From f6527f1b250fdd5dce906cbff730c9858ad01f98 Mon Sep 17 00:00:00 2001 From: Christina Diaz Date: Mon, 16 Mar 2026 19:36:40 -0400 Subject: [PATCH 1/5] =?UTF-8?q?=F0=9F=9A=A7=20Add=20files=20model=20ideas?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../schema/include_access_model.yaml | 179 +++++++++++++++++- 1 file changed, 169 insertions(+), 10 deletions(-) diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index 99145db..0d5d3b2 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -310,32 +310,148 @@ classes: identifier: true File: title: File - description: File + description: An object and its metadata that exists in s3. is_a: Record slots: - - file_id - - subject_id + - file_id + - subject_id # do we need both a subject and sample id in this table? - sample_id - - filename - - format - - data_category - - data_type + - file_name - format + # - data_category - might be better suited for an assay model + # - data_type - same as ^ + # below are the file fields d3b use from automatic file inventorying in aws; many fields decscibe object metadata + - file_category + description: a high level classfication of the file (e.g., omics file, imaging file) - size + - s3_file_path # can name this url if more appropriate + description: full s3 url of an file's location in aws + - s3_key + - file_extension + - data_transfer_id + description: jira ticket number associated with a file transfer request to production bucket + - aws_account_id + - account_name + - account_alias + - bucket_study_id + description: global study ID used to create the bucket + - bucket + - s3_created_at + - s3_modified_at + - intelligent_tiering_access + - is_delete_marker + description: notes whether a file has been deleted from s3 + - is_latest + - storage_class + - hash + - manifest_hash_value + - file_hash_validation_status + - file_type + - access_url + - drs_uri + + # not sure if these are actual useful - but are in the d3b model + - encryption_status + - is_multipart_uploaded + - object_lock_leval_hold_status + - object_lock_mode + - object_lock_retain_until_date + - replication_status + - version_id + + + #TODO: I'm not convinced this is the right strategy- access model vs operations +# this might be good to have in a separate model for drs management - staging_url - release_url - - drs_uri - - hash + # - drs_uri + # - hash slot_usage: file_id: range: string required: true identifier: true subject_id: - multivalued: true + multivalued: true sample_id: multivalued: true + file_name: + range: string + required: true + format: + range: string + required: true + file_category: + range: string + required: true + size: + range: integer + required: true + s3_file_path: + range: string + required: true + s3_key: + range: string + required: true + file_extension: + range: string + required: true + data_transfer_id: + range: string + required: false + aws_account_id: + range: string + required: true + account_name: + range: string + required: true + account_alias: + range: string + required: true + bucket_study_id: + range: string + required: false + bucket: + range: string + required: false + s3_created_at: + range: date + required: true + s3_modified_at: + range: date + required: true + intelligent_tiering_access: + range: string + required: true + is_delete_marker: + range: boolean + required: true + is_latest: + range: boolean + required: true + storage_class: + range: string + required: true + hash: + range: + required: true + manifest_hash_value: + range: + required: false + file_hash_validation_status: + range: string + required: false + file_type: + range: string + required: true + access_url: + range: string + required: false + drs_uri: + range: string + required: false + FileHash: title: File Hash description: Type and value of a file content hash. @@ -343,6 +459,49 @@ classes: - hash_type - hash_value + FileDrs: + title: File DRS + description: Access control information for files accessed through a DRS service. + slots: + - file_id + description: unique file identifier assigned to a file + - staging_url + description: s3 location of a file before its made public + - release_url + description: production location of a publically available file + - hash + - access_type + description: notes wheter a file is controlled, open, or registered-tier access + - access_url + - drs_uri + - acl + description: access control list for the file + + slot_usage: + file_id: + range: string + required: true + identifier: true + staging_url: + range: string + required: true + release_url: + range: string + required: true + hash: + range: + required: true + access_type: + range: string + required: true + access_url: + range: string + requried: true + acl: + range: string + required: true + multivalued: true + slots: From 038d9b7e97001c011b23f911e3c399e8f73421bc Mon Sep 17 00:00:00 2001 From: Christina Diaz Date: Mon, 16 Mar 2026 19:42:49 -0400 Subject: [PATCH 2/5] =?UTF-8?q?=F0=9F=9A=A7=20Adding=20stuff?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../schema/include_access_model.yaml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index 0d5d3b2..4b3a8dc 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -318,8 +318,9 @@ classes: - sample_id - file_name - format - # - data_category - might be better suited for an assay model - # - data_type - same as ^ + - data_category # might be better suited for the assay model + - data_type # same as ^ + # below are the file fields d3b use from automatic file inventorying in aws; many fields decscibe object metadata - file_category description: a high level classfication of the file (e.g., omics file, imaging file) @@ -359,12 +360,18 @@ classes: - replication_status - version_id + # new proposed fields + - is_released + description: notes whether a file has been released to the public + - is_registered + description: notes whether a file has been registered to a drs service + #TODO: I'm not convinced this is the right strategy- access model vs operations # this might be good to have in a separate model for drs management - - staging_url - - release_url + # - staging_url + # - release_url # - drs_uri # - hash slot_usage: @@ -470,9 +477,11 @@ classes: - release_url description: production location of a publically available file - hash + description: file hash value - access_type description: notes wheter a file is controlled, open, or registered-tier access - access_url + description: - drs_uri - acl description: access control list for the file From b8a58ed9eef0517c8ec92f960b5c3e9a2ed21fce Mon Sep 17 00:00:00 2001 From: Christina Diaz Date: Thu, 26 Mar 2026 10:35:03 -0400 Subject: [PATCH 3/5] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20Update=20files=20model?