDEDCC.down_syndrome_status, name="down_syndrome_status", curie=INCLUDEDCC.curie('down_syndrome_status'), - model_uri=INCLUDEDCC.down_syndrome_status, domain=None, range=Union[str, "EnumDownSyndromeStatus"]) - -slots.age_at_first_engagement = Slot(uri=INCLUDEDCC.age_at_first_engagement, name="age_at_first_engagement", curie=INCLUDEDCC.curie('age_at_first_engagement'), - model_uri=INCLUDEDCC.age_at_first_engagement, domain=None, range=Optional[int]) - -slots.vital_status = Slot(uri=INCLUDEDCC.vital_status, name="vital_status", curie=INCLUDEDCC.curie('vital_status'), - model_uri=INCLUDEDCC.vital_status, domain=None, range=Optional[Union[str, "EnumVitalStatus"]]) - -slots.age_at_last_vital_status = Slot(uri=INCLUDEDCC.age_at_last_vital_status, name="age_at_last_vital_status", curie=INCLUDEDCC.curie('age_at_last_vital_status'), - model_uri=INCLUDEDCC.age_at_last_vital_status, domain=None, range=Optional[int]) - -slots.assertion_provenance = Slot(uri=INCLUDEDCC.assertion_provenance, name="assertion_provenance", curie=INCLUDEDCC.curie('assertion_provenance'), - model_uri=INCLUDEDCC.assertion_provenance, domain=None, range=Optional[Union[str, "EnumAssertionProvenance"]]) - -slots.age_at_assertion = Slot(uri=INCLUDEDCC.age_at_assertion, name="age_at_assertion", curie=INCLUDEDCC.curie('age_at_assertion'), - model_uri=INCLUDEDCC.age_at_assertion, domain=None, range=Optional[int]) - -slots.age_at_event = Slot(uri=INCLUDEDCC.age_at_event, name="age_at_event", curie=INCLUDEDCC.curie('age_at_event'), - model_uri=INCLUDEDCC.age_at_event, domain=None, range=Optional[int]) - -slots.age_at_resolution = Slot(uri=INCLUDEDCC.age_at_resolution, name="age_at_resolution", curie=INCLUDEDCC.curie('age_at_resolution'), - model_uri=INCLUDEDCC.age_at_resolution, domain=None, range=Optional[int]) - -slots.concept = Slot(uri=INCLUDEDCC.concept, name="concept", curie=INCLUDEDCC.curie('concept'), - model_uri=INCLUDEDCC.concept, domain=None, range=Optional[Union[Union[str, ConceptConceptCurie], list[Union[str, ConceptConceptCurie]]]]) - -slots.concept_curie = Slot(uri=INCLUDEDCC.concept_curie, name="concept_curie", curie=INCLUDEDCC.curie('concept_curie'), - model_uri=INCLUDEDCC.concept_curie, domain=None, range=Optional[Union[str, URIorCURIE]]) - -slots.display = Slot(uri=INCLUDEDCC.display, name="display", curie=INCLUDEDCC.curie('display'), - model_uri=INCLUDEDCC.display, domain=None, range=Optional[str]) - -slots.concept_source = Slot(uri=INCLUDEDCC.concept_source, name="concept_source", curie=INCLUDEDCC.curie('concept_source'), - model_uri=INCLUDEDCC.concept_source, domain=None, range=Optional[str]) - -slots.value_concept = Slot(uri=INCLUDEDCC.value_concept, name="value_concept", curie=INCLUDEDCC.curie('value_concept'), - model_uri=INCLUDEDCC.value_concept, domain=None, range=Optional[Union[Union[str, ConceptConceptCurie], list[Union[str, ConceptConceptCurie]]]]) - -slots.value_number = Slot(uri=INCLUDEDCC.value_number, name="value_number", curie=INCLUDEDCC.curie('value_number'), - model_uri=INCLUDEDCC.value_number, domain=None, range=Optional[float]) - -slots.value_source = Slot(uri=INCLUDEDCC.value_source, name="value_source", curie=INCLUDEDCC.curie('value_source'), - model_uri=INCLUDEDCC.value_source, domain=None, range=Optional[str]) - -slots.value_unit = Slot(uri=INCLUDEDCC.value_unit, name="value_unit", curie=INCLUDEDCC.curie('value_unit'), - model_uri=INCLUDEDCC.value_unit, domain=None, range=Optional[Union[str, ConceptConceptCurie]]) - -slots.value_unit_source = Slot(uri=INCLUDEDCC.value_unit_source, name="value_unit_source", curie=INCLUDEDCC.curie('value_unit_source'), - model_uri=INCLUDEDCC.value_unit_source, domain=None, range=Optional[str]) - -slots.sample_id = Slot(uri=INCLUDEDCC.sample_id, name="sample_id", curie=INCLUDEDCC.curie('sample_id'), - model_uri=INCLUDEDCC.sample_id, domain=None, range=Optional[Union[str, SampleSampleId]]) - -slots.parent_sample_id = Slot(uri=INCLUDEDCC.parent_sample_id, name="parent_sample_id", curie=INCLUDEDCC.curie('parent_sample_id'), - model_uri=INCLUDEDCC.parent_sample_id, domain=None, range=Optional[Union[str, SampleSampleId]]) - -slots.biospecimen_collection_id = Slot(uri=INCLUDEDCC.biospecimen_collection_id, name="biospecimen_collection_id", curie=INCLUDEDCC.curie('biospecimen_collection_id'), - model_uri=INCLUDEDCC.biospecimen_collection_id, domain=None, range=Optional[Union[str, BiospecimenCollectionBiospecimenCollectionId]]) - -slots.aliquot_id = Slot(uri=INCLUDEDCC.aliquot_id, name="aliquot_id", curie=INCLUDEDCC.curie('aliquot_id'), - model_uri=INCLUDEDCC.aliquot_id, domain=None, range=Optional[Union[str, AliquotAliquotId]]) - -slots.sample_type = Slot(uri=INCLUDEDCC.sample_type, name="sample_type", curie=INCLUDEDCC.curie('sample_type'), - model_uri=INCLUDEDCC.sample_type, domain=None, range=Union[str, URIorCURIE]) - -slots.processing = Slot(uri=INCLUDEDCC.processing, name="processing", curie=INCLUDEDCC.curie('processing'), - model_uri=INCLUDEDCC.processing, domain=None, range=Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]]) - -slots.availablity_status = Slot(uri=INCLUDEDCC.availablity_status, name="availablity_status", curie=INCLUDEDCC.curie('availablity_status'), - model_uri=INCLUDEDCC.availablity_status, domain=None, range=Optional[Union[str, "EnumAvailabilityStatus"]]) - -slots.storage_method = Slot(uri=INCLUDEDCC.storage_method, name="storage_method", curie=INCLUDEDCC.curie('storage_method'), - model_uri=INCLUDEDCC.storage_method, domain=None, range=Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]]) - -slots.quantity_number = Slot(uri=INCLUDEDCC.quantity_number, name="quantity_number", curie=INCLUDEDCC.curie('quantity_number'), - model_uri=INCLUDEDCC.quantity_number, domain=None, range=Optional[float]) - -slots.quantity_unit = Slot(uri=INCLUDEDCC.quantity_unit, name="quantity_unit", curie=INCLUDEDCC.curie('quantity_unit'), - model_uri=INCLUDEDCC.quantity_unit, domain=None, range=Optional[Union[str, ConceptConceptCurie]]) - -slots.concentration_number = Slot(uri=INCLUDEDCC.concentration_number, name="concentration_number", curie=INCLUDEDCC.curie('concentration_number'), - model_uri=INCLUDEDCC.concentration_number, domain=None, range=Optional[float]) - -slots.concentration_unit = Slot(uri=INCLUDEDCC.concentration_unit, name="concentration_unit", curie=INCLUDEDCC.curie('concentration_unit'), - model_uri=INCLUDEDCC.concentration_unit, domain=None, range=Optional[Union[str, ConceptConceptCurie]]) - -slots.age_at_collection = Slot(uri=INCLUDEDCC.age_at_collection, name="age_at_collection", curie=INCLUDEDCC.curie('age_at_collection'), - model_uri=INCLUDEDCC.age_at_collection, domain=None, range=Optional[float]) - -slots.method = Slot(uri=INCLUDEDCC.method, name="method", curie=INCLUDEDCC.curie('method'), - model_uri=INCLUDEDCC.method, domain=None, range=Optional[Union[str, "EnumSampleCollectionMethod"]]) - -slots.site = Slot(uri=INCLUDEDCC.site, name="site", curie=INCLUDEDCC.curie('site'), - model_uri=INCLUDEDCC.site, domain=None, range=Optional[Union[str, "EnumSite"]]) - -slots.spatial_qualifier = Slot(uri=INCLUDEDCC.spatial_qualifier, name="spatial_qualifier", curie=INCLUDEDCC.curie('spatial_qualifier'), - model_uri=INCLUDEDCC.spatial_qualifier, domain=None, range=Optional[Union[str, "EnumSpatialQualifiers"]]) - -slots.laterality = Slot(uri=INCLUDEDCC.laterality, name="laterality", curie=INCLUDEDCC.curie('laterality'), - model_uri=INCLUDEDCC.laterality, domain=None, range=Optional[Union[str, "EnumLaterality"]]) - -slots.encounter_id = Slot(uri=INCLUDEDCC.encounter_id, name="encounter_id", curie=INCLUDEDCC.curie('encounter_id'), - model_uri=INCLUDEDCC.encounter_id, domain=None, range=Optional[Union[str, EncounterEncounterId]]) - -slots.description = Slot(uri=INCLUDEDCC.description, name="description", curie=INCLUDEDCC.curie('description'), - model_uri=INCLUDEDCC.description, domain=None, range=Optional[str]) - -slots.encounter_definition_id = Slot(uri=INCLUDEDCC.encounter_definition_id, name="encounter_definition_id", curie=INCLUDEDCC.curie('encounter_definition_id'), - model_uri=INCLUDEDCC.encounter_definition_id, domain=None, range=Optional[Union[str, EncounterDefinitionEncounterDefinitionId]]) - -slots.activity_definition_id = Slot(uri=INCLUDEDCC.activity_definition_id, name="activity_definition_id", curie=INCLUDEDCC.curie('activity_definition_id'), - model_uri=INCLUDEDCC.activity_definition_id, domain=None, range=Optional[Union[str, ActivityDefinitionActivityDefinitionId]]) - -slots.file_id = Slot(uri=INCLUDEDCC.file_id, name="file_id", curie=INCLUDEDCC.curie('file_id'), - model_uri=INCLUDEDCC.file_id, domain=None, range=Optional[Union[str, FileFileId]]) - -slots.filename = Slot(uri=INCLUDEDCC.filename, name="filename", curie=INCLUDEDCC.curie('filename'), - model_uri=INCLUDEDCC.filename, domain=None, range=Optional[str]) - -slots.format = Slot(uri=INCLUDEDCC.format, name="format", curie=INCLUDEDCC.curie('format'), - model_uri=INCLUDEDCC.format, domain=None, range=Optional[Union[str, "EnumEDAMFormats"]]) - -slots.data_type = Slot(uri=INCLUDEDCC.data_type, name="data_type", curie=INCLUDEDCC.curie('data_type'), - model_uri=INCLUDEDCC.data_type, domain=None, range=Optional[Union[str, "EnumEDAMDataTypes"]]) - -slots.size = Slot(uri=INCLUDEDCC.size, name="size", curie=INCLUDEDCC.curie('size'), - model_uri=INCLUDEDCC.size, domain=None, range=Optional[int]) - -slots.staging_url = Slot(uri=INCLUDEDCC.staging_url, name="staging_url", curie=INCLUDEDCC.curie('staging_url'), - model_uri=INCLUDEDCC.staging_url, domain=None, range=Optional[Union[str, URIorCURIE]]) - -slots.release_url = Slot(uri=INCLUDEDCC.release_url, name="release_url", curie=INCLUDEDCC.curie('release_url'), - model_uri=INCLUDEDCC.release_url, domain=None, range=Optional[Union[str, URIorCURIE]]) - -slots.drs_uri = Slot(uri=INCLUDEDCC.drs_uri, name="drs_uri", curie=INCLUDEDCC.curie('drs_uri'), - model_uri=INCLUDEDCC.drs_uri, domain=None, range=Optional[Union[str, URIorCURIE]]) - -slots.hash = Slot(uri=INCLUDEDCC.hash, name="hash", curie=INCLUDEDCC.curie('hash'), - model_uri=INCLUDEDCC.hash, domain=None, range=Optional[Union[dict, FileHash]]) - -slots.hash_type = Slot(uri=INCLUDEDCC.hash_type, name="hash_type", curie=INCLUDEDCC.curie('hash_type'), - model_uri=INCLUDEDCC.hash_type, domain=None, range=Optional[Union[str, "EnumFileHashType"]]) - -slots.hash_value = Slot(uri=INCLUDEDCC.hash_value, name="hash_value", curie=INCLUDEDCC.curie('hash_value'), - model_uri=INCLUDEDCC.hash_value, domain=None, range=Optional[str]) - -slots.dataset_id = Slot(uri=INCLUDEDCC.dataset_id, name="dataset_id", curie=INCLUDEDCC.curie('dataset_id'), - model_uri=INCLUDEDCC.dataset_id, domain=None, range=Optional[Union[str, DatasetDatasetId]]) - -slots.data_collection_start = Slot(uri=INCLUDEDCC.data_collection_start, name="data_collection_start", curie=INCLUDEDCC.curie('data_collection_start'), - model_uri=INCLUDEDCC.data_collection_start, domain=None, range=Optional[str]) - -slots.data_collection_end = Slot(uri=INCLUDEDCC.data_collection_end, name="data_collection_end", curie=INCLUDEDCC.curie('data_collection_end'), - model_uri=INCLUDEDCC.data_collection_end, domain=None, range=Optional[str]) - -slots.Study_study_id = Slot(uri=INCLUDEDCC.study_id, name="Study_study_id", curie=INCLUDEDCC.curie('study_id'), - model_uri=INCLUDEDCC.Study_study_id, domain=Study, range=Union[str, StudyStudyId]) - -slots.StudyMetadata_study_id = Slot(uri=INCLUDEDCC.study_id, name="StudyMetadata_study_id", curie=INCLUDEDCC.curie('study_id'), - model_uri=INCLUDEDCC.StudyMetadata_study_id, domain=StudyMetadata, range=Union[str, StudyMetadataStudyId]) - -slots.StudyMetadata_data_category = Slot(uri=INCLUDEDCC.data_category, name="StudyMetadata_data_category", curie=INCLUDEDCC.curie('data_category'), - model_uri=INCLUDEDCC.StudyMetadata_data_category, domain=StudyMetadata, range=Union[Union[str, "EnumDataCategory"], list[Union[str, "EnumDataCategory"]]]) - -slots.DOI_do_id = Slot(uri=INCLUDEDCC.do_id, name="DOI_do_id", curie=INCLUDEDCC.curie('do_id'), - model_uri=INCLUDEDCC.DOI_do_id, domain=DOI, range=Union[str, DOIDoId]) - -slots.Subject_subject_id = Slot(uri=INCLUDEDCC.subject_id, name="Subject_subject_id", curie=INCLUDEDCC.curie('subject_id'), - model_uri=INCLUDEDCC.Subject_subject_id, domain=Subject, range=Union[str, SubjectSubjectId]) - -slots.Demographics_subject_id = Slot(uri=INCLUDEDCC.subject_id, name="Demographics_subject_id", curie=INCLUDEDCC.curie('subject_id'), - model_uri=INCLUDEDCC.Demographics_subject_id, domain=Demographics, range=Union[str, DemographicsSubjectId]) - -slots.SubjectAssertion_assertion_id = Slot(uri=INCLUDEDCC.assertion_id, name="SubjectAssertion_assertion_id", curie=INCLUDEDCC.curie('assertion_id'), - model_uri=INCLUDEDCC.SubjectAssertion_assertion_id, domain=SubjectAssertion, range=Union[str, SubjectAssertionAssertionId]) - -slots.Concept_concept_curie = Slot(uri=INCLUDEDCC.concept_curie, name="Concept_concept_curie", curie=INCLUDEDCC.curie('concept_curie'), - model_uri=INCLUDEDCC.Concept_concept_curie, domain=Concept, range=Union[str, ConceptConceptCurie]) - -slots.Sample_sample_id = Slot(uri=INCLUDEDCC.sample_id, name="Sample_sample_id", curie=INCLUDEDCC.curie('sample_id'), - model_uri=INCLUDEDCC.Sample_sample_id, domain=Sample, range=Union[str, SampleSampleId]) - -slots.Sample_biospecimen_collection_id = Slot(uri=INCLUDEDCC.biospecimen_collection_id, name="Sample_biospecimen_collection_id", curie=INCLUDEDCC.curie('biospecimen_collection_id'), - model_uri=INCLUDEDCC.Sample_biospecimen_collection_id, domain=Sample, range=Optional[Union[str, BiospecimenCollectionBiospecimenCollectionId]]) - -slots.BiospecimenCollection_biospecimen_collection_id = Slot(uri=INCLUDEDCC.biospecimen_collection_id, name="BiospecimenCollection_biospecimen_collection_id", curie=INCLUDEDCC.curie('biospecimen_collection_id'), - model_uri=INCLUDEDCC.BiospecimenCollection_biospecimen_collection_id, domain=BiospecimenCollection, range=Union[str, BiospecimenCollectionBiospecimenCollectionId]) - -slots.Aliquot_aliquot_id = Slot(uri=INCLUDEDCC.aliquot_id, name="Aliquot_aliquot_id", curie=INCLUDEDCC.curie('aliquot_id'), - model_uri=INCLUDEDCC.Aliquot_aliquot_id, domain=Aliquot, range=Union[str, AliquotAliquotId]) - -slots.Encounter_encounter_id = Slot(uri=INCLUDEDCC.encounter_id, name="Encounter_encounter_id", curie=INCLUDEDCC.curie('encounter_id'), - model_uri=INCLUDEDCC.Encounter_encounter_id, domain=Encounter, range=Union[str, EncounterEncounterId]) - -slots.EncounterDefinition_encounter_definition_id = Slot(uri=INCLUDEDCC.encounter_definition_id, name="EncounterDefinition_encounter_definition_id", curie=INCLUDEDCC.curie('encounter_definition_id'), - model_uri=INCLUDEDCC.EncounterDefinition_encounter_definition_id, domain=EncounterDefinition, range=Union[str, EncounterDefinitionEncounterDefinitionId]) - -slots.EncounterDefinition_activity_definition_id = Slot(uri=INCLUDEDCC.activity_definition_id, name="EncounterDefinition_activity_definition_id", curie=INCLUDEDCC.curie('activity_definition_id'), - model_uri=INCLUDEDCC.EncounterDefinition_activity_definition_id, domain=EncounterDefinition, range=Optional[Union[Union[str, ActivityDefinitionActivityDefinitionId], list[Union[str, ActivityDefinitionActivityDefinitionId]]]]) - -slots.ActivityDefinition_activity_definition_id = Slot(uri=INCLUDEDCC.activity_definition_id, name="ActivityDefinition_activity_definition_id", curie=INCLUDEDCC.curie('activity_definition_id'), - model_uri=INCLUDEDCC.ActivityDefinition_activity_definition_id, domain=ActivityDefinition, range=Union[str, ActivityDefinitionActivityDefinitionId]) - -slots.File_file_id = Slot(uri=INCLUDEDCC.file_id, name="File_file_id", curie=INCLUDEDCC.curie('file_id'), - model_uri=INCLUDEDCC.File_file_id, domain=File, range=Union[str, FileFileId]) - -slots.File_subject_id = Slot(uri=INCLUDEDCC.subject_id, name="File_subject_id", curie=INCLUDEDCC.curie('subject_id'), - model_uri=INCLUDEDCC.File_subject_id, domain=File, range=Optional[Union[Union[str, SubjectSubjectId], list[Union[str, SubjectSubjectId]]]]) - -slots.File_sample_id = Slot(uri=INCLUDEDCC.sample_id, name="File_sample_id", curie=INCLUDEDCC.curie('sample_id'), - model_uri=INCLUDEDCC.File_sample_id, domain=File, range=Optional[Union[Union[str, SampleSampleId], list[Union[str, SampleSampleId]]]]) - -slots.Dataset_dataset_id = Slot(uri=INCLUDEDCC.dataset_id, name="Dataset_dataset_id", curie=INCLUDEDCC.curie('dataset_id'), - model_uri=INCLUDEDCC.Dataset_dataset_id, domain=Dataset, range=Union[str, DatasetDatasetId]) - -slots.Dataset_file_id = Slot(uri=INCLUDEDCC.file_id, name="Dataset_file_id", curie=INCLUDEDCC.curie('file_id'), - model_uri=INCLUDEDCC.Dataset_file_id, domain=Dataset, range=Optional[Union[Union[str, FileFileId], list[Union[str, FileFileId]]]]) diff --git a/src/include_access_model/datamodel/include_access_model_pydantic.py b/src/include_access_model/datamodel/include_access_model_pydantic.py deleted file mode 100644 index 5fef463..0000000 --- a/src/include_access_model/datamodel/include_access_model_pydantic.py +++ /dev/null @@ -1,882 +0,0 @@ -from __future__ import annotations - -import re -import sys -from datetime import ( - date, - datetime, - time -) -from decimal import Decimal -from enum import Enum -from typing import ( - Any, - ClassVar, - Literal, - Optional, - Union -) - -from pydantic import ( - BaseModel, - ConfigDict, - Field, - RootModel, - SerializationInfo, - SerializerFunctionWrapHandler, - field_validator, - model_serializer -) - - -metamodel_version = "None" -version = "None" - - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - serialize_by_alias = True, - validate_by_name = True, - validate_assignment = True, - validate_default = True, - extra = "forbid", - arbitrary_types_allowed = True, - use_enum_values = True, - strict = False, - ) - - @model_serializer(mode='wrap', when_used='unless-none') - def treat_empty_lists_as_none( - self, handler: SerializerFunctionWrapHandler, - info: SerializationInfo) -> dict[str, Any]: - if info.exclude_none: - _instance = self.model_copy() - for field, field_info in type(_instance).model_fields.items(): - if getattr(_instance, field) == [] and not( - field_info.is_required()): - setattr(_instance, field, None) - else: - _instance = self - return handler(_instance, info) - - - -class LinkMLMeta(RootModel): - root: dict[str, Any] = {} - model_config = ConfigDict(frozen=True) - - def __getattr__(self, key:str): - return getattr(self.root, key) - - def __getitem__(self, key:str): - return self.root[key] - - def __setitem__(self, key:str, value): - self.root[key] = value - - def __contains__(self, key:str) -> bool: - return key in self.root - - -linkml_meta = LinkMLMeta({'default_prefix': 'includedcc', - 'default_range': 'string', - 'description': 'LinkML Schema for the internal INCLUDE DCC Access Model', - 'id': 'https://includedcc.org/include-access-model', - 'imports': ['linkml:types'], - 'license': 'MIT', - 'name': 'include-access-model', - 'prefixes': {'HP': {'prefix_prefix': 'HP', - 'prefix_reference': 'http://purl.obolibrary.org/obo/HP_'}, - 'MONDO': {'prefix_prefix': 'MONDO', - 'prefix_reference': 'http://purl.obolibrary.org/obo/MONDO_'}, - 'NCIT': {'prefix_prefix': 'NCIT', - 'prefix_reference': 'http://purl.obolibrary.org/obo/NCIT_'}, - 'PATO': {'prefix_prefix': 'PATO', - 'prefix_reference': 'http://purl.obolibrary.org/obo/PATO_'}, - 'cdc_race_eth': {'prefix_prefix': 'cdc_race_eth', - 'prefix_reference': 'urn:oid:2.16.840.1.113883.6.238/'}, - 'hl7_null': {'prefix_prefix': 'hl7_null', - 'prefix_reference': 'http://terminology.hl7.org/CodeSystem/v3-NullFlavor/'}, - 'ig2_biospecimen_availability': {'prefix_prefix': 'ig2_biospecimen_availability', - 'prefix_reference': 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/biospecimen-availability/'}, - 'ig2dac': {'prefix_prefix': 'ig2dac', - 'prefix_reference': 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code/'}, - 'ig2dat': {'prefix_prefix': 'ig2dat', - 'prefix_reference': 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type/'}, - 'ig_dob_method': {'prefix_prefix': 'ig_dob_method', - 'prefix_reference': 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/'}, - 'igcondtype': {'prefix_prefix': 'igcondtype', - 'prefix_reference': 'https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/'}, - 'includedcc': {'prefix_prefix': 'includedcc', - 'prefix_reference': 'https://includedcc.org/include-access-model/'}, - 'linkml': {'prefix_prefix': 'linkml', - 'prefix_reference': 'https://w3id.org/linkml/'}, - 'mesh': {'prefix_prefix': 'mesh', - 'prefix_reference': 'http://id.nlm.nih.gov/mesh/'}, - 'schema': {'prefix_prefix': 'schema', - 'prefix_reference': 'http://schema.org/'}, - 'snomed_ct': {'prefix_prefix': 'snomed_ct', - 'prefix_reference': 'http://snomed.info/id/'}}, - 'see_also': ['https://includedcc.github.io/include-access-model'], - 'source_file': 'src/include_access_model/schema/include_access_model.yaml', - 'title': 'INCLUDE DCC Access Model'} ) - -class EnumProgram(str, Enum): - """ - Funding programs relevant to inform operations. - """ - INCLUDE = "include" - KF = "kf" - Other = "other" - - -class EnumResearchDomain(str, Enum): - """ - Domains of Research used to find studies. - """ - Behavior_and_Behavior_Mechanisms = "behavior_and_behavior_mechanisms" - Congenital_Heart_Defects = "congenital_heart_defects" - Immune_System_Diseases = "immune_system_diseases" - Hematologic_Diseases = "hematologic_diseases" - Neurodevelopment = "neurodevelopment" - Sleep_Wake_Disorders = "sleep_wake_disorders" - All_Co_occurring_Conditions = "all_co_occurring_conditions" - Physical_Fitness = "physical_fitness" - Other = "other" - - -class EnumParticipantLifespanStage(str, Enum): - """ - Stages of life during which participants may be recruited. - """ - Fetal = "fetal" - """ - Before birth - """ - Neonatal = "neonatal" - """ - 0-28 days old - """ - Pediatric = "pediatric" - """ - Birth-17 years old - """ - Adult = "adult" - """ - 18+ years old - """ - - -class EnumStudyDesign(str, Enum): - """ - Approaches for collecting data, investigating interventions, and/or analyzing data. - """ - Case_Control = "case_control" - Case_Set = "case_set" - Control_Set = "control_set" - Clinical_Trial = "clinical_trial" - Cross_Sectional = "cross_sectional" - FamilySOLIDUSTwinsSOLIDUSTrios = "family_twins_trios" - Interventional = "interventional" - Longitudinal = "longitudinal" - Trial_Readiness_Study = "trial_readiness_study" - Tumor_vs_Matched_Normal = "tumor_vs_matched_normal" - - -class EnumClinicalDataSourceType(str, Enum): - """ - Approaches to ascertain clinical information about a participant. - """ - Medical_Record = "medical_record" - """ - Data obtained directly from medical record - """ - Investigator_Assessment = "investigator_assessment" - """ - Data obtained by examination, interview, etc. with investigator - """ - Participant_or_Caregiver_Report = "participant_or_caregiver_report" - """ - Data obtained from survey, questionnaire, etc. filled out by participant or caregiver - """ - Other = "other" - """ - Data obtained from other source, such as tissue bank - """ - Unknown = "unknown" - - -class EnumDataCategory(str, Enum): - """ - Categories of data which may be collected about participants. - """ - Unharmonized_DemographicSOLIDUSClinical_Data = "unharmonized_demographic_clinical_data" - Harmonized_DemographicSOLIDUSClinical_Data = "harmonized_demographic_clinical_data" - Genomics = "genomics" - Transcriptomics = "transcriptomics" - Epigenomics = "epigenomics" - Proteomics = "proteomics" - Metabolomics = "metabolomics" - CognitiveSOLIDUSBehavioral = "cognitive_behavioral" - Immune_Profiling = "immune_profiling" - Imaging = "imaging" - Microbiome = "microbiome" - Fitness = "fitness" - Physical_Activity = "physical_activity" - Other = "other" - Sleep_Study = "sleep_study" - - -class EnumSubjectType(str, Enum): - """ - Types of Subject entities - """ - participant = "participant" - """ - Study participant with consent, assent, or waiver of consent. - """ - non_participant = "non_participant" - """ - An individual associated with a study who was not explictly consented, eg, the subject of a reported family history. - """ - cell_line = "cell_line" - """ - Cell Line - """ - animal_model = "animal_model" - """ - Animal model - """ - group = "group" - """ - A group of individuals or entities. - """ - other = "other" - """ - A different entity type- ideally this will be resolved! - """ - - -class EnumDownSyndromeStatus(str, Enum): - """ - Down syndrome / chromosome 21 status - """ - D21 = "d21" - """ - Disomy 21 (euploid) - """ - T21 = "t21" - """ - Trisomy 21 (Down syndrome) - """ - - -class EnumSex(str, Enum): - """ - Subject Sex - """ - Female = "female" - Male = "male" - Other = "other" - Unknown = "unknown" - - -class EnumRace(str, Enum): - """ - Participant Race - """ - American_Indian_or_Alaska_Native = "american_indian_or_alaska_native" - Asian = "asian" - Black_or_African_American = "black_or_african_american" - More_than_one_race = "more_than_one_race" - Native_Hawaiian_or_Other_Pacific_Islander = "native_hawaiian_or_other_pacific_islander" - Other = "other" - White = "white" - Prefer_not_to_answer = "prefer_not_to_answer" - Unknown = "unknown" - East_Asian = "east_asian" - """ - UK only; do not use for US data - """ - Latin_American = "latin_american" - """ - UK only; do not use for US data - """ - Middle_Eastern_or_North_African = "middle_eastern_or_north_african" - """ - UK only; do not use for US data - """ - South_Asian = "south_asian" - """ - UK only; do not use for US data - """ - - -class EnumEthnicity(str, Enum): - """ - Participant ethnicity, specific to Hispanic or Latino. - """ - Hispanic_or_Latino = "hispanic_or_latino" - Not_Hispanic_or_Latino = "not_hispanic_or_latino" - Prefer_not_to_answer = "prefer_not_to_answer" - Unknown = "unknown" - - -class EnumVitalStatus(str, Enum): - """ - Descriptions of a Subject's vital status - """ - Dead = "dead" - Alive = "alive" - - -class EnumNull(str, Enum): - """ - Base enumeration providing null options. - """ - Unknown = "unknown" - - -class EnumAssertionProvenance(str, Enum): - """ - Possible data sources for assertions. - """ - Medical_Record = "medical_record" - """ - Data obtained from a medical record - """ - Investigator_Assessment = "investigator_assessment" - """ - Data obtained by examination, interview, etc. with investigator - """ - Participant_or_Caregiver_Report = "participant_or_caregiver_report" - """ - Data obtained from survey, questionnaire, etc. filled out by participant or caregiver - """ - Other = "other" - """ - Data obtained from other source, such as tissue bank - """ - - -class EnumAvailabilityStatus(str, Enum): - """ - Is the biospecimen available for use? - """ - Available = "available" - """ - Biospecimen is Available - """ - Unavailable = "unavailable" - """ - Biospecimen is Unavailable - """ - - -class EnumSampleCollectionMethod(str): - """ - The approach used to collect the biospecimen. [LOINC](https://loinc.org) is recommended. - """ - pass - - -class EnumSite(str): - """ - The location of the specimen collection. [SNOMED Body Site](https://hl7.org/fhir/R4B/valueset-body-site.html) is recommended. - """ - pass - - -class EnumSpatialQualifiers(str): - """ - Any spatial/location qualifiers. - """ - pass - - -class EnumLaterality(str): - """ - Laterality information for the site - """ - pass - - -class EnumEDAMFormats(str): - """ - Data formats from the EDAM ontology. - """ - pass - - -class EnumEDAMDataTypes(str): - """ - Data types from the EDAM ontology. - """ - pass - - -class EnumFileHashType(str, Enum): - """ - Types of file hashes supported. - """ - MD5 = "md5" - ETag = "etag" - SHA_1 = "sha1" - - - -class Record(ConfiguredBaseModel): - """ - One row / entity within the database - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, - 'from_schema': 'https://includedcc.org/include-access-model', - 'title': 'Record'}) - - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Study(Record): - """ - Study Metadata - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'study_id': {'identifier': True, - 'name': 'study_id', - 'range': 'string', - 'required': True}}, - 'title': 'Research Study'}) - - study_id: str = Field(default=..., title="Study ID", description="""INCLUDE Global ID for the study""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'StudyMetadata']} }) - parent_study: Optional[str] = Field(default=None, title="Parent Study", description="""The parent study for this study, if it is a nested study.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - study_title: str = Field(default=..., description="""Full Study Title""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - study_code: str = Field(default=..., title="Study Code", description="""Unique identifier for the study (generally a short acronym)""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - study_short_name: Optional[str] = Field(default=None, title="Study Code", description="""Short name for the study""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - program: list[EnumProgram] = Field(default=..., title="Program", description="""Funding source(s) for the study""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - funding_source: Optional[list[str]] = Field(default=[], title="Funding Source", description="""The funding source(s) of the study.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - principal_investigator: list[Investigator] = Field(default=..., title="Principal Investigator", description="""The Principal Investigator(s) responsible for the study.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - contact: list[Investigator] = Field(default=..., title="Contact Person", description="""The individual to contact with questions about this record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'VirtualBiorepository']} }) - study_description: str = Field(default=..., title="Study Description", description="""Brief description of the study (2-4 sentences)""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - website: Optional[str] = Field(default=None, title="Website", description="""Website for the Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'VirtualBiorepository', 'Publication']} }) - publication: Optional[list[Publication]] = Field(default=[], title="Publication", description="""Publications associated with this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'Dataset']} }) - acknowledgments: Optional[str] = Field(default=None, title="Acknowledgments", description="""Funding statement and acknowledgments for this study""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - citation_statement: Optional[str] = Field(default=None, title="Citation Statement", description="""Statement that secondary data users should use to acknowledge use of this study or dataset. E.g., \"The results analyzed and here are based in whole or in part upon data generated by the INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project , and were accessed from the INCLUDE Data Hub and .\"""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} }) - do_id: Optional[str] = Field(default=None, title="DOI", description="""Digital Object Identifier (DOI) for this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'DOI', 'Dataset']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class StudyMetadata(Record): - """ - Additional features about studies that may not apply to all studies - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'data_category': {'multivalued': True, - 'name': 'data_category', - 'required': True}, - 'study_id': {'identifier': True, - 'name': 'study_id', - 'required': True}}, - 'title': 'Study Metadata'}) - - study_id: str = Field(default=..., title="Study ID", description="""INCLUDE Global ID for the study""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'StudyMetadata']} }) - participant_lifespan_stage: list[EnumParticipantLifespanStage] = Field(default=..., title="Participant Lifespan Stage", description="""Focus age group(s) of the study population""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - selection_criteria: Optional[str] = Field(default=None, title="Selection Criteria", description="""Brief description of inclusion and/or exclusion criteria for the study""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - study_design: list[EnumStudyDesign] = Field(default=..., title="Study Design", description="""Overall design of study, including whether it is longitudinal and whether family members/unrelated controls are also enrolled""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - clinical_data_source_type: list[EnumClinicalDataSourceType] = Field(default=..., title="Clinical Data Source Type", description="""Source(s) of data collected from study participants""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - data_category: list[EnumDataCategory] = Field(default=..., title="Data Category", description="""General category of data in this Record (e.g. Clinical, Genomics, etc)""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata', 'File']} }) - vbr: Optional[VirtualBiorepository] = Field(default=None, title="Virtual Biorepository", description="""Information about the study's Virtual Biorepository, if participating""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - research_domain: list[EnumResearchDomain] = Field(default=..., description="""Main research domain(s) of the study, other than Down syndrome""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - expected_number_of_participants: int = Field(default=..., title="Expected Number of Participants", description="""Total expected number of participants to be recruited.""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - actual_number_of_participants: int = Field(default=..., title="Actual Number of Participants", description="""Total participants included at this time.""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class VirtualBiorepository(Record): - """ - An organization that can provide access to specimen for further analysis. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'title': 'Virtual BioRepository (VBR)'}) - - name: Optional[str] = Field(default=None, title="Name", description="""Name of the entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository', - 'Investigator', - 'EncounterDefinition', - 'ActivityDefinition', - 'Dataset']} }) - institution: Optional[str] = Field(default=None, title="Institution", description="""Name of the institution this record is associated with.""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository', 'Investigator']} }) - contact: list[Investigator] = Field(default=..., title="Contact Person", description="""The individual to contact with questions about this record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'VirtualBiorepository']} }) - website: Optional[str] = Field(default=None, title="Website", description="""Website for the Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'VirtualBiorepository', 'Publication']} }) - vbr_readme: Optional[str] = Field(default=None, title="VBR Readme", description="""Instructions for contacting or requesting samples from Virtual Biorepository, if participating""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class DOI(Record): - """ - A DOI is a permanent reference with metadata about a digital object. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'do_id': {'identifier': True, - 'name': 'do_id', - 'range': 'string', - 'required': True}}, - 'title': 'Digital Object Identifier (DOI)'}) - - do_id: str = Field(default=..., title="DOI", description="""Digital Object Identifier (DOI) for this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'DOI', 'Dataset']} }) - bibliographic_reference: Optional[str] = Field(default=None, title="Bibiliographic Reference", description="""Text use to reference this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['DOI', 'Publication']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Investigator(Record): - """ - An individual who made contributions to the collection, analysis, or sharing of data. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'title': 'Investigator'}) - - name: Optional[str] = Field(default=None, title="Name", description="""Name of the entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository', - 'Investigator', - 'EncounterDefinition', - 'ActivityDefinition', - 'Dataset']} }) - institution: Optional[str] = Field(default=None, title="Institution", description="""Name of the institution this record is associated with.""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository', 'Investigator']} }) - investigator_title: Optional[str] = Field(default=None, title="Investigator Title", description="""The title of the Investigator, eg, \"Assistant Professor\"""", json_schema_extra = { "linkml_meta": {'domain_of': ['Investigator']} }) - email: Optional[str] = Field(default=None, title="Email Address", description="""An email address to reach the entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Investigator']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Publication(Record): - """ - Information about a specific publication. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'title': 'Publication'}) - - bibliographic_reference: Optional[str] = Field(default=None, title="Bibiliographic Reference", description="""Text use to reference this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['DOI', 'Publication']} }) - website: Optional[str] = Field(default=None, title="Website", description="""Website for the Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'VirtualBiorepository', 'Publication']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Subject(Record): - """ - This entity is the subject about which data or references are recorded. This includes the idea of a human participant in a study, a cell line, an animal model, or any other similar entity. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'subject_id': {'identifier': True, - 'name': 'subject_id', - 'range': 'string', - 'required': True}}, - 'title': 'Subject'}) - - subject_id: str = Field(default=..., title="Study ID", description="""INCLUDE Global ID for the Subject""", json_schema_extra = { "linkml_meta": {'domain_of': ['Subject', - 'Demographics', - 'SubjectAssertion', - 'Encounter', - 'File']} }) - subject_type: EnumSubjectType = Field(default=..., title="Subject Type", description="""Type of entity this record represents""", json_schema_extra = { "linkml_meta": {'domain_of': ['Subject']} }) - organism_type: Optional[str] = Field(default=None, title="Organism Type", description="""Organism Type""", json_schema_extra = { "linkml_meta": {'domain_of': ['Subject']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Demographics(Record): - """ - Basic participant demographics summary - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'subject_id': {'identifier': True, - 'name': 'subject_id', - 'required': True}}, - 'title': 'Demographics'}) - - subject_id: str = Field(default=..., title="Study ID", description="""INCLUDE Global ID for the Subject""", json_schema_extra = { "linkml_meta": {'domain_of': ['Subject', - 'Demographics', - 'SubjectAssertion', - 'Encounter', - 'File']} }) - sex: EnumSex = Field(default=..., title="Sex", description="""Sex of Participant""", json_schema_extra = { "linkml_meta": {'domain_of': ['Demographics']} }) - race: list[EnumRace] = Field(default=..., title="Race", description="""Race of Participant""", json_schema_extra = { "linkml_meta": {'domain_of': ['Demographics']} }) - ethnicity: EnumEthnicity = Field(default=..., title="Ethnicity", description="""Ethnicity of Participant""", json_schema_extra = { "linkml_meta": {'domain_of': ['Demographics']} }) - down_syndrome_status: EnumDownSyndromeStatus = Field(default=..., title="Down Syndrome Status", description="""Down Syndrome status of participant""", json_schema_extra = { "linkml_meta": {'domain_of': ['Demographics']} }) - age_at_last_vital_status: Optional[int] = Field(default=None, title="Age at Last Vital Status", description="""Age in days when participant's vital status was last recorded""", ge=-365, le=32507, json_schema_extra = { "linkml_meta": {'domain_of': ['Demographics'], 'unit': {'ucum_code': 'd'}} }) - vital_status: Optional[EnumVitalStatus] = Field(default=None, title="Vital Status", description="""Whether participant is alive or dead""", json_schema_extra = { "linkml_meta": {'domain_of': ['Demographics']} }) - age_at_first_engagement: Optional[int] = Field(default=None, title="Age at First Participant Engagement", description="""Age in days of Participant at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available.""", ge=-365, le=32507, json_schema_extra = { "linkml_meta": {'domain_of': ['Demographics'], 'unit': {'ucum_code': 'd'}} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class SubjectAssertion(Record): - """ - Assertion about a particular Subject. May include Conditions, Measurements, etc. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'assertion_id': {'identifier': True, - 'name': 'assertion_id', - 'range': 'string', - 'required': True}}, - 'title': 'Subject Assertion'}) - - assertion_id: str = Field(default=..., title="Assertion ID", description="""INCLUDE Global ID for the Assertion""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - subject_id: Optional[str] = Field(default=None, title="Study ID", description="""INCLUDE Global ID for the Subject""", json_schema_extra = { "linkml_meta": {'domain_of': ['Subject', - 'Demographics', - 'SubjectAssertion', - 'Encounter', - 'File']} }) - encounter_id: Optional[str] = Field(default=None, title="Encounter ID", description="""Unique identifier for this Encounter.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion', 'BiospecimenCollection', 'Encounter']} }) - assertion_provenance: Optional[EnumAssertionProvenance] = Field(default=None, title="Assertion Provenance", description="""The original source of this assertion""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - age_at_assertion: Optional[int] = Field(default=None, title="Age at assertion", description="""The age in days of the Subject when the assertion was made.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion'], 'unit': {'ucum_code': 'd'}} }) - age_at_event: Optional[int] = Field(default=None, title="Age at event", description="""The age in days of the Subject at the time point which the assertion describes, eg, age of onset or when a measurement was performed.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion', 'Encounter'], 'unit': {'ucum_code': 'd'}} }) - age_at_resolution: Optional[int] = Field(default=None, title="Age at resolution", description="""The age in days of the Subject when the asserted state was resolved.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion'], 'unit': {'ucum_code': 'd'}} }) - concept: Optional[list[str]] = Field(default=[], title="Concept", description="""The structured term defining the meaning of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - concept_source: Optional[str] = Field(default=None, title="Concept Source Text", description="""The source text yielding the standardized concept.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - value_concept: Optional[list[str]] = Field(default=[], title="Value concept", description="""The structured term defining the value of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - value_number: Optional[float] = Field(default=None, title="Value Number", description="""The numeric value of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - value_source: Optional[str] = Field(default=None, title="Value Source Text", description="""The source text yielding the value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - value_unit: Optional[str] = Field(default=None, title="Value Units", description="""The structured term defining the units of the value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - value_unit_source: Optional[str] = Field(default=None, title="Value Units Source Text", description="""The source text yielding the value's units.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Concept(ConfiguredBaseModel): - """ - A standardized concept with display information. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'concept_curie': {'identifier': True, - 'name': 'concept_curie', - 'required': True}}, - 'title': 'Concept'}) - - concept_curie: str = Field(default=..., title="Concept Curie", description="""The standardized curie for the term.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Concept']} }) - display: Optional[str] = Field(default=None, title="Display String", description="""The friendly display string of the coded term.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Concept']} }) - - -class Sample(Record): - """ - A functionally equivalent specimen taken from a participant or processed from such a sample. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'biospecimen_collection_id': {'description': 'Biospecimen ' - 'Collection ' - 'during which ' - 'this sample was ' - 'generated.', - 'name': 'biospecimen_collection_id'}, - 'sample_id': {'identifier': True, - 'name': 'sample_id', - 'range': 'string', - 'required': True}}, - 'title': 'Sample'}) - - sample_id: str = Field(default=..., title="Sample ID", description="""The unique identifier for this Sample.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot', 'File']} }) - biospecimen_collection_id: Optional[str] = Field(default=None, title="Biospecimen Collection ID", description="""Biospecimen Collection during which this sample was generated.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'BiospecimenCollection']} }) - parent_sample_id: Optional[str] = Field(default=None, title="Parent Sample ID", description="""Sample from which this sample is derived""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample']} }) - sample_type: str = Field(default=..., title="Sample Type", description="""Type of material of which this Sample is comprised""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample']} }) - processing: Optional[list[str]] = Field(default=[], title="Sample Processing", description="""Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample']} }) - availablity_status: Optional[EnumAvailabilityStatus] = Field(default=None, title="Sample Availability", description="""Can this Sample be requested for further analysis?""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot']} }) - storage_method: Optional[list[str]] = Field(default=[], title="Sample Storage Method", description="""Sample storage method, eg, Frozen or with additives""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample']} }) - quantity_number: Optional[float] = Field(default=None, title="Quantity", description="""The total quantity of the specimen""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot']} }) - quantity_unit: Optional[str] = Field(default=None, title="Quantity Units", description="""The structured term defining the units of the quantity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class BiospecimenCollection(Record): - """ - A biospecimen collection event which yields one or more Samples. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'biospecimen_collection_id': {'identifier': True, - 'name': 'biospecimen_collection_id', - 'range': 'string', - 'required': True}}, - 'title': 'BiospecimenCollection'}) - - biospecimen_collection_id: str = Field(default=..., title="Biospecimen Collection ID", description="""Unique identifier for this Biospecimen Collection.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'BiospecimenCollection']} }) - age_at_collection: Optional[float] = Field(default=None, title="Age at Biospecimen Collection", description="""The age at which this biospecimen was collected in decimal years.""", json_schema_extra = { "linkml_meta": {'domain_of': ['BiospecimenCollection'], 'unit': {'ucum_code': 'a'}} }) - method: Optional[EnumSampleCollectionMethod] = Field(default=None, title="Biospecimen Collection Method", description="""The approach used to collect the biospecimen.""", json_schema_extra = { "linkml_meta": {'domain_of': ['BiospecimenCollection']} }) - site: Optional[EnumSite] = Field(default=None, title="Biospecimen Collection Site", description="""The location of the specimen collection.""", json_schema_extra = { "linkml_meta": {'domain_of': ['BiospecimenCollection']} }) - spatial_qualifier: Optional[EnumSpatialQualifiers] = Field(default=None, title="Spatial Qualifier", description="""Qualifier that further refine the specific location of biospecimen collection""", json_schema_extra = { "linkml_meta": {'domain_of': ['BiospecimenCollection']} }) - laterality: Optional[EnumLaterality] = Field(default=None, title="Location Laterality", description="""Laterality that further refine the specific location of biospecimen collection""", json_schema_extra = { "linkml_meta": {'domain_of': ['BiospecimenCollection']} }) - encounter_id: Optional[str] = Field(default=None, title="Encounter ID", description="""Unique identifier for this Encounter.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion', 'BiospecimenCollection', 'Encounter']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Aliquot(Record): - """ - A specific tube or amount of a biospecimen associated with a Sample. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'aliquot_id': {'identifier': True, - 'name': 'aliquot_id', - 'range': 'string', - 'required': True}}, - 'title': 'Aliquot'}) - - aliquot_id: str = Field(default=..., title="Aliquot ID", description="""Unique identifier for an Aliquot.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Aliquot']} }) - sample_id: Optional[str] = Field(default=None, title="Sample ID", description="""The unique identifier for this Sample.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot', 'File']} }) - availablity_status: Optional[EnumAvailabilityStatus] = Field(default=None, title="Sample Availability", description="""Can this Sample be requested for further analysis?""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot']} }) - quantity_number: Optional[float] = Field(default=None, title="Quantity", description="""The total quantity of the specimen""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot']} }) - quantity_unit: Optional[str] = Field(default=None, title="Quantity Units", description="""The structured term defining the units of the quantity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot']} }) - concentration_number: Optional[float] = Field(default=None, title="Concentration", description="""What is the concentration of the analyte in the Aliquot?""", json_schema_extra = { "linkml_meta": {'domain_of': ['Aliquot']} }) - concentration_unit: Optional[str] = Field(default=None, title="Concentration Units", description="""Units associated with the concentration of the analyte in the Aliquot.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Aliquot']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class Encounter(Record): - """ - An event at which data was collected about a participant, an intervention was made, or information about a participant was recorded. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'encounter_id': {'identifier': True, - 'name': 'encounter_id', - 'range': 'string', - 'required': True}}, - 'title': 'Participant Encounter'}) - - encounter_id: str = Field(default=..., title="Encounter ID", description="""Unique identifier for this Encounter.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion', 'BiospecimenCollection', 'Encounter']} }) - subject_id: Optional[str] = Field(default=None, title="Study ID", description="""INCLUDE Global ID for the Subject""", json_schema_extra = { "linkml_meta": {'domain_of': ['Subject', - 'Demographics', - 'SubjectAssertion', - 'Encounter', - 'File']} }) - encounter_definition_id: Optional[str] = Field(default=None, title="Encounter Definition ID", description="""Unique identifier for this Encounter Definition.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Encounter', 'EncounterDefinition']} }) - age_at_event: Optional[int] = Field(default=None, title="Age at event", description="""The age in days of the Subject at the time point which the assertion describes, eg, age of onset or when a measurement was performed.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion', 'Encounter'], 'unit': {'ucum_code': 'd'}} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class EncounterDefinition(Record): - """ - A definition of an encounter type in this study, ie, an event at which data was collected about a participant, an intervention was made, or information about a participant was recorded. This may be something planned by a study or a type of data collection. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'activity_definition_id': {'multivalued': True, - 'name': 'activity_definition_id'}, - 'encounter_definition_id': {'identifier': True, - 'name': 'encounter_definition_id', - 'range': 'string', - 'required': True}}, - 'title': 'Encounter Definition'}) - - encounter_definition_id: str = Field(default=..., title="Encounter Definition ID", description="""Unique identifier for this Encounter Definition.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Encounter', 'EncounterDefinition']} }) - name: Optional[str] = Field(default=None, title="Name", description="""Name of the entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository', - 'Investigator', - 'EncounterDefinition', - 'ActivityDefinition', - 'Dataset']} }) - description: Optional[str] = Field(default=None, title="Description", description="""Description for this entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['EncounterDefinition', 'ActivityDefinition', 'Dataset']} }) - activity_definition_id: Optional[list[str]] = Field(default=[], title="Activity Definition ID", description="""Unique identifier for this Activity Definition.""", json_schema_extra = { "linkml_meta": {'domain_of': ['EncounterDefinition', 'ActivityDefinition']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class ActivityDefinition(Record): - """ - A definition of an activity in this study, eg, a biospecimen collection, intervention, survey, or assessment. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'activity_definition_id': {'identifier': True, - 'name': 'activity_definition_id', - 'range': 'string', - 'required': True}}, - 'title': 'Activity Definition'}) - - activity_definition_id: str = Field(default=..., title="Activity Definition ID", description="""Unique identifier for this Activity Definition.""", json_schema_extra = { "linkml_meta": {'domain_of': ['EncounterDefinition', 'ActivityDefinition']} }) - name: Optional[str] = Field(default=None, title="Name", description="""Name of the entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository', - 'Investigator', - 'EncounterDefinition', - 'ActivityDefinition', - 'Dataset']} }) - description: Optional[str] = Field(default=None, title="Description", description="""Description for this entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['EncounterDefinition', 'ActivityDefinition', 'Dataset']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class File(Record): - """ - File - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'file_id': {'identifier': True, - 'name': 'file_id', - 'range': 'string', - 'required': True}, - 'sample_id': {'multivalued': True, 'name': 'sample_id'}, - 'subject_id': {'multivalued': True, 'name': 'subject_id'}}, - 'title': 'File'}) - - file_id: str = Field(default=..., title="File ID", description="""Unique identifier for this File.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File', 'Dataset']} }) - subject_id: Optional[list[str]] = Field(default=[], title="Study ID", description="""INCLUDE Global ID for the Subject""", json_schema_extra = { "linkml_meta": {'domain_of': ['Subject', - 'Demographics', - 'SubjectAssertion', - 'Encounter', - 'File']} }) - sample_id: Optional[list[str]] = Field(default=[], title="Sample ID", description="""The unique identifier for this Sample.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Sample', 'Aliquot', 'File']} }) - filename: Optional[str] = Field(default=None, title="Filename", description="""The name of the file.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File']} }) - format: Optional[EnumEDAMFormats] = Field(default=None, title="File Format", description="""The format of the file.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File']} }) - data_category: Optional[EnumDataCategory] = Field(default=None, title="Data Category", description="""General category of data in this Record (e.g. Clinical, Genomics, etc)""", json_schema_extra = { "linkml_meta": {'domain_of': ['StudyMetadata', 'File']} }) - data_type: Optional[EnumEDAMDataTypes] = Field(default=None, title="Data Type", description="""The type of data within this file.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File']} }) - size: Optional[int] = Field(default=None, title="File Size", description="""Size of the file, in Bytes.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File'], 'unit': {'ucum_code': 'By'}} }) - staging_url: Optional[str] = Field(default=None, title="Staging Location", description="""URL for internal access to the data. May be temporary.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File']} }) - release_url: Optional[str] = Field(default=None, title="Release Location", description="""URL for controlled or open access to the data.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File']} }) - drs_uri: Optional[str] = Field(default=None, title="DRS URI", description="""DRS location to access the data.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File']} }) - hash: Optional[FileHash] = Field(default=None, title="File Hash", description="""File hash information""", json_schema_extra = { "linkml_meta": {'domain_of': ['File']} }) - external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} }) - - -class FileHash(ConfiguredBaseModel): - """ - Type and value of a file content hash. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'title': 'File Hash'}) - - hash_type: Optional[EnumFileHashType] = Field(default=None, title="File Hash Type", description="""The type of file hash, eg, md5""", json_schema_extra = { "linkml_meta": {'domain_of': ['FileHash']} }) - hash_value: Optional[str] = Field(default=None, title="File Hash Value", description="""The value of the file hash""", json_schema_extra = { "linkml_meta": {'domain_of': ['FileHash']} }) - - -class Dataset(ConfiguredBaseModel): - """ - Set of files grouped together for release. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model', - 'slot_usage': {'dataset_id': {'identifier': True, - 'name': 'dataset_id', - 'range': 'string', - 'required': True}, - 'file_id': {'description': 'The list of files comprising this ' - 'dataset.', - 'multivalued': True, - 'name': 'file_id'}}, - 'title': 'Dataset'}) - - dataset_id: str = Field(default=..., title="Dataset ID", description="""Unique identifier for a Dataset.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Dataset']} }) - name: Optional[str] = Field(default=None, title="Name", description="""Name of the entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['VirtualBiorepository', - 'Investigator', - 'EncounterDefinition', - 'ActivityDefinition', - 'Dataset']} }) - description: Optional[str] = Field(default=None, title="Description", description="""Description for this entity.""", json_schema_extra = { "linkml_meta": {'domain_of': ['EncounterDefinition', 'ActivityDefinition', 'Dataset']} }) - do_id: Optional[str] = Field(default=None, title="DOI", description="""Digital Object Identifier (DOI) for this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'DOI', 'Dataset']} }) - file_id: Optional[list[str]] = Field(default=[], title="File ID", description="""The list of files comprising this dataset.""", json_schema_extra = { "linkml_meta": {'domain_of': ['File', 'Dataset']} }) - publication: Optional[list[Publication]] = Field(default=[], title="Publication", description="""Publications associated with this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'Dataset']} }) - data_collection_start: Optional[str] = Field(default=None, title="Data Collection Start", description="""The date that data collection started. May include only a year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Dataset']} }) - data_collection_end: Optional[str] = Field(default=None, title="Data Collection End", description="""The date that data collection started. May include only a year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Dataset']} }) - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Record.model_rebuild() -Study.model_rebuild() -StudyMetadata.model_rebuild() -VirtualBiorepository.model_rebuild() -DOI.model_rebuild() -Investigator.model_rebuild() -Publication.model_rebuild() -Subject.model_rebuild() -Demographics.model_rebuild() -SubjectAssertion.model_rebuild() -Concept.model_rebuild() -Sample.model_rebuild() -BiospecimenCollection.model_rebuild() -Aliquot.model_rebuild() -Encounter.model_rebuild() -EncounterDefinition.model_rebuild() -ActivityDefinition.model_rebuild() -File.model_rebuild() -FileHash.model_rebuild() -Dataset.model_rebuild() diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index 5d22101..83ea94c 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -25,6 +25,7 @@ prefixes: mesh: http://id.nlm.nih.gov/mesh/ NCIT: http://purl.obolibrary.org/obo/NCIT_ PATO: http://purl.obolibrary.org/obo/PATO_ + DUO: http://purl.obolibrary.org/obo/DUO_ default_prefix: includedcc default_range: string @@ -39,6 +40,23 @@ classes: abstract: true slots: - external_id + - access_policy_id + AccessPolicy: + title: Access Policy + description: The access policy that describes the controls around use of data + slots: + - access_policy_id + - data_use_accession + - data_use_permission + - data_use_modifier + - disease_limitation + - access_description + - website + slot_usage: + access_policy_id: + range: string + required: true + identifier: true Study: title: Research Study description: Study Metadata @@ -370,6 +388,34 @@ slots: description: INCLUDE Global ID for the study range: Study multivalued: false + access_policy_id: + title: Access Policy ID + description: Global identifier for the access policy that applies to + this row of data. + range: AccessPolicy + data_use_accession: + title: Data Use Accession + description: Accession used to provision access to the record, eg, + a dbGaP phsID. + range: uriorcurie + data_use_permission: + title: Data Use Permission + description: Broad category of restrictions on data use. + range: EnumDataUsePermission + required: true + data_use_modifier: + title: Data Use Modifier + description: Additional modifiers that limit data use. + range: EnumDataUseModifier + disease_limitation: + title: Data Use Disease Limitation + description: If the access is limited to a specific disease purpose, + it is specified here. + range: string + access_description: + title: Access Description + description: Any additional information to support access requests. + range: string do_id: title: DOI description: Digital Object Identifier (DOI) for this Record. @@ -457,7 +503,7 @@ slots: required: true website: title: Website - description: Website for the Record. + description: Website with more information about this entity. range: uri contact: title: Contact Person @@ -798,6 +844,27 @@ slots: range: string enums: + EnumDataUsePermission: + title: Data Use Permission + description: Data Use Ontology (DUO) terms for data use permissions. + #Do we need a "registered tier" item? + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000001 + is_direct: false + relationship_types: + - rdfs:subClassOf + EnumDataUseModifier: + title: Data Use Modifier + description: Data Use Ontology (DUO) terms for data use modifiers. + reachable_from: + source_ontology: bioregistry:duo + source_nodes: + - DUO:0000017 + is_direct: false + relationship_types: + - rdfs:subClassOf EnumProgram: title: Funding Programs description: Funding programs relevant to inform operations.