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/schema/include_access_model.yaml | 2651 ----------------- .../schema/include_access_model.yaml | 232 +- 2 files changed, 147 insertions(+), 2736 deletions(-) diff --git a/docs/schema/include_access_model.yaml b/docs/schema/include_access_model.yaml index b0a4b4e..e69de29 100644 --- a/docs/schema/include_access_model.yaml +++ b/docs/schema/include_access_model.yaml @@ -1,2651 +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: DOI - domain_of: - - Study - - DOI - 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: ActivityDefinition - domain_of: - - VirtualBiorepository - - Investigator - - EncounterDefinition - - ActivityDefinition - 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: Study - domain_of: - - Study - 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: Assertion 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: ActivityDefinition - domain_of: - - EncounterDefinition - - ActivityDefinition - 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: File - domain_of: - - File - 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 - 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 -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: 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 -metamodel_version: 1.7.0 -source_file: include_access_model.yaml -source_file_date: '2026-03-09T16:30:20' -source_file_size: 35097 -generation_date: '2026-03-09T16:31:10' - diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index 4b3a8dc..38e6459 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -310,23 +310,120 @@ classes: identifier: true File: title: File - description: An object and its metadata that exists in s3. + # subset of info; ideally pulls from a file universe table and some kind of assay table + description: Required information for portal use. is_a: Record slots: + - study_id + description: unique global study identifier file belongs to - file_id + description: unique file identifier assigned to a file - subject_id # do we need both a subject and sample id in this table? - sample_id + - s3_file_path # can name this url if more appropriate + description: full s3 url of an file's location in aws - file_name + - size - format - - data_category # might be better suited for the assay model - - data_type # same as ^ + - data_category + - data_type + - experimental_strategy + - acl + description: access control list for the file + - access_type + description: notes wheter a file is controlled, open, or registered-tier access + - access_url + - drs_uri + - is_released # maybe can leave this out? should only release ready data be in this model? + description: notes whether a file has been released to the public + - is_registered + description: notes whether a file has been registered to a drs service + - repository + description: name of drs service files are registered to + - hash + description: file hash value - # below are the file fields d3b use from automatic file inventorying in aws; many fields decscibe object metadata + slot_usage: + study_id: + range: string + required: true + identifier: true + file_id: + range: string + required: true + identifier: true + subject_id: + multivalued: true + sample_id: + multivalued: true + file_name: + range: string + required: true + format: + range: string + required: true + size: + range: integer + required: true + s3_file_path: + range: string + required: true + hash: + range: + required: true + access_url: + range: string + required: false + drs_uri: + range: string + required: false + data_category: + range: string + required: true + data_type: + range: string + required: true + experimental_strategy: + range: string + required: true + access_type: + range: string + required: true + is_released: + range: boolean + required: true + is_registered: + range: boolean + required: true + repository: + range: string + required: true + access_url: + range: string + required: true + + FileHash: + title: File Hash + description: Type and value of a file content hash. + slots: + - hash_type + - hash_value + + FileAdmin: # names are TBD; can change - idea is this is operational or file universe model + title: File Admin + description: File unvierse; contains all information about a file that may be needed for operational work + slots: + - study_id + description: unique global study identifier file belongs to + - file_id + description: unique file identifier assigned to a file + - subject_id # do we need both a subject and sample id in this table? + - sample_id + - s3_file_path # can name this url if more appropriate + description: full s3 url of an file's location in aws - file_category description: a high level classfication of the file (e.g., omics file, imaging file) - size - - s3_file_path # can name this url if more appropriate - description: full s3 url of an file's location in aws - s3_key - file_extension - data_transfer_id @@ -344,14 +441,9 @@ classes: description: notes whether a file has been deleted from s3 - is_latest - storage_class - - hash - manifest_hash_value - file_hash_validation_status - file_type - - access_url - - drs_uri - - # not sure if these are actual useful - but are in the d3b model - encryption_status - is_multipart_uploaded - object_lock_leval_hold_status @@ -359,45 +451,39 @@ classes: - object_lock_retain_until_date - replication_status - version_id + - staging_url + description: s3 location of a file before its made public + - release_url + description: production location of a publically available file + - hash + description: file hash value + - access_type + description: notes wheter a file is controlled, open, or registered-tier access + - access_url + description: + - drs_uri + - acl + description: access control list for the file + - is_released + description: notes whether a file has been released to the public + - is_registered + description: notes whether a file has been registered to a drs service + - repository + description: name of drs service files are registered to + - experiment_strategy - # new proposed fields - - is_released - description: notes whether a file has been released to the public - - is_registered - description: notes whether a file has been registered to a drs service - - - -#TODO: I'm not convinced this is the right strategy- access model vs operations -# this might be good to have in a separate model for drs management - # - staging_url - # - release_url - # - drs_uri - # - hash - slot_usage: - file_id: - range: string - required: true - identifier: true - subject_id: - multivalued: true - sample_id: - multivalued: true - file_name: + slot_usage: + study_id: range: string required: true - format: + identifier: true + file_id: range: string required: true - file_category: + identifier: true + file_category: range: string required: true - size: - range: integer - required: true - s3_file_path: - range: string - required: true s3_key: range: string required: true @@ -440,9 +526,6 @@ classes: storage_class: range: string required: true - hash: - range: - required: true manifest_hash_value: range: required: false @@ -452,45 +535,6 @@ classes: file_type: range: string required: true - access_url: - range: string - required: false - drs_uri: - range: string - required: false - - FileHash: - title: File Hash - description: Type and value of a file content hash. - slots: - - hash_type - - hash_value - - FileDrs: - title: File DRS - description: Access control information for files accessed through a DRS service. - slots: - - file_id - description: unique file identifier assigned to a file - - staging_url - description: s3 location of a file before its made public - - release_url - description: production location of a publically available file - - hash - description: file hash value - - access_type - description: notes wheter a file is controlled, open, or registered-tier access - - access_url - description: - - drs_uri - - acl - description: access control list for the file - - slot_usage: - file_id: - range: string - required: true - identifier: true staging_url: range: string required: true @@ -510,6 +554,24 @@ classes: range: string required: true multivalued: true + repository: + range: string + required: true + is_released: + range: boolean + required: true + is_registered: + range: boolean + required: true + experimental_strategy: + range: string + required: true + data_category: + range: string + required: true + data_type: + range: string + required: true From 93f9b1790c5ac80eaf914d5482aad4e9769a9f03 Mon Sep 17 00:00:00 2001 From: Christina Diaz Date: Thu, 26 Mar 2026 11:38:23 -0400 Subject: [PATCH 4/5] =?UTF-8?q?=F0=9F=9A=A7=20Working=20on=20assay=20model?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../schema/include_access_model.yaml | 61 ++++++++++++++++++- 1 file changed, 60 insertions(+), 1 deletion(-) diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index 38e6459..afdd81a 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -336,7 +336,7 @@ classes: - drs_uri - is_released # maybe can leave this out? should only release ready data be in this model? description: notes whether a file has been released to the public - - is_registered + - is_registered # maybe can leave this out? should only drs registered data be in this model? description: notes whether a file has been registered to a drs service - repository description: name of drs service files are registered to @@ -535,6 +535,9 @@ classes: file_type: range: string required: true + size: + range: integer + required: true staging_url: range: string required: true @@ -569,10 +572,66 @@ classes: data_category: range: string required: true + description: high-level category of the data used for filtering data_type: range: string required: true + FileAssay: + title: File Assay + # for now group all types into one table; but we may want to split out since different + # assay types collect different types of information + # this is a basic model + description: A file produced by or associated with an assay or data + acquisition process including omics, imaging, actigraphy, and other experimental or observational data. + slots: + file_id: + range: string + required: true + identifier: true + subject_id: + range: string + required: true + sample_id: + range: string + required: true + data_category: + range: string + required: true + description: high-level category of the data used for filtering + experimental_strategy: + range: string + required: true + descirption: method or assay used to generate the data + data_type: + range: string + required: true + description: specific type of data contained in the file + format: + range: string + required: true + size: + range: integer + required: true + access_type: + range: string + required: true + assay_center: + range: string + required: false + description: the organization or center that generated the file + platform: + range: string + required: false + description: instrument or platform family name + workflow_name: + range: string + required: false + description: processing tool that produced the file + workflow_version: + range: string + required: false + slots: From fe360b3ed995da1fe45bbe12bdcbaf4b0a7479df Mon Sep 17 00:00:00 2001 From: Christina Diaz Date: Thu, 26 Mar 2026 11:45:50 -0400 Subject: [PATCH 5/5] =?UTF-8?q?=F0=9F=92=A1=20Updating=20comments?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/include_access_model/schema/include_access_model.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index afdd81a..5db89ef 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -410,6 +410,7 @@ classes: - hash_value FileAdmin: # names are TBD; can change - idea is this is operational or file universe model + # probs doesn't go into the "access model" - but here is what could go there title: File Admin description: File unvierse; contains all information about a file that may be needed for operational work slots: