diff --git a/base/base.yaml b/base/base.yaml index b5670f6..c5f81cf 100644 --- a/base/base.yaml +++ b/base/base.yaml @@ -1130,6 +1130,31 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64} + submitter_participant_ids: + name: submitter_participant_ids + description: A list of Unique identifiers (min 1) for participants within the study, assigned by + the data provider. + title: Submitter Participant Ids + examples: + - value: '90234' + - value: BLD_donor_89 + - value: AML-90 + exact_mappings: + - ARGO.v1.34:donor.submitter_donor_id + - Beacon.v2.2.0:individual.id + - CQDG:submitter_participant_id + - FHIR.v5.0.0:Patient.identifier + - mCODE.v4.0.0:Patient.identifier + - MOHCCN.v3.1:Donor.submitter_donor_id + - Phenopackets.v2.0:Individual.id + annotations: + specifications: "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" + range: string + required: true + pattern: ^[A-Za-z0-9\-\._]{1,64} + multivalued: true + minimum_cardinality: 1 + list_elements_unique: true vital_status: name: vital_status description: Participant's last known state of living or deceased. @@ -1681,6 +1706,31 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_specimen_ids: + name: submitter_specimen_ids + description: List of Unique identifiers (min 1) for specimens within the study, assigned by the + data provider. + title: Submitter Specimen Ids + examples: + - value: LAML_PO + - value: '00445' + - value: THY_099-tumour + exact_mappings: + - ARGO.v1.34:specimen.submitter_specimen_id + - Beacon.v2.2.0:biosample.id + - CQDG:submitter_biospecimen_id + - FHIR.v5.0.0:Specimen.identifier + - mCODE.v4.0.0:Specimen.identifier + - MOHCCN.v3.1:specimen.submitter_specimen_id + - Phenopackets.v2.0:Biosample.derived_from_id + annotations: + specifications: "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier" + range: string + required: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + multivalued: true + minimum_cardinality: 1 + list_elements_unique: true age_at_diagnosis: name: age_at_diagnosis description: Age of participant (in days) at time of diagnosis of the condition. @@ -1962,6 +2012,27 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_sample_ids: + name: submitter_sample_ids + description: 'List of Unique identifiers (min 1) for samples within the study, assigned by the + data provider. + + ' + title: Submitter Sample Ids + examples: + - value: hnc_12 + - value: CCG_34_94583 + - value: BRCA47832-3239 + exact_mappings: + - ARGO.v1.34:sample_registration.submitter_sample_id + - MOHCCN.v3.1:Sample_registration.submitter_sample_id + - Phenopackets.v2.0:Biosample.id + range: string + required: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + multivalued: true + minimum_cardinality: 1 + list_elements_unique: true sample_status: name: sample_status description: "Indicate the status of the sample for data analysis.\nCase sample refers to a sample that meets the disease or exposure criteria under investigation.\nControl sample refers to of the same type that does not meet the criteria, representing a normal or baseline state for comparison." @@ -1978,6 +2049,19 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_experiment_ids: + name: submitter_experiment_ids + description: A list of Unique identifiers (min 1) for experiments within the study, assigned by + the data provider. + title: Submitter Experiment Ids + exact_mappings: + - ARGO.v1.34:experiment.submitter_sequencing_experiment_id + range: string + required: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + multivalued: true + minimum_cardinality: 1 + list_elements_unique: true experiment_type: name: experiment_type description: "Indicate NCIt (NCI Thesaurus) code and term to denote the broad type of sequencing experiment performed. A mixture of library strategy and source." @@ -4019,10 +4103,10 @@ classes: title: Analysis slots: - submitter_analysis_id - - submitter_experiment_id - - submitter_participant_id - - submitter_sample_id - - submitter_specimen_id + - submitter_experiment_ids + - submitter_participant_ids + - submitter_sample_ids + - submitter_specimen_ids - analysisType - data_category - genome_annotation diff --git a/custom/pcgl/pcgl_dh.yaml b/custom/pcgl/pcgl_dh.yaml index c5846c3..8d8f0e8 100644 --- a/custom/pcgl/pcgl_dh.yaml +++ b/custom/pcgl/pcgl_dh.yaml @@ -1135,6 +1135,33 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64} + submitter_participant_ids: + name: submitter_participant_ids + annotations: + specifications: + tag: specifications + value: FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier + description: A list of Unique identifiers (min 1) for participants within the + study, assigned by the data provider. + title: submitter_participant_ids + examples: + - value: '90234' + - value: BLD_donor_89 + - value: AML-90 + exact_mappings: + - ARGO.v1.34:donor.submitter_donor_id + - Beacon.v2.2.0:individual.id + - CQDG:submitter_participant_id + - FHIR.v5.0.0:Patient.identifier + - mCODE.v4.0.0:Patient.identifier + - MOHCCN.v3.1:Donor.submitter_donor_id + - Phenopackets.v2.0:Individual.id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64} + minimum_cardinality: 1 vital_status: name: vital_status annotations: @@ -1821,6 +1848,33 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_specimen_ids: + name: submitter_specimen_ids + annotations: + specifications: + tag: specifications + value: FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier + description: List of Unique identifiers (min 1) for specimens within the study, + assigned by the data provider. + title: submitter_specimen_ids + examples: + - value: LAML_PO + - value: '00445' + - value: THY_099-tumour + exact_mappings: + - ARGO.v1.34:specimen.submitter_specimen_id + - Beacon.v2.2.0:biosample.id + - CQDG:submitter_biospecimen_id + - FHIR.v5.0.0:Specimen.identifier + - mCODE.v4.0.0:Specimen.identifier + - MOHCCN.v3.1:specimen.submitter_specimen_id + - Phenopackets.v2.0:Biosample.derived_from_id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + minimum_cardinality: 1 age_at_diagnosis: name: age_at_diagnosis annotations: @@ -2149,6 +2203,27 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_sample_ids: + name: submitter_sample_ids + description: 'List of Unique identifiers (min 1) for samples within the study, + assigned by the data provider. + + ' + title: submitter_sample_ids + examples: + - value: hnc_12 + - value: CCG_34_94583 + - value: BRCA47832-3239 + exact_mappings: + - ARGO.v1.34:sample_registration.submitter_sample_id + - MOHCCN.v3.1:Sample_registration.submitter_sample_id + - Phenopackets.v2.0:Biosample.id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + minimum_cardinality: 1 sample_status: name: sample_status description: 'Indicate the status of the sample for data analysis. @@ -2171,6 +2246,19 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_experiment_ids: + name: submitter_experiment_ids + description: A list of Unique identifiers (min 1) for experiments within the study, + assigned by the data provider. + title: submitter_experiment_ids + exact_mappings: + - ARGO.v1.34:experiment.submitter_sequencing_experiment_id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + minimum_cardinality: 1 experiment_type: name: experiment_type description: Indicate NCIt (NCI Thesaurus) code and term to denote the broad type @@ -4409,13 +4497,13 @@ classes: title: Analysis slots: - submitter_analysis_id - - submitter_experiment_id - - submitter_participant_id - - submitter_sample_id - - submitter_specimen_id - analysisType - data_category - studyId + - submitter_experiment_ids + - submitter_participant_ids + - submitter_sample_ids + - submitter_specimen_ids - genome_annotation - genome_build - variant_calling_strategy @@ -4425,32 +4513,32 @@ classes: name: submitter_analysis_id rank: 1 slot_group: Database Identifiers - submitter_experiment_id: - name: submitter_experiment_id - rank: 2 - slot_group: Database Identifiers - submitter_participant_id: - name: submitter_participant_id - rank: 3 - slot_group: Database Identifiers - submitter_sample_id: - name: submitter_sample_id - rank: 4 - slot_group: Database Identifiers - submitter_specimen_id: - name: submitter_specimen_id - rank: 5 - slot_group: Database Identifiers analysisType: name: analysisType - rank: 6 + rank: 2 slot_group: Analysis data_category: name: data_category - rank: 7 + rank: 3 slot_group: Analysis studyId: name: studyId + rank: 4 + slot_group: Analysis + submitter_experiment_ids: + name: submitter_experiment_ids + rank: 5 + slot_group: Analysis + submitter_participant_ids: + name: submitter_participant_ids + rank: 6 + slot_group: Analysis + submitter_sample_ids: + name: submitter_sample_ids + rank: 7 + slot_group: Analysis + submitter_specimen_ids: + name: submitter_specimen_ids rank: 8 slot_group: Analysis genome_annotation: diff --git a/custom/pcgl/pcgl_full.yaml b/custom/pcgl/pcgl_full.yaml index 488ef9a..c35fbec 100644 --- a/custom/pcgl/pcgl_full.yaml +++ b/custom/pcgl/pcgl_full.yaml @@ -1135,6 +1135,33 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64} + submitter_participant_ids: + name: submitter_participant_ids + annotations: + specifications: + tag: specifications + value: FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier + description: A list of Unique identifiers (min 1) for participants within the + study, assigned by the data provider. + title: submitter_participant_ids + examples: + - value: '90234' + - value: BLD_donor_89 + - value: AML-90 + exact_mappings: + - ARGO.v1.34:donor.submitter_donor_id + - Beacon.v2.2.0:individual.id + - CQDG:submitter_participant_id + - FHIR.v5.0.0:Patient.identifier + - mCODE.v4.0.0:Patient.identifier + - MOHCCN.v3.1:Donor.submitter_donor_id + - Phenopackets.v2.0:Individual.id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64} + minimum_cardinality: 1 vital_status: name: vital_status annotations: @@ -1821,6 +1848,33 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_specimen_ids: + name: submitter_specimen_ids + annotations: + specifications: + tag: specifications + value: FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier + description: List of Unique identifiers (min 1) for specimens within the study, + assigned by the data provider. + title: submitter_specimen_ids + examples: + - value: LAML_PO + - value: '00445' + - value: THY_099-tumour + exact_mappings: + - ARGO.v1.34:specimen.submitter_specimen_id + - Beacon.v2.2.0:biosample.id + - CQDG:submitter_biospecimen_id + - FHIR.v5.0.0:Specimen.identifier + - mCODE.v4.0.0:Specimen.identifier + - MOHCCN.v3.1:specimen.submitter_specimen_id + - Phenopackets.v2.0:Biosample.derived_from_id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + minimum_cardinality: 1 age_at_diagnosis: name: age_at_diagnosis annotations: @@ -2149,6 +2203,27 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_sample_ids: + name: submitter_sample_ids + description: 'List of Unique identifiers (min 1) for samples within the study, + assigned by the data provider. + + ' + title: submitter_sample_ids + examples: + - value: hnc_12 + - value: CCG_34_94583 + - value: BRCA47832-3239 + exact_mappings: + - ARGO.v1.34:sample_registration.submitter_sample_id + - MOHCCN.v3.1:Sample_registration.submitter_sample_id + - Phenopackets.v2.0:Biosample.id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + minimum_cardinality: 1 sample_status: name: sample_status description: 'Indicate the status of the sample for data analysis. @@ -2171,6 +2246,19 @@ slots: range: string required: true pattern: ^[A-Za-z0-9\-\._]{1,64}$ + submitter_experiment_ids: + name: submitter_experiment_ids + description: A list of Unique identifiers (min 1) for experiments within the study, + assigned by the data provider. + title: submitter_experiment_ids + exact_mappings: + - ARGO.v1.34:experiment.submitter_sequencing_experiment_id + list_elements_unique: true + range: string + required: true + multivalued: true + pattern: ^[A-Za-z0-9\-\._]{1,64}$ + minimum_cardinality: 1 experiment_type: name: experiment_type description: Indicate NCIt (NCI Thesaurus) code and term to denote the broad type @@ -4390,13 +4478,13 @@ classes: title: Analysis slots: - submitter_analysis_id - - submitter_experiment_id - - submitter_participant_id - - submitter_sample_id - - submitter_specimen_id - analysisType - data_category - studyId + - submitter_experiment_ids + - submitter_participant_ids + - submitter_sample_ids + - submitter_specimen_ids - genome_annotation - genome_build - variant_calling_strategy @@ -4406,32 +4494,32 @@ classes: name: submitter_analysis_id rank: 1 slot_group: Database Identifiers - submitter_experiment_id: - name: submitter_experiment_id - rank: 2 - slot_group: Database Identifiers - submitter_participant_id: - name: submitter_participant_id - rank: 3 - slot_group: Database Identifiers - submitter_sample_id: - name: submitter_sample_id - rank: 4 - slot_group: Database Identifiers - submitter_specimen_id: - name: submitter_specimen_id - rank: 5 - slot_group: Database Identifiers analysisType: name: analysisType - rank: 6 + rank: 2 slot_group: Analysis data_category: name: data_category - rank: 7 + rank: 3 slot_group: Analysis studyId: name: studyId + rank: 4 + slot_group: Analysis + submitter_experiment_ids: + name: submitter_experiment_ids + rank: 5 + slot_group: Analysis + submitter_participant_ids: + name: submitter_participant_ids + rank: 6 + slot_group: Analysis + submitter_sample_ids: + name: submitter_sample_ids + rank: 7 + slot_group: Analysis + submitter_specimen_ids: + name: submitter_specimen_ids rank: 8 slot_group: Analysis genome_annotation: diff --git a/lectern/pcgl/pcgl_lectern.json b/lectern/pcgl/pcgl_lectern.json index 0faedff..a7b5d3b 100644 --- a/lectern/pcgl/pcgl_lectern.json +++ b/lectern/pcgl/pcgl_lectern.json @@ -1,4070 +1,4038 @@ { - "description": "The PCGL Data Dictionary specifies the standardized data elements, controlled vocabulary, data types, validation rules, and interoperability mappings for all health and genomic data submitted to the Pan-Canadian Genome Library.", - "meta": { - "version": { - "base": "1.0", - "extension": "0.0" + "name": "prod_pcgl_schema", + "description": "The PCGL Data Dictionary specifies the standardized data elements, controlled vocabulary, data types, validation rules, and interoperability mappings for all health and genomic data submitted to the Pan-Canadian Genome Library.", + "version": "2.0", + "meta": { + "version": { + "base": "1.0", + "extension": "0.0" + } + }, + "schemas": [ + { + "name": "study", + "description": "Study refers to a specific research project conducted as part of a larger program. It involves data collection, analysis, and interpretation related to the program's goals. Each study is focused on particular research questions related to set of objectives. Upon registration will be provided a PCGL ID following the regex convention: `PCGLST[0-9]{4}`", + "fields": [ + { + "meta": { + "displayName": "dac_id" + }, + "name": "dac_id", + "description": "Unique identifier of the Data Access Committee (DAC) in PCGL to which the study is assigned. This will be supplied by PCGL Admin", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "context" + }, + "name": "context", + "description": "Indicate if the study was conducted in a clinical setting or as part of a research project.", + "restrictions": { + "required": true, + "codeList": [ + "Clinical", + "Research" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "domain" + }, + "name": "domain", + "description": "List of specific scientific or clinical domains addressed by the study. In case there are several, place each on separate line.", + "restrictions": { + "required": true, + "codeList": [ + "Aging", + "Birth Defects", + "Cancer", + "Circulatory and Respiratory Health", + "General Health", + "Infection and Immunity", + "Musculoskeletal Health and Arthritis", + "Neurodevelopmental Conditions", + "Neurosciences, Mental Health and Addiction", + "Nutrition, Metabolism and Diabetes", + "Population Genomics", + "Rare Diseases", + "Other" + ] + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "funding_sources", + "examples": [ + "National Example Foundation, NEF-12345", + "Example Health Research Council" + ] + }, + "name": "funding_sources", + "description": "List of organizations or agencies funding the study. \n\nIn case there are several, please list each funding source on a separate line in the format:\nFunder name, Grant number", + "restrictions": { + "required": true + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "lead_organizations" + }, + "name": "lead_organizations", + "description": "List of institutions or organizations leading the study.\nIn case there are several, please list each lead organization on a separate line using its full official name.", + "restrictions": { + "required": true + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "principal_investigators", + "examples": [ + "John Doe, Example Research Institute" + ] + }, + "name": "principal_investigators", + "description": "List of lead researchers responsible for the study.\nIn case there are several, please list each investigator on a separate line in the format:\nFirstName LastName, Affiliation", + "restrictions": { + "required": true + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "status" + }, + "name": "status", + "description": "Indicate if the study is completed or ongoing.", + "restrictions": { + "required": true, + "codeList": [ + "Ongoing", + "Completed" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "study_description" + }, + "name": "study_description", + "description": "A detailed description of the study's purpose, hypothesis, and design.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "study_name" + }, + "name": "study_name", + "description": "The official name of the study", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "collaborators", + "examples": [ + "Biotech Inc., Industry Partner", + "Emily John, Data Contributor" + ] + }, + "name": "collaborators", + "description": "List of researchers, institutions or companies involved in the study.\n\nIn case there are several, please list each collaborator on a separate line in the format:\nFirstName LastName (if individual) or Organization full official name, Role", + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "keywords" + }, + "name": "keywords", + "description": "List of specific terms that describe the focus and content of the study. In case there are several, place each on separate line.", + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "participant_criteria" + }, + "name": "participant_criteria", + "description": "Inclusion/exclusion criteria for participants (e.g., specific cancer type, age range).", + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "program_name" + }, + "name": "program_name", + "description": "Indicate the overarching program the study belongs to (if applicable)", + "valueType": "string" + }, + { + "meta": { + "displayName": "publication_links" + }, + "name": "publication_links", + "description": "List of URL links to academic papers or reports associated with the study. \nIn case there are several, please list each publication on a separate line by providing a DOI URL formatted as https://doi.org/ followed by the DOI number.", + "valueType": "string", + "isArray": true, + "delimiter": "|" } + ] }, - "name": "Pan-Canadian Genome Library Data Dictionary", - "schemas": [ + { + "name": "dac", + "description": "A group of individuals responsible for reviewing and approving or denying access requests to data based on established policies. Upon registration will be provided a PCGL ID following the regex convention: `PCGLDA[0-9]{4}`", + "fields": [ { - "description": "Study refers to a specific research project conducted as part of a larger program. It involves data collection, analysis, and interpretation related to the program's goals. Each study is focused on particular research questions related to set of objectives. Upon registration will be provided a PCGL ID following the regex convention: `PCGLST[0-9]{4}`", - "fields": [ - { - "description": "The official name of the study", - "meta": { - "displayName": "study_name" - }, - "name": "study_name", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "A detailed description of the study's purpose, hypothesis, and design.", - "meta": { - "displayName": "study_description" - }, - "name": "study_description", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate the overarching program the study belongs to (if applicable)", - "meta": { - "displayName": "program_name" - }, - "name": "program_name", - "valueType": "string" - }, - { - "delimiter": "|", - "description": "List of specific terms that describe the focus and content of the study. In case there are several, place each on separate line.", - "isArray": true, - "meta": { - "displayName": "keywords" - }, - "name": "keywords", - "valueType": "string" - }, - { - "description": "Indicate if the study is completed or ongoing.", - "meta": { - "displayName": "status" - }, - "name": "status", - "restrictions": { - "codeList": [ - "Ongoing", - "Completed" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate if the study was conducted in a clinical setting or as part of a research project.", - "meta": { - "displayName": "context" - }, - "name": "context", - "restrictions": { - "codeList": [ - "Clinical", - "Research" - ], - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "List of specific scientific or clinical domains addressed by the study. In case there are several, place each on separate line.", - "isArray": true, - "meta": { - "displayName": "domain" - }, - "name": "domain", - "restrictions": { - "codeList": [ - "Aging", - "Birth Defects", - "Cancer", - "Circulatory and Respiratory Health", - "General Health", - "Infection and Immunity", - "Musculoskeletal Health and Arthritis", - "Neurodevelopmental Conditions", - "Neurosciences, Mental Health and Addiction", - "Nutrition, Metabolism and Diabetes", - "Population Genomics", - "Rare Diseases", - "Other" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the Data Access Committee (DAC) in PCGL to which the study is assigned. This will be supplied by PCGL Admin", - "meta": { - "displayName": "dac_id" - }, - "name": "dac_id", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "Inclusion/exclusion criteria for participants (e.g., specific cancer type, age range).", - "isArray": true, - "meta": { - "displayName": "participant_criteria" - }, - "name": "participant_criteria", - "valueType": "string" - }, - { - "delimiter": "|", - "description": "List of lead researchers responsible for the study.\nIn case there are several, please list each investigator on a separate line in the format:\nFirstName LastName, Affiliation", - "isArray": true, - "meta": { - "displayName": "principal_investigators", - "examples": [ - "John Doe, Example Research Institute" - ] - }, - "name": "principal_investigators", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "List of institutions or organizations leading the study.\nIn case there are several, please list each lead organization on a separate line using its full official name.", - "isArray": true, - "meta": { - "displayName": "lead_organizations" - }, - "name": "lead_organizations", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "List of researchers, institutions or companies involved in the study.\n\nIn case there are several, please list each collaborator on a separate line in the format:\nFirstName LastName (if individual) or Organization full official name, Role", - "isArray": true, - "meta": { - "displayName": "collaborators", - "examples": [ - "Biotech Inc., Industry Partner", - "Emily John, Data Contributor" - ] - }, - "name": "collaborators", - "valueType": "string" - }, - { - "delimiter": "|", - "description": "List of organizations or agencies funding the study. \n\nIn case there are several, please list each funding source on a separate line in the format:\nFunder name, Grant number", - "isArray": true, - "meta": { - "displayName": "funding_sources", - "examples": [ - "National Example Foundation, NEF-12345", - "Example Health Research Council" - ] - }, - "name": "funding_sources", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "List of URL links to academic papers or reports associated with the study. \nIn case there are several, please list each publication on a separate line by providing a DOI URL formatted as https://doi.org/ followed by the DOI number.", - "isArray": true, - "meta": { - "displayName": "publication_links" - }, - "name": "publication_links", - "valueType": "string" - } + "meta": { + "displayName": "contact_email" + }, + "name": "contact_email", + "description": "Contact email for communication.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "contact_name", + "examples": [ + "Jone Smith" + ] + }, + "name": "contact_name", + "description": "The full name of the primary contact person. Please provide in the format: FirstName LastName", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "dac_description" + }, + "name": "dac_description", + "description": "An in-depth description of the DAC, including its overall purpose, scope and responsibilities.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "dac_name" + }, + "name": "dac_name", + "description": "Full name of the DAC.", + "restrictions": { + "required": true + }, + "valueType": "string" + } + ] + }, + { + "name": "participant", + "description": "The collection of all data related to a specific individual human in the context of a specific study.", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" ], - "name": "study" + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string", + "unique": true }, { - "description": "A group of individuals responsible for reviewing and approving or denying access requests to data based on established policies. Upon registration will be provided a PCGL ID following the regex convention: `PCGLDA[0-9]{4}`", - "fields": [ - { - "description": "Full name of the DAC.", - "meta": { - "displayName": "dac_name" - }, - "name": "dac_name", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "An in-depth description of the DAC, including its overall purpose, scope and responsibilities.", - "meta": { - "displayName": "dac_description" - }, - "name": "dac_description", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "The full name of the primary contact person. Please provide in the format: FirstName LastName", - "meta": { - "displayName": "contact_name", - "examples": [ - "Jone Smith" - ] - }, - "name": "contact_name", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "Contact email for communication.", - "meta": { - "displayName": "contact_email" - }, - "name": "contact_email", - "restrictions": { - "required": true - }, - "valueType": "string" + "meta": { + "displayName": "duo_permission", + "exact_mappings": { + "CQDG": "duo_permission" + } + }, + "name": "duo_permission", + "description": "Select one of the Data Use Ontology (DUO) codes in Compact URI (CURIE) pattern to indicate permitted uses or focused areas of research for the Participant data.", + "restrictions": { + "required": true, + "codeList": [ + "DUO:0000042 (general research use)", + "DUO:0000006 (health or medical or biomedical research)", + "DUO:0000007 (disease specific research)", + "DUO:0000011 (population origins or ancestry research only)", + "DUO:0000004 (no restriction)" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "disease_specific_modifier", + "examples": [ + "MONDO:0000001" + ] + }, + "name": "disease_specific_modifier", + "description": "If the permission is DUO:0000007 (disease specific research), then MONDO codes must be provided to specify which disease(s) apply.", + "valueType": "string", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "duo_permission" + ], + "match": { + "value": "DUO:0000007 (disease specific research)" + }, + "case": "all" } + ] + }, + "then": { + "required": true, + "regex": "^MONDO:\\d{7}$" + }, + "else": { + "required": false, + "empty": true + } + }, + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "duo_modifier", + "exact_mappings": { + "CQDG": "duo_modifier" + } + }, + "name": "duo_modifier", + "description": "Collection of Data Use Ontology (DUO) codes in Compact URI (CURIE) pattern to add requirements, limitations, or prohibitions within the permitted boundary for the Participant data.", + "valueType": "string", + "restrictions": { + "codeList": [ + "DUO:0000043 (clinical care use)", + "DUO:0000029 (return to database or resource)", + "DUO:0000028 (institution specific restriction)", + "DUO:0000027 (project specific restriction)", + "DUO:0000026 (user specific restriction)", + "DUO:0000025 (time limit on use)", + "DUO:0000024 (publication moratorium)", + "DUO:0000022 (geographical restriction)", + "DUO:0000021 (ethics approval required)", + "DUO:0000020 (collaboration required)", + "DUO:0000019 (publication required)", + "DUO:0000018 (not for profit, non commercial use only)", + "DUO:0000046 (non-commercial use only)", + "DUO:0000045 (not for profit organisation use only)", + "DUO:0000016 (genetic studies only)", + "DUO:0000015 (no general methods research)", + "DUO:0000012 (research specific restrictions)", + "DUO:00000044 (population origins or ancestry research prohibited)" + ] + }, + "isArray": true, + "delimiter": "|" + } + ] + }, + { + "name": "sociodemographic", + "description": "Captures sociodemographic characteristics of an individual that may vary over time and can influence health status, access to care, or disease outcomes. These factors are often collected longitudinally and reflect broader social determinants of health. The PCGL requires information on eight key sociodemographic variables defined by the Canadian Institute for Health Information (CIHI).", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" ], - "name": "dac" + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" }, { - "description": "The collection of all data related to a specific individual human in the context of a specific study.", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Select one of the Data Use Ontology (DUO) codes in Compact URI (CURIE) pattern to indicate permitted uses or focused areas of research for the Participant data.", - "meta": { - "displayName": "duo_permission", - "exact_mappings": { - "CQDG": "duo_permission" - } - }, - "name": "duo_permission", - "restrictions": { - "codeList": [ - "DUO:0000042 (general research use)", - "DUO:0000006 (health or medical or biomedical research)", - "DUO:0000007 (disease specific research)", - "DUO:0000011 (population origins or ancestry research only)", - "DUO:0000004 (no restriction)" - ], - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "Collection of Data Use Ontology (DUO) codes in Compact URI (CURIE) pattern to add requirements, limitations, or prohibitions within the permitted boundary for the Participant data.", - "isArray": true, - "meta": { - "displayName": "duo_modifier", - "exact_mappings": { - "CQDG": "duo_modifier" - } - }, - "name": "duo_modifier", - "restrictions": { - "codeList": [ - "DUO:0000043 (clinical care use)", - "DUO:0000029 (return to database or resource)", - "DUO:0000028 (institution specific restriction)", - "DUO:0000027 (project specific restriction)", - "DUO:0000026 (user specific restriction)", - "DUO:0000025 (time limit on use)", - "DUO:0000024 (publication moratorium)", - "DUO:0000022 (geographical restriction)", - "DUO:0000021 (ethics approval required)", - "DUO:0000020 (collaboration required)", - "DUO:0000019 (publication required)", - "DUO:0000018 (not for profit, non commercial use only)", - "DUO:0000046 (non-commercial use only)", - "DUO:0000045 (not for profit organisation use only)", - "DUO:0000016 (genetic studies only)", - "DUO:0000015 (no general methods research)", - "DUO:0000012 (research specific restrictions)", - "DUO:00000044 (population origins or ancestry research prohibited)" - ] - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "If the permission is DUO:0000007 (disease specific research), then MONDO codes must be provided to specify which disease(s) apply.", - "isArray": true, - "meta": { - "displayName": "disease_specific_modifier", - "examples": [ - "MONDO:0000001" - ] - }, - "name": "disease_specific_modifier", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "all", - "fields": [ - "duo_permission" - ], - "match": { - "value": "DUO:0000007 (disease specific research)" - } - } - ] - }, - "then": { - "regex": "^MONDO:\\d{7}$", - "required": true - } - }, - "valueType": "string" + "meta": { + "displayName": "submitter_sociodem_id", + "examples": [ + "90234", + "BLD_participant_89", + "AML-90" + ] + }, + "name": "submitter_sociodem_id", + "description": "Unique identifier for the sociodemographic record, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "age_at_sociodem_collection", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "age_at_sociodem_collection", + "description": "Age (in days) of the participant at the time of sociodemographic data collection", + "restrictions": { + "required": true + }, + "valueType": "integer" + }, + { + "meta": { + "displayName": "education", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "education", + "description": "The highest level of education attained.", + "restrictions": { + "required": true, + "codeList": [ + "No formal education", + "Elementary school or equivalent", + "High school (secondary school) diploma or equivalency certificate", + "Certificate of Apprenticeship, Certificate of Qualification (Journeyperson's designation), or other trades certificate or diploma", + "College, CEGEP, or other non-university certificate or diploma", + "Bachelor's degree", + "Degree in medicine, dentistry, veterinary medicine or optometry", + "Master's degree", + "Doctoral degree", + "Post-doctoral fellowship or training", + "Prefer not to answer", + "Not applicable", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "education_collect_method" + }, + "name": "education_collect_method", + "description": "Studies must report how the education data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", + "restrictions": { + "required": true, + "codeList": [ + "Self-identified", + "Derived", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "ethnicity", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + }, + "comments": [ + "EDI indicator" + ] + }, + "name": "ethnicity", + "description": "Ethnicity is a 'multi-dimensional concept referring to community belonging and a shared cultural group membership.\nIt is related to sociodemographic characteristics, including language, religion, geographic origin, nationality, cultural traditions, ancestry and migration history, among others,'\n[REF: Canadian Institute for Health Information. Guidance on the Use of Standards for Race-Based and Indigenous Identity Data Collection and Health Reporting in Canada (2022)][REF: Canadian Institute for Health Information.Guidance on the Use of Standards for Race-Based and Indigenous Identity Data Collection and Health Reporting in Canada.(2022)](https://www.cihi.ca/sites/default/files/document/guidance-and-standards-for-race-based-and-indigenous-identity-data-en.pdf).\nParticipants may have multiple ethnic and/or cultural identities.\nAll categories entered by the participants should be reported.", + "restrictions": { + "required": true, + "codeList": [ + "Free text input", + "Another Ethnic or Cultural Origin", + "Do not know", + "Prefer not to answer", + "Not applicable", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "ethnicity_collect_method" + }, + "name": "ethnicity_collect_method", + "description": "Studies must report how the ethnicity data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", + "restrictions": { + "required": true, + "codeList": [ + "Socially assigned", + "Self-identified", + "Derived", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "gender", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0", + "Phenopackets.v2.0": "Individual.gender" + }, + "comments": [ + "EDI indicator" + ] + }, + "name": "gender", + "description": "Gender refers to the socially constructed roles, behaviours, expressions and identities of girls, women, boys, men, and gender diverse people.\nA person\u2019s gender may be the same as or different from their assigned sex at birth and may change over time.", + "restrictions": { + "required": true, + "codeList": [ + "Man", + "Woman", + "Another Gender", + "Prefer not to answer", + "Not applicable", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "gender_collect_method" + }, + "name": "gender_collect_method", + "description": "Studies must report how the gender data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", + "restrictions": { + "required": true, + "codeList": [ + "Self-identified", + "Other", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "geographic_location", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "geographic_location", + "description": "A participant's postal code at their current address of residence.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z][0-9][A-Za-z][0-9][A-Za-z][0-9]$|^Missing \\- Unknown$|^Missing \\- Not collected$|^Missing \\- Not provided$|^Missing \\- Restricted access$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "geographic_location_collect_method" + }, + "name": "geographic_location_collect_method", + "description": "Studies must report how the geographic_location data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", + "restrictions": { + "required": true, + "codeList": [ + "Self-identified", + "Derived", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "personal_income", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "personal_income", + "description": "Personal annual income from all sources after taxes.", + "restrictions": { + "required": true, + "codeList": [ + "Less than $15,000", + "$ 15,000 - $ 19,999", + "$ 20,000 - $ 29,000", + "$ 30,000 - $ 49,999", + "$ 50,000 - $ 69,999", + "$ 70,000 - $ 84,999", + "$ 85,000 - $ 99,999", + "$ 100,000 - $ 124,999", + "$ 125,000 - $ 149,999", + "$ 150,000 or more", + "Prefer not to answer", + "Not applicable", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "personal_income_collect_method" + }, + "name": "personal_income_collect_method", + "description": "Studies must report how the personal_income data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", + "restrictions": { + "required": true, + "codeList": [ + "Self-identified", + "Derived", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "race", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + }, + "comments": [ + "EDI indicator" + ] + }, + "name": "race", + "description": "Race is a social construct used to judge and categorize people based on perceived differences in physical appearance in ways that create and maintain power differentials within social hierarchies.\nThere is no scientifically supported biological basis for discrete racial groups\n[REF: Canadian Institute for Health Information.Guidance on the Use of Standards for Race-Based and Indigenous Identity Data Collection and Health Reporting in Canada. (2022)](https://www.cihi.ca/sites/default/files/document/guidance-and-standards-for-race-based-and-indigenous-identity-data-en.pdf).\nParticipants may have multiple racial identities.\nAll categories selected by the participants should be reported.", + "restrictions": { + "required": true, + "codeList": [ + "Black", + "East Asian", + "Indigenous (First Nations, Inuk/Inuit, M\u00e9tis)", + "Latin American", + "Middle Eastern or North African", + "South Asian", + "Southeast Asian", + "White", + "Another Racial Category", + "Do not know", + "Prefer not to answer", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "race_collect_method" + }, + "name": "race_collect_method", + "description": "Studies must report how race data was collected\n. This is necessary to enable data aggregation, harmonization, and reproducibility.\nResponses from prospective projects should always be self-identified.\nTo respect participants' autonomy and right to self-determination, as well as to avoid conflating differences in (genetic) population structure with socially constructed racial categories,responses that were self-identified should not be aggregated with responses that were socially assigned or derived.", + "restrictions": { + "required": true, + "codeList": [ + "Socially assigned", + "Self-identified", + "Derived", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "sex_at_birth", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0", + "Phenopackets.v2.0": "Individual.sex" + } + }, + "name": "sex_at_birth", + "description": "Sex is a biological concept that has been historically defined solely based on external anatomy; however, sex is also influenced by our physiology, genes, and hormones.", + "restrictions": { + "required": true, + "codeList": [ + "Male", + "Female", + "Intersex", + "Another Sex", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "sex_collect_method" + }, + "name": "sex_collect_method", + "description": "Studies must report how the sex_at_birth data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", + "restrictions": { + "required": true, + "codeList": [ + "Self-identified", + "Clinician-recorded", + "Derived", + "Other", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "sociodem_date_collection", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "sociodem_date_collection", + "description": "Many sociodemographic variables are social constructs, and the way participants self-identify may evolve over time. \nPlease indicate the actual date when the data was collected in format: YYYY-MM-DD, if available. \nIf the exact day is unknown, partial dates are acceptable:\n- Use YYYY-MM if the day is unknown but the month and year are known\n- Use YYYY if only the year is known", + "restrictions": { + "required": true, + "regex": "^(?:\\d{4}|\\d{4}-\\d{2}|\\d{4}-\\d{2}-\\d{2})$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "sociodem_question" + }, + "name": "sociodem_question", + "description": "Indicate whether the questions asked for the sociodemographic variable follow the PCGL reference question and standard reporting categories.", + "restrictions": { + "required": true, + "codeList": [ + "PCGL reference question", + "Another question", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "ethnicity_another_category", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "ethnicity_another_category", + "description": "A response which does not fall into any of the previous categories. For example, a response of \u201cOther\u201d from retrospective studies. Prospective projects should instead allow participants to freely self-identify.", + "valueType": "string", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "ethnicity" + ], + "match": { + "codeList": [ + "Free text input" + ] + }, + "case": "any" } - ], - "name": "participant" + ] + }, + "then": { + "required": true + }, + "else": { + "required": false, + "empty": true + } + } }, { - "description": "Captures sociodemographic characteristics of an individual that may vary over time and can influence health status, access to care, or disease outcomes. These factors are often collected longitudinally and reflect broader social determinants of health. The PCGL requires information on eight key sociodemographic variables defined by the Canadian Institute for Health Information (CIHI).", - "fields": [ - { - "description": "Unique identifier for the sociodemographic record, assigned by the data provider.", - "meta": { - "displayName": "submitter_sociodem_id", - "examples": [ - "90234", - "BLD_participant_89", - "AML-90" - ] - }, - "name": "submitter_sociodem_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Age (in days) of the participant at the time of sociodemographic data collection", - "meta": { - "displayName": "age_at_sociodem_collection", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "age_at_sociodem_collection", - "restrictions": { - "required": true - }, - "valueType": "integer" - }, - { - "description": "Many sociodemographic variables are social constructs, and the way participants self-identify may evolve over time. \nPlease indicate the actual date when the data was collected in format: YYYY-MM-DD, if available. \nIf the exact day is unknown, partial dates are acceptable:\n- Use YYYY-MM if the day is unknown but the month and year are known\n- Use YYYY if only the year is known", - "meta": { - "displayName": "sociodem_date_collection", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "sociodem_date_collection", - "restrictions": { - "regex": "^(?:\\d{4}|\\d{4}-\\d{2}|\\d{4}-\\d{2}-\\d{2})$", - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "Race is a social construct used to judge and categorize people based on perceived differences in physical appearance in ways that create and maintain power differentials within social hierarchies.\nThere is no scientifically supported biological basis for discrete racial groups\n[REF: Canadian Institute for Health Information.Guidance on the Use of Standards for Race-Based and Indigenous Identity Data Collection and Health Reporting in Canada. (2022)](https://www.cihi.ca/sites/default/files/document/guidance-and-standards-for-race-based-and-indigenous-identity-data-en.pdf).\nParticipants may have multiple racial identities.\nAll categories selected by the participants should be reported.", - "isArray": true, - "meta": { - "comments": [ - "EDI indicator" - ], - "displayName": "race", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "race", - "restrictions": { - "codeList": [ - "Black", - "East Asian", - "Indigenous (First Nations, Inuk/Inuit, M\u00e9tis)", - "Latin American", - "Middle Eastern or North African", - "South Asian", - "Southeast Asian", - "White", - "Another Racial Category", - "Do not know", - "Prefer not to answer", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "A response which does not fall into any of the previous racial reporting categories (e.g., Pacific Islander, Indigenous identities outside of North America, etc.).", - "meta": { - "displayName": "race_another_racial_category", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "race_another_racial_category", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "all", - "fields": [ - "race" - ], - "match": { - "codeList": [ - "Another Racial Category" - ] - } - } - ] - }, - "then": { - "required": true - } - }, - "valueType": "string" - }, - { - "description": "Studies must report how race data was collected\n. This is necessary to enable data aggregation, harmonization, and reproducibility.\nResponses from prospective projects should always be self-identified.\nTo respect participants' autonomy and right to self-determination, as well as to avoid conflating differences in (genetic) population structure with socially constructed racial categories,responses that were self-identified should not be aggregated with responses that were socially assigned or derived.", - "meta": { - "displayName": "race_collect_method" - }, - "name": "race_collect_method", - "restrictions": { - "codeList": [ - "Socially assigned", - "Self-identified", - "Derived", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Gender refers to the socially constructed roles, behaviours, expressions and identities of girls, women, boys, men, and gender diverse people.\nA person\u2019s gender may be the same as or different from their assigned sex at birth and may change over time.", - "meta": { - "comments": [ - "EDI indicator" - ], - "displayName": "gender", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0", - "Phenopackets.v2.0": "Individual.gender" - } - }, - "name": "gender", - "restrictions": { - "codeList": [ - "Man", - "Woman", - "Another Gender", - "Prefer not to answer", - "Not applicable", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "A response which does not fall into any of the previous gender reporting categories.", - "meta": { - "displayName": "gender_another_gender", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "gender_another_gender", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "all", - "fields": [ - "gender" - ], - "match": { - "value": "Another Gender" - } - } - ] - }, - "then": { - "required": true - } - }, - "valueType": "string" - }, - { - "description": "Studies must report how the gender data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", - "meta": { - "displayName": "gender_collect_method" - }, - "name": "gender_collect_method", - "restrictions": { - "codeList": [ - "Self-identified", - "Other", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "delimiter": "|", - "description": "Ethnicity is a 'multi-dimensional concept referring to community belonging and a shared cultural group membership.\nIt is related to sociodemographic characteristics, including language, religion, geographic origin, nationality, cultural traditions, ancestry and migration history, among others,'\n[REF: Canadian Institute for Health Information. Guidance on the Use of Standards for Race-Based and Indigenous Identity Data Collection and Health Reporting in Canada (2022)][REF: Canadian Institute for Health Information.Guidance on the Use of Standards for Race-Based and Indigenous Identity Data Collection and Health Reporting in Canada.(2022)](https://www.cihi.ca/sites/default/files/document/guidance-and-standards-for-race-based-and-indigenous-identity-data-en.pdf).\nParticipants may have multiple ethnic and/or cultural identities.\nAll categories entered by the participants should be reported.", - "isArray": true, - "meta": { - "comments": [ - "EDI indicator" - ], - "displayName": "ethnicity", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "ethnicity", - "restrictions": { - "codeList": [ - "Free text input", - "Another Ethnic or Cultural Origin", - "Do not know", - "Prefer not to answer", - "Not applicable", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "A response which does not fall into any of the previous categories. For example, a response of \u201cOther\u201d from retrospective studies. Prospective projects should instead allow participants to freely self-identify.", - "meta": { - "displayName": "ethnicity_another_category", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "ethnicity_another_category", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "any", - "fields": [ - "ethnicity" - ], - "match": { - "codeList": [ - "Free text input" - ] - } - } - ] - }, - "then": { - "required": true - } - }, - "valueType": "string" - }, - { - "description": "Studies must report how the ethnicity data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", - "meta": { - "displayName": "ethnicity_collect_method" - }, - "name": "ethnicity_collect_method", - "restrictions": { - "codeList": [ - "Socially assigned", - "Self-identified", - "Derived", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Sex is a biological concept that has been historically defined solely based on external anatomy; however, sex is also influenced by our physiology, genes, and hormones.", - "meta": { - "displayName": "sex_at_birth", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0", - "Phenopackets.v2.0": "Individual.sex" - } - }, - "name": "sex_at_birth", - "restrictions": { - "codeList": [ - "Male", - "Female", - "Intersex", - "Another Sex", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "A response which does not fall into any of the previous categories. ", - "meta": { - "displayName": "sex_another_category", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "sex_another_category", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "any", - "fields": [ - "sex_at_birth" - ], - "match": { - "value": "Another Sex" - } - } - ] - }, - "then": { - "required": true - } - }, - "valueType": "string" - }, - { - "description": "Studies must report how the sex_at_birth data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", - "meta": { - "displayName": "sex_collect_method" - }, - "name": "sex_collect_method", - "restrictions": { - "codeList": [ - "Self-identified", - "Clinician-recorded", - "Derived", - "Other", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "The highest level of education attained.", - "meta": { - "displayName": "education", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "education", - "restrictions": { - "codeList": [ - "No formal education", - "Elementary school or equivalent", - "High school (secondary school) diploma or equivalency certificate", - "Certificate of Apprenticeship, Certificate of Qualification (Journeyperson's designation), or other trades certificate or diploma", - "College, CEGEP, or other non-university certificate or diploma", - "Bachelor's degree", - "Degree in medicine, dentistry, veterinary medicine or optometry", - "Master's degree", - "Doctoral degree", - "Post-doctoral fellowship or training", - "Prefer not to answer", - "Not applicable", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Studies must report how the education data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", - "meta": { - "displayName": "education_collect_method" - }, - "name": "education_collect_method", - "restrictions": { - "codeList": [ - "Self-identified", - "Derived", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Personal annual income from all sources after taxes.", - "meta": { - "displayName": "personal_income", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "personal_income", - "restrictions": { - "codeList": [ - "Less than $15,000", - "$ 15,000 - $ 19,999", - "$ 20,000 - $ 29,000", - "$ 30,000 - $ 49,999", - "$ 50,000 - $ 69,999", - "$ 70,000 - $ 84,999", - "$ 85,000 - $ 99,999", - "$ 100,000 - $ 124,999", - "$ 125,000 - $ 149,999", - "$ 150,000 or more", - "Prefer not to answer", - "Not applicable", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Studies must report how the personal_income data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", - "meta": { - "displayName": "personal_income_collect_method" - }, - "name": "personal_income_collect_method", - "restrictions": { - "codeList": [ - "Self-identified", - "Derived", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "A participant's postal code at their current address of residence.", - "meta": { - "displayName": "geographic_location", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "geographic_location", - "restrictions": { - "regex": "^[A-Za-z][0-9][A-Za-z][0-9][A-Za-z][0-9]$|^Missing \\- Unknown$|^Missing \\- Not collected$|^Missing \\- Not provided$|^Missing \\- Restricted access$", - "required": true - }, - "valueType": "string" - }, - { - "description": "When postal code is less specific, additional information may be reported.", - "meta": { - "displayName": "geographic_location_additional" - }, - "name": "geographic_location_additional", - "valueType": "string" - }, - { - "description": "Studies must report how the geographic_location data was collected. This is necessary to enable data aggregation, harmonization, and reproducibility. ", - "meta": { - "displayName": "geographic_location_collect_method" - }, - "name": "geographic_location_collect_method", - "restrictions": { - "codeList": [ - "Self-identified", - "Derived", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate whether the questions asked for the sociodemographic variable follow the PCGL reference question and standard reporting categories.", - "meta": { - "displayName": "sociodem_question" - }, - "name": "sociodem_question", - "restrictions": { - "codeList": [ - "PCGL reference question", - "Another question", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Report the questions asked for the sociodemographic variable, including the provided response options/reporting categories if it does not follow the PCGL reference question and standard reporting categories.", - "meta": { - "displayName": "sociodem_question_detail", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - } - }, - "name": "sociodem_question_detail", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "any", - "fields": [ - "sociodem_question" - ], - "match": { - "codeList": [ - "PCGL reference question", - "Another question" - ] - } - } - ] - }, - "then": { - "required": true - } - }, - "valueType": "string" - }, - { - "description": "Studies may choose to report whether potential bias may exist due to the way reporting categories were defined and handled.", - "meta": { - "displayName": "sociodem_notes", - "exact_mappings": { - "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" - }, - "examples": [ - "For example, in the Canadian Census, the order of the provided response options for ethnicity were shown to influence number of received responses per reporting option. \n\nOther examples may include inclusion/exclusion criteria based on sociodemographic variables." - ] - }, - "name": "sociodem_notes", - "valueType": "string" + "meta": { + "displayName": "gender_another_gender", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "gender_another_gender", + "description": "A response which does not fall into any of the previous gender reporting categories.", + "valueType": "string", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "gender" + ], + "match": { + "value": "Another Gender" + }, + "case": "all" } - ], - "name": "sociodemographic", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Data for the characterization of the participant by means of segmenting the population (e.g., characterization by age, sex, or race).", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Age (in days) of participant at time of enrollment into the study", - "meta": { - "displayName": "age_at_enrollment" - }, - "name": "age_at_enrollment", - "valueType": "integer" - }, - { - "description": "Participant's last known state of living or deceased.", - "meta": { - "displayName": "vital_status", - "exact_mappings": { - "ARGO.v1.34": "donor.vital_status", - "CQDG": "vital_status", - "MOHCCN.v3.1": "Donor.is_deceased", - "Phenopackets.v2.0": "Individual.vital_status" - }, - "related_mappings": { - "FHIR.v5.0.0": "derive_from_Patient.deceased.boolean" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.deceased_x_" - ] - }, - "name": "vital_status", - "restrictions": { - "codeList": [ - "Alive", - "Deceased", - "Not applicable", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ] - }, - "valueType": "string" - }, - { - "description": "Indicate the cause of a participant's death.", - "meta": { - "displayName": "cause_of_death", - "exact_mappings": { - "ARGO.v1.34": "donor.cause_of_death", - "MOHCCN.v3.1": "Donor.cause_of_death", - "Phenopackets.v2.0": "VitalStatus.cause_of_death" - } - }, - "name": "cause_of_death", - "restrictions": { - "codeList": [ - "Died of cancer", - "Died of other reasons", - "Not applicable", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access" - ] - }, - "valueType": "string" - }, - { - "description": "Age of participant (in days) at time of death", - "meta": { - "displayName": "age_at_death", - "exact_mappings": { - "ARGO.v1.34": "donor.survival_time", - "Phenopackets.v2.0": "VitalStatus.survival_time_in_days" - }, - "related_mappings": { - "FHIR.v5.0.0": "Patient.deceased.dateTime-Patient.birthDate", - "MOHCCN.v3.1": "Donor.date_at_death-Donor.date_of_birth", - "mCODE.v4.0.0": "Patient.deceased.dateTime-Patient.birthDate" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.deceased_x_", - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" - ] - }, - "name": "age_at_death", - "valueType": "integer" + ] + }, + "then": { + "required": true + }, + "else": { + "required": false, + "empty": true + } + } + }, + { + "meta": { + "displayName": "geographic_location_additional" + }, + "name": "geographic_location_additional", + "description": "When postal code is less specific, additional information may be reported.", + "valueType": "string" + }, + { + "meta": { + "displayName": "race_another_racial_category", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "race_another_racial_category", + "description": "A response which does not fall into any of the previous racial reporting categories (e.g., Pacific Islander, Indigenous identities outside of North America, etc.).", + "valueType": "string", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "race" + ], + "match": { + "codeList": [ + "Another Racial Category" + ] + }, + "case": "all" } - ], - "name": "demographic", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "The disease that is inferred to be present in the individual, family or cohort being analyzed.", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the primary diagnosis event, assigned by the data provider.", - "meta": { - "displayName": "submitter_diagnosis_id", - "exact_mappings": { - "ARGO.v1.34": "primary_diagnosis.submitter_diagnosis_id", - "FHIR.v5.0.0": "Condition.identifier", - "MOHCCN.v3.1": "primary_diagnosis.submitter_diagnosis_id", - "mCODE.v4.0.0": "Condition.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.identifier" - ] - }, - "name": "submitter_diagnosis_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Age of participant (in days) at time of diagnosis of the condition.", - "meta": { - "displayName": "age_at_diagnosis", - "exact_mappings": { - "ARGO.v1.34": "primary_diagnosis.age_at_diagnosis", - "FHIR.v5.0.0": "Condition.onset.onsetAge", - "Phenopackets.v2.0": "Disease.onset", - "mCODE.v4.0.0": "Condition.onset" - }, - "related_mappings": { - "MOHCCN.v3.1": "primary_diagnosis.date_of_diagnosis-donor.date_of_birth" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.onset_x_" - ] - }, - "name": "age_at_diagnosis", - "valueType": "integer" - }, - { - "description": "Use ICD-10 code or MONDO code to represent the disease diagnosed. Provide code in Compact URI (CURIE) pattern.", - "meta": { - "comments": [ - "Provide code in Compact URI (CURIE) pattern. ICD-10 code: refer to https://icd.who.int/browse10/2019/en MONDO code: refer to https://www.ebi.ac.uk/ols/ontologies/mondo" - ], - "displayName": "disease_code", - "exact_mappings": { - "ARGO.v1.34": "primary_diagnosis.cancer_type_code", - "CQDG": "disease_code", - "FHIR.v5.0.0": "Condition.code.coding.code", - "MOHCCN.v3.1": "primary_diagnosis.cancer_type_code", - "Phenopackets.v2.0": "Disease.term.id", - "mCODE.v4.0.0": "Condition.code.coding.code" - }, - "examples": [ - "MONDO:0000001", - "icd10:C34" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" - ] - }, - "name": "disease_code", - "restrictions": { - "regex": "^icd10:[A-Z][0-9][A-Z0-9](\\.[A-Z0-9]{1,4})?$|^MONDO:\\d{7}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the disease_code", - "meta": { - "displayName": "disease_term", - "exact_mappings": { - "FHIR.v5.0.0": "Condition.code.coding.display", - "Phenopackets.v2.0": "Disease.term.label", - "mCODE.v4.0.0": "Condition.code.coding.display" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" - ] - }, - "name": "disease_term", - "valueType": "string" + ] + }, + "then": { + "required": true + }, + "else": { + "required": false, + "empty": true + } + } + }, + { + "meta": { + "displayName": "sex_another_category", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "sex_another_category", + "description": "A response which does not fall into any of the previous categories. ", + "valueType": "string", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "sex_at_birth" + ], + "match": { + "value": "Another Sex" + }, + "case": "any" } - ], - "name": "diagnosis", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Medications, procedures, other actions taken for clinical management", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the treatment, assigned by the data provider.", - "meta": { - "displayName": "submitter_treatment_id", - "exact_mappings": { - "FHIR.v5.0.0": "Procedure.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" - ] - }, - "name": "submitter_treatment_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "The category or method of treatment administered", - "meta": { - "displayName": "treatment_type" - }, - "name": "treatment_type", - "restrictions": { - "codeList": [ - "Medication", - "Procedure", - "Radiation therapy", - "Other" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the primary diagnosis event, assigned by the data provider.", - "meta": { - "displayName": "submitter_diagnosis_id", - "exact_mappings": { - "ARGO.v1.34": "primary_diagnosis.submitter_diagnosis_id", - "FHIR.v5.0.0": "Condition.identifier", - "MOHCCN.v3.1": "primary_diagnosis.submitter_diagnosis_id", - "mCODE.v4.0.0": "Condition.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.identifier" - ] - }, - "name": "submitter_diagnosis_id", - "restrictions": { - "if": { - "conditions": [ - { - "case": "all", - "fields": [ - "submitter_treatment_id" - ], - "match": { - "exists": false - } - } - ] - }, - "then": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": false - } - }, - "valueType": "string" - }, - { - "description": "Age (in days) of the participant at the time the treatment was administered.", - "meta": { - "displayName": "age_at_treatment", - "related_mappings": { - "ARGO.v1.34": "treatment.treatment_start_interval+donor.age_at_diagnosis", - "FHIR.v5.0.0": "Procedure.occurrenceDateTime-Patient.birthDate", - "MOHCCN.v3.1": "Systemic_therapy.start_date-Donor.date_of_birth", - "Phenopackets.v2.0": "TherapeuticRegimen.end_time-Individual.date_of_birth" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.occurrence_x_", - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" - ] - }, - "name": "age_at_treatment", - "valueType": "integer" - }, - { - "description": "The length of time (in days) over which the treatment was administered.", - "meta": { - "displayName": "treatment_duration", - "exact_mappings": { - "ARGO.v1.34": "treatment.treatment_duration", - "FHIR.v5.0.0": "Procedure.occurrencePeriod" - }, - "related_mappings": { - "MOHCCN.v3.1": "Systemic_therapy.start_date-Systemic_therapy.end_date", - "Phenopackets.v2.0": "TreatmentRegimen.end_time-TreatmentRegimen.start_time" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.occurrence_x_" - ] - }, - "name": "treatment_duration", - "valueType": "integer" - }, - { - "description": "The purpose of the treatment or the desired effect or outcome resulting from the treatment.", - "meta": { - "displayName": "treatment_intent", - "exact_mappings": { - "ARGO.v1.34": "treatment.treatment_intent", - "MOHCCN.v3.1": "Treatment.treatment_intent" - } - }, - "name": "treatment_intent", - "restrictions": { - "codeList": [ - "Curative", - "Diagnostic", - "Forensic", - "Guidance", - "Palliative", - "Preventative", - "Screening", - "Supportive", - "Other", - "Missing - Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Not applicable" - ] - }, - "valueType": "string" - }, - { - "description": "The outcome of the treatment, indicating how the patient responded to the intervention", - "meta": { - "displayName": "treatment_response", - "exact_mappings": { - "ARGO.v1.34": "treatment.response_to_treatment", - "CQDG": "treatment_response", - "MOHCCN.v3.1": "Treatment.response_to_treatment" - } - }, - "name": "treatment_response", - "restrictions": { - "codeList": [ - "Clinical remission", - "Disease Progression", - "Improvement of symptoms", - "No improvement of symptoms", - "No sign of disease", - "Partial Response", - "Stable Disease", - "Treatment cessation due to toxicity", - "Worsening of symptoms", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown", - "Not applicable" - ] - }, - "valueType": "string" - }, - { - "description": "Indicate the participant's status of the prescribed treatment.", - "meta": { - "displayName": "treatment_status", - "exact_mappings": { - "ARGO.v1.34": "treatment.outcome_of_treatment", - "MOHCCN.v3.1": "Treatment.status_of_treatment" - } - }, - "name": "treatment_status", - "restrictions": { - "codeList": [ - "Other", - "Patient choice (stopped or interrupted treatment)", - "Physician decision (stopped or interrupted treatment)", - "Treatment completed as prescribed", - "Treatment incomplete because patient died", - "Treatment incomplete due to technical or organizational problems", - "Treatment ongoing", - "Treatment stopped due to acute toxicity", - "Treatment stopped due to lack of efficacy (disease progression)", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown", - "Not applicable" - ] - }, - "valueType": "string" + ] + }, + "then": { + "required": true + }, + "else": { + "required": false, + "empty": true + } + } + }, + { + "meta": { + "displayName": "sociodem_notes", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + }, + "examples": [ + "For example, in the Canadian Census, the order of the provided response options for ethnicity were shown to influence number of received responses per reporting option. \n\nOther examples may include inclusion/exclusion criteria based on sociodemographic variables." + ] + }, + "name": "sociodem_notes", + "description": "Studies may choose to report whether potential bias may exist due to the way reporting categories were defined and handled.", + "valueType": "string" + }, + { + "meta": { + "displayName": "sociodem_question_detail", + "exact_mappings": { + "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0": "PCGL.Reference.Survey.v1.0.and.PCGL.Guidance.Document.for.Participant.Sociodemographic.Data.v1.0" + } + }, + "name": "sociodem_question_detail", + "description": "Report the questions asked for the sociodemographic variable, including the provided response options/reporting categories if it does not follow the PCGL reference question and standard reporting categories.", + "valueType": "string", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "sociodem_question" + ], + "match": { + "codeList": [ + "PCGL reference question", + "Another question" + ] + }, + "case": "any" } + ] + }, + "then": { + "required": true + }, + "else": { + "required": false, + "empty": true + } + } + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "demographic", + "description": "Data for the characterization of the participant by means of segmenting the population (e.g., characterization by age, sex, or race).", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" ], - "name": "treatment", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_diagnosis_id", - "local": "submitter_diagnosis_id" - } - ], - "schema": "diagnosis" - }, - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Any point of contact with a patient after primary diagnosis. ", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Participant's age (in days) at time of the follow up event", - "meta": { - "displayName": "age_at_followup", - "related_mappings": { - "ARGO.v1.34": "primary_diagnosis.age_at_diagnosis+followup.interval_of_followup", - "FHIR.v5.0.0": "Observation.effectiveDateTime-Patient.birthDate", - "MOHCCN.v3.1": "Follow_up.date_of_followup-Donor.date_of_birth" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_", - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" - ] - }, - "name": "age_at_followup", - "valueType": "integer" - }, - { - "description": "Indicate the participant's disease status at time of follow-up", - "meta": { - "displayName": "disease_status_at_followup", - "exact_mappings": { - "ARGO.v1.34": "follow_up.disease_status_at_followup", - "MOHCCN.v3.1": "Follow_up.disease_status_at_followup" - } - }, - "name": "disease_status_at_followup", - "restrictions": { - "codeList": [ - "Complete remission", - "Distant progression", - "Loco-regional progression", - "No evidence of disease", - "Partial remission", - "Progression NOS", - "Relapse or recurrence", - "Stable" - ], - "required": true - }, - "valueType": "string" - } + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_death", + "exact_mappings": { + "ARGO.v1.34": "donor.survival_time", + "Phenopackets.v2.0": "VitalStatus.survival_time_in_days" + }, + "related_mappings": { + "FHIR.v5.0.0": "Patient.deceased.dateTime-Patient.birthDate", + "mCODE.v4.0.0": "Patient.deceased.dateTime-Patient.birthDate", + "MOHCCN.v3.1": "Donor.date_at_death-Donor.date_of_birth" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.deceased_x_", + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" + ] + }, + "name": "age_at_death", + "description": "Age of participant (in days) at time of death", + "valueType": "integer" + }, + { + "meta": { + "displayName": "age_at_enrollment" + }, + "name": "age_at_enrollment", + "description": "Age (in days) of participant at time of enrollment into the study", + "valueType": "integer" + }, + { + "meta": { + "displayName": "cause_of_death", + "exact_mappings": { + "ARGO.v1.34": "donor.cause_of_death", + "MOHCCN.v3.1": "Donor.cause_of_death", + "Phenopackets.v2.0": "VitalStatus.cause_of_death" + } + }, + "name": "cause_of_death", + "description": "Indicate the cause of a participant's death.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Died of cancer", + "Died of other reasons", + "Not applicable", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + } + }, + { + "meta": { + "displayName": "vital_status", + "exact_mappings": { + "ARGO.v1.34": "donor.vital_status", + "CQDG": "vital_status", + "MOHCCN.v3.1": "Donor.is_deceased", + "Phenopackets.v2.0": "Individual.vital_status" + }, + "related_mappings": { + "FHIR.v5.0.0": "derive_from_Patient.deceased.boolean" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.deceased_x_" + ] + }, + "name": "vital_status", + "description": "Participant's last known state of living or deceased.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Alive", + "Deceased", + "Not applicable", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access" + ] + } + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "diagnosis", + "description": "The disease that is inferred to be present in the individual, family or cohort being analyzed.", + "fields": [ + { + "meta": { + "displayName": "submitter_diagnosis_id", + "exact_mappings": { + "ARGO.v1.34": "primary_diagnosis.submitter_diagnosis_id", + "FHIR.v5.0.0": "Condition.identifier", + "mCODE.v4.0.0": "Condition.identifier", + "MOHCCN.v3.1": "primary_diagnosis.submitter_diagnosis_id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.identifier" ], - "name": "follow_up", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "A clinical procedure performed on a subject. For example a surgical or diagnostic procedure such as a biopsy.", - "fields": [ - { - "description": "Unique identifier of the treatment, assigned by the data provider.", - "meta": { - "displayName": "submitter_treatment_id", - "exact_mappings": { - "FHIR.v5.0.0": "Procedure.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" - ] - }, - "name": "submitter_treatment_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Use code from NCIt, SNOMED-CT, UMLS or CCI to represent the procedure performed. Provide code in Compact URI (CURIE) pattern.\n\nNCIt URL:\nhttp://purl.obolibrary.org/obo/NCIT_{code}\nSNOMED-CT URL:\nhttp://snomed.info/id/{code}\nUMLS URL:\nhttps://uts.nlm.nih.gov/uts/umls/concept/{code}\nCCI URL:\nhttps://www.cihi.ca/en/cci-coding-structure", - "meta": { - "comments": [ - "Provide code in Compact URI (CURIE) pattern. NCIt URL: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C\n SNOMED-CT URL: http://snomed.info/id/\n UMLS URL: https://uts.nlm.nih.gov/uts/umls/concept/ CCI URL:https://www.cihi.ca/en/cci-coding-structure" - ], - "displayName": "procedure_code", - "exact_mappings": { - "Phenopackets.v2.0": "Procedure.code.id" - }, - "examples": [ - "NCIT:C51894", - "snomedct:284196006", - "umls:C2584994", - "CCI:1CA14STCDR" - ], - "related_mappings": { - "FHIR.v5.0.0": "Procedure.code.coding.system:Procedure.code" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" - ] - }, - "name": "procedure_code", - "restrictions": { - "regex": "^NCIT:C\\d+$|^snomedct:(\\w+)?\\d+$|^umls:C\\d+$|^CCI:[A-Z0-9]([0-9]{2}|[A-Z]{2}){3}(([0-9]{2}|[A-Z]{2})[A-Z0-9]?)?$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the procedure_code", - "meta": { - "displayName": "procedure_term", - "exact_mappings": { - "FHIR.v5.0.0": "Procedure.code.display", - "Phenopackets.v2.0": "Procedure.code.label" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" - ] - }, - "name": "procedure_term", - "valueType": "string" - }, - { - "description": "Indicate the ICD-O-3 topography code or UBERON code for the anatomic location of a specimen when it was collected. Please use C80.9 if the anatomic location of a specimen is Unknown.", - "meta": { - "displayName": "procedure_body_site_code", - "exact_mappings": { - "ARGO.v1.34": "surgery.surgery_site", - "FHIR.v5.0.0": "Procedure.bodySite.coding.code", - "MOHCCN.v3.1": "Surgery.surgery_site", - "Phenopackets.v2.0": "Procedure.body_site.id", - "mCODE.v4.0.0": "Specimen.collection.bodySite" - }, - "examples": [ - "C50.1", - "C18" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.bodySite" - ] - }, - "name": "procedure_body_site_code", - "restrictions": { - "regex": "^ICDO3:[C][0-9]{2}(.[0-9]{1})?$|^UBERON:\\d{7,}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the procedure_body_site_code", - "meta": { - "displayName": "procedure_body_site_term", - "exact_mappings": { - "FHIR.v5.0.0": "Procedure.bodySite.coding.display", - "Phenopackets.v2.0": "Procedure.body_site.label" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.bodySite" - ] - }, - "name": "procedure_body_site_term", - "valueType": "string" - } + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_diagnosis_id", + "description": "Unique identifier of the primary diagnosis event, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" ], - "name": "procedure", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_treatment_id", - "local": "submitter_treatment_id" - } - ], - "schema": "treatment" - } - ] - } - }, - { - "description": "An agent such as a drug (pharmaceutical agent), broadly defined as prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies.", - "fields": [ - { - "description": "Unique identifier of the treatment, assigned by the data provider.", - "meta": { - "displayName": "submitter_treatment_id", - "exact_mappings": { - "FHIR.v5.0.0": "Procedure.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" - ] - }, - "name": "submitter_treatment_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized code from RxNorm, KEGG drug database, PubChem Compound or NCIt to represent the drug.\nProvide code in Compact URI (CURIE) pattern.\nRxNorm URL:\nhttps://rxnav.nlm.nih.gov/REST/rxcui/{code}\nKEGG URL:\nhttps://www.kegg.jp/entry/{code}\nPubChem URL:\nhttps://pubchem.ncbi.nlm.nih.gov/compound/{code}\nNCIt URL:\nhttps://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C{code}'", - "meta": { - "comments": [ - "Provide code in Compact URI (CURIE) pattern. RxNorm URL: https://rxnav.nlm.nih.gov/REST/rxcui/{code} KEGG URL: https://www.kegg.jp/entry/{code} PubChem URL: https://pubchem.ncbi.nlm.nih.gov/compound/{code} NCIt URL: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C{code}" - ], - "displayName": "drug_code", - "examples": [ - "rxnorm:221058", - "kegg.drug:D00123", - "pubchem.compound:100101", - "NCIT:C138986" - ], - "related_mappings": { - "ARGO.v1.34": "chemotherapy.drug_database:chemotherapy.drug_rxnormcui,chemotherapy.drug_id,hormone_therapy.drug_database:hormone_therapy.drug_rxnormcui,hormone_therapy.drug_id,immunotherapy.drug_database:immunotherapy.drug_rxnormcui,immunotherapy.drug_id", - "FHIR.v5.0.0": "MedicationAdministration.medication.code.coding.system:MedicationAdministration.medication.code.coding.code", - "MOHCCN.v3.1": "Systemic_therapy.drug_reference_database:Systemic_therapy.drug_reference_identifier" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/medicationadministration-definitions.html#MedicationAdministration.medication" - ] - }, - "name": "drug_code", - "restrictions": { - "regex": "^rxnorm:\\d{1,8}$|^kegg\\.drug:D\\d+$|^pubchem\\.chem:\\d+$|^NCIT:C\\d{1,7}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the drug_code", - "meta": { - "displayName": "drug_term", - "exact_mappings": { - "MOHCCN.v3.1": "Systemic_therapy.drug_name" - }, - "related_mappings": { - "ARGO.v1.34": "chemotherapy.drug_name,hormone_therapy.drug_name,immunotherapy.drug_name" - } - }, - "name": "drug_term", - "valueType": "string" - }, - { - "description": "Provide the ontology of standardized units to indicate units used to record drug dose.", - "meta": { - "displayName": "drug_dose_units", - "exact_mappings": { - "MOHCCN.v3.1": "Systemic_therapy.drug_dose_units" - }, - "related_mappings": { - "ARGO.v1.34": "chemotherapy.chemotherapy_drug_dose_units,hormone_therapy.hormone_drug_dose_units,immunotherapy.immunotherapy_drug_dose_units" - } - }, - "name": "drug_dose_units", - "restrictions": { - "regex": "^UO:\\d{7}$" - }, - "valueType": "string" - }, - { - "description": "Indicate the total prescribed cumulative drug dose in the same units specified in drug_dose_units.", - "meta": { - "displayName": "prescribed_cumulative_drug_dose", - "exact_mappings": { - "FHIR": "MedicationAdministration.medication.code.coding.display", - "MOHCCN.v3.1": "Systemic_therapy.prescribed_cumulative_drug_dose" - }, - "related_mappings": { - "ARGO.v1.34": "chemotherapy.prescribed_cumulative_drug_dose,hormone_therapy.prescribed_cumulative_drug_dose,immunotherapy.prescribed_cumulative_drug_dose" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/medicationadministration-definitions.html#MedicationAdministration.medication" - ] - }, - "name": "prescribed_cumulative_drug_dose", - "valueType": "number" - }, - { - "description": "Indicate the total actual cumulative drug dose in the same units specified in drug_dose_units.", - "meta": { - "displayName": "actual_cumulative_drug_dose", - "exact_mappings": { - "MOHCCN.v3.1": "Systemic_therapy.actual_cumulative_drug_dose" - }, - "related_mappings": { - "ARGO.v1.34": "chemotherapy.actual_cumulative_drug_dose,hormone_therapy.actual_cumulative_drug_dose,immunotherapy.actual_cumulative_drug_dose" - } - }, - "name": "actual_cumulative_drug_dose", - "valueType": "number" - } + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "disease_code", + "exact_mappings": { + "ARGO.v1.34": "primary_diagnosis.cancer_type_code", + "CQDG": "disease_code", + "FHIR.v5.0.0": "Condition.code.coding.code", + "mCODE.v4.0.0": "Condition.code.coding.code", + "MOHCCN.v3.1": "primary_diagnosis.cancer_type_code", + "Phenopackets.v2.0": "Disease.term.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" ], - "name": "medication", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_treatment_id", - "local": "submitter_treatment_id" - } - ], - "schema": "treatment" - } - ] - } - }, - { - "description": "Uses ionizing radiation, generally as part of cancer treatment to control or kill malignant cells.", - "fields": [ - { - "description": "Unique identifier of the treatment, assigned by the data provider.", - "meta": { - "displayName": "submitter_treatment_id", - "exact_mappings": { - "FHIR.v5.0.0": "Procedure.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" - ] - }, - "name": "submitter_treatment_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate NCIt code to denote the modality of radiation therapy.\nProvide code in Compact URI (CURIE) pattern.", - "meta": { - "displayName": "radiation_modality_code", - "exact_mappings": { - "Phenopackets.v2.0": "RadiationTherapy.modality" - }, - "examples": [ - "NCIT:C28039" - ], - "related_mappings": { - "FHIR.v5.0.0": "Procedure.code.coding.system:Procedure.code" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" - ] - }, - "name": "radiation_modality_code", - "restrictions": { - "regex": "^NCIT:C\\d+$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the radiation modality code.", - "meta": { - "displayName": "radiation_modality_term", - "exact_mappings": { - "FHIR.v5.0.0": "Procedure.code.coding.display" - }, - "examples": [ - "Electron Beam" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" - ] - }, - "name": "radiation_modality_term", - "valueType": "string" - }, - { - "description": "Indicate the total number of fractions delivered as part of treatment.", - "meta": { - "displayName": "radiation_fractions", - "exact_mappings": { - "ARGO.v1.34": "radiation.radiation_therapy_fractions", - "MOHCCN.v3.1": "Radiation.radiation_therapy_fractions", - "Phenopackets.v2.0": "RadiationTherapy.fractions" - } - }, - "name": "radiation_fractions", - "valueType": "integer" - }, - { - "description": "Indicate the total dose given in units of Gray (Gy).", - "meta": { - "comments": [ - "For FHIR.v5.0.0 mapping:Observation.valueQuantity and link Observation to radiation therapy Procedure using Observation.partOf -> Procedure" - ], - "displayName": "radiation_dosage", - "exact_mappings": { - "ARGO.v1.34": "radiation.radiation_therapy_dosage", - "MOHCCN.v3.1": "Radiation.radiation_therapy_dosage", - "Phenopackets.v2.0": "RadiationTherapy.dosage" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_", - "FHIRSpec.v5.0.0:http://hl7.org/fhir/observation-definitions.html#Observation.partOf" - ] - }, - "name": "radiation_dosage", - "valueType": "integer" - }, - { - "description": "Indicate the ICD-O-3 topography code or UBERON code for the anatomic location where radiation therapy was administered.\n Please use C80.9 if the anatomic location is Unknown. Provide code in Compact URI (CURIE) pattern.\n\n Refer to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3) manual for guidelines at https://apps.who.int/iris/handle/10665/42344\n\n UBERON URL: http://purl.obolibrary.org/obo/UBERON_{code}", - "meta": { - "comments": [ - "Refer to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3) manual for guidelines at https://apps.who.int/iris/handle/10665/42344" - ], - "displayName": "anatomical_site_irradiated_code", - "exact_mappings": { - "ARGO.v1.34": "radiation.anatomical_site_irradiated_code", - "FHIR.v5.0.0": "Procedure.bodySite", - "MOHCCN.v3.1": "Radiation.anatomical_site_irradiated_code", - "Phenopackets.v2.0": "RadiationTherapy.body_site", - "mCODE.v4.0.0": "Specimen.collection.bodySite" - }, - "examples": [ - "C50.1", - "C18" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.bodySite" - ] - }, - "name": "anatomical_site_irradiated_code", - "restrictions": { - "regex": "^ICDO3:[C][0-9]{2}(.[0-9]{1})?$|^UBERON:\\d{7,}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the anatomical_site_irradiated_code", - "meta": { - "displayName": "anatomical_site_irradiated_term" - }, - "name": "anatomical_site_irradiated_term", - "valueType": "string" - } + "comments": [ + "Provide code in Compact URI (CURIE) pattern. ICD-10 code: refer to https://icd.who.int/browse10/2019/en MONDO code: refer to https://www.ebi.ac.uk/ols/ontologies/mondo" ], - "name": "radiation", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_treatment_id", - "local": "submitter_treatment_id" - } - ], - "schema": "treatment" - } - ] - } - }, - { - "description": "Record individual measurements to capture quantitative, ordinal (e.g., absent/present), or categorical measurements.", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Age (in days) of the participant at the time the lab test or measurement was conducted.", - "meta": { - "displayName": "age_at_measurement", - "exact_mappings": { - "Phenopackets.v2.0": "Measurement.timeObserved.timeElement.age" - }, - "related_mappings": { - "FHIR.v5.0.0": "Observation.effectiveDateTime-Patient.birthDate" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_", - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" - ] - }, - "name": "age_at_measurement", - "valueType": "integer" - }, - { - "description": "Use standardized LOINC (Logical Observation Identifiers Names and Codes) code to represent quantitative, ordinal, or categorical measurements.\nProvide code in Compact URI (CURIE) pattern.", - "meta": { - "comments": [ - "Provide code in Compact URI (CURIE) pattern. LOINC URL: https://loinc.org/{code}" - ], - "displayName": "measurement_code", - "exact_mappings": { - "Phenopackets.v2.0": "Measurement.assay.id" - }, - "related_mappings": { - "FHIR.v5.0.0": "Observation.code.coding.system:Observation.code.coding.code" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" - ] - }, - "name": "measurement_code", - "restrictions": { - "regex": "^LOINC:[0-9]{1,5}-[0-9]$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the measurement_code", - "meta": { - "displayName": "measurement_term", - "exact_mappings": { - "FHIR.v5.0.0": "Observation.code.coding.display", - "Phenopackets.v2.0": "Measurement.assay.label" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" - ] - }, - "name": "measurement_term", - "valueType": "string" - }, - { - "description": "The numeric result of the lab test or measurement.", - "meta": { - "displayName": "measurement_result_numeric", - "exact_mappings": { - "FHIR.v5.0.0": "Observation.value.valueQuantity.value", - "Phenopackets.v2.0": "Measurement.measurement.value.quantity.value" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_" - ] - }, - "name": "measurement_result_numeric", - "valueType": "number" - }, - { - "description": "Provide the ontology of standardized units to indicate units used to record measurement result. Provide code in Compact URI (CURIE) pattern. UO URL: http://purl.obolibrary.org/obo/UO_{code}", - "meta": { - "displayName": "measurement_unit", - "exact_mappings": { - "FHIR.v5.0.0": "Observation.value.valueQuantity.unit", - "Phenopackets.v2.0": "Measurement.measurement.value.quantity.unit" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_" - ] - }, - "name": "measurement_unit", - "restrictions": { - "regex": "^UO:\\d{7}$" - }, - "valueType": "string" - }, - { - "description": "The categorical result of the lab test or measurement.", - "meta": { - "displayName": "measurement_result_categorical", - "exact_mappings": { - "FHIR.v5.0.0": "Observation.value.valueCodeableConcept", - "Phenopackets.v2.0": "Measurement.measurement.value.quantity.value" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_" - ] - }, - "name": "measurement_result_categorical", - "valueType": "string" - } + "examples": [ + "MONDO:0000001", + "icd10:C34" + ] + }, + "name": "disease_code", + "description": "Use ICD-10 code or MONDO code to represent the disease diagnosed. Provide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^icd10:[A-Z][0-9][A-Z0-9](\\.[A-Z0-9]{1,4})?$|^MONDO:\\d{7}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_diagnosis", + "exact_mappings": { + "ARGO.v1.34": "primary_diagnosis.age_at_diagnosis", + "FHIR.v5.0.0": "Condition.onset.onsetAge", + "mCODE.v4.0.0": "Condition.onset", + "Phenopackets.v2.0": "Disease.onset" + }, + "related_mappings": { + "MOHCCN.v3.1": "primary_diagnosis.date_of_diagnosis-donor.date_of_birth" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.onset_x_" + ] + }, + "name": "age_at_diagnosis", + "description": "Age of participant (in days) at time of diagnosis of the condition.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "disease_term", + "exact_mappings": { + "FHIR.v5.0.0": "Condition.code.coding.display", + "mCODE.v4.0.0": "Condition.code.coding.display", + "Phenopackets.v2.0": "Disease.term.label" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" + ] + }, + "name": "disease_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the disease_code", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "treatment", + "description": "Medications, procedures, other actions taken for clinical management", + "fields": [ + { + "meta": { + "displayName": "submitter_diagnosis_id", + "exact_mappings": { + "ARGO.v1.34": "primary_diagnosis.submitter_diagnosis_id", + "FHIR.v5.0.0": "Condition.identifier", + "mCODE.v4.0.0": "Condition.identifier", + "MOHCCN.v3.1": "primary_diagnosis.submitter_diagnosis_id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.identifier" ], - "name": "measurement", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Individual phenotypic features, observed as either present or absent (excluded), with possible onset, modifiers and frequency", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Participant's age (in days) when phenotype was observed", - "meta": { - "comments": [ - "EDI indicator" - ], - "displayName": "age_at_phenotype", - "exact_mappings": { - "Phenopackets.v2.0": "PhenotypicFeature.onset" - }, - "related_mappings": { - "FHIR.v5.0.0": "Observation.effectiveDateTime-Patient.birthDate" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_", - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" - ] - }, - "name": "age_at_phenotype", - "valueType": "integer" - }, - { - "description": "Use standardized HPO (Human Phenotype Ontology) codes to represent the phenotype.\nProvide code in Compact URI (CURIE) pattern.", - "meta": { - "comments": [ - "Provide code in Compact URI (CURIE) pattern. HPO URL: https://hpo.jax.org/app/browse/term/HP:" - ], - "displayName": "phenotype_code", - "exact_mappings": { - "FHIR.v5.0.0": "Observation.code.coding.code", - "Phenopackets.v2.0": "PhenotypicFeature.type.id" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" - ] - }, - "name": "phenotype_code", - "restrictions": { - "regex": "^HP:[0-9]{7}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the phenotype_code.", - "meta": { - "displayName": "phenotype_term", - "exact_mappings": { - "FHIR.v5.0.0": "Observation.code.coding.display", - "Phenopackets.v2.0": "PhenotypicFeature.type.label" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" - ] - }, - "name": "phenotype_term", - "valueType": "string" - }, - { - "description": "Indicate whether the phenotype was observed in the participant.", - "meta": { - "displayName": "phenotype_observed" - }, - "name": "phenotype_observed", - "restrictions": { - "codeList": [ - "No", - "Unknown", - "Yes" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate the length of time (in days) over which the phenotype was observed in the participant.", - "meta": { - "displayName": "phenotype_duration", - "exact_mappings": { - "FHIR.v5.0.0": "Observation.effectivePeriod" - }, - "related_mappings": { - "Phenopackets.v2.0": "PhenotypicFeature.resolution-PhenotypicFeature.onset" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_" - ] - }, - "name": "phenotype_duration", - "valueType": "integer" - }, - { - "description": "The degree or severity of the observed phenotype.", - "meta": { - "comments": [ - "Permissible values from https://hpo.jax.org/browse/term/HP:0012824" - ], - "displayName": "phenotype_severity", - "exact_mappings": { - "Phenopackets.v2.0": "PhenotypicFeature.severity" - } - }, - "name": "phenotype_severity", - "restrictions": { - "codeList": [ - "Borderline", - "Mild", - "Moderate", - "Profound", - "Severe" - ] - }, - "valueType": "string" + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_diagnosis_id", + "description": "Unique identifier of the primary diagnosis event, assigned by the data provider.", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "submitter_treatment_id" + ], + "match": { + "exists": false + }, + "case": "all" } + ] + }, + "then": { + "required": false, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + } + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" ], - "name": "phenotype", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Any medical conditions (e.g diabetes, prior cancer malignancies) that have existed or may occur during the clinical course of the participant who has the index disease under study.", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate the age (in days) of comorbidity diagnosis.", - "meta": { - "displayName": "age_at_comorbidity_diagnosis", - "exact_mappings": { - "ARGO.v1.34": "Comorbidity.age_at_comorbidity_diagnosis", - "MOHCCN.v3.1": "Comorbidity.age_at_comorbidity_diagnosis" - }, - "related_mappings": { - "FHIR.v5.0.0": "Condition.onsetDateTime-Patient.birthDate" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.onset_x_", - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" - ] - }, - "name": "age_at_comorbidity_diagnosis", - "valueType": "integer" - }, - { - "description": "Use ICD-10 code or Mondo code to indicate the comorbidity diagnosed. Provide code in Compact URI (CURIE) pattern.", - "meta": { - "comments": [ - "Provide code in Compact URI (CURIE) pattern. ICD-10 code: refer to https://icd.who.int/browse10/2019/en MONDO code: refer to https://www.ebi.ac.uk/ols/ontologies/mondo" - ], - "displayName": "comorbidity_code", - "exact_mappings": { - "ARGO.v1.34": "Comorbidity.comorbidity_type_code", - "FHIR.v.5.0.0": "Condition.code.coding.code", - "MOHCCN.v3.1": "Comorbidity.comorbidity_type_code" - }, - "examples": [ - "MONDO:0000001", - "icd10:C34" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" - ] - }, - "name": "comorbidity_code", - "restrictions": { - "regex": "^icd10:[A-Z][0-9][A-Z0-9](\\.[A-Z0-9]{1,4})?$|^MONDO:\\d{7}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the comorbidity_code", - "meta": { - "displayName": "comorbidity_term", - "exact_mappings": { - "FHIR.v5.0.0": "Condition.code.coding.display", - "Phenopackets.v2.0": "Disease.term", - "mCODE.v4.0.0": "condition.code.coding.display" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" - ] - }, - "name": "comorbidity_term", - "valueType": "string" - }, - { - "description": "Indicate whether the comorbid condition is currently being treated or not.", - "meta": { - "displayName": "comorbidity_treatment_status" - }, - "name": "comorbidity_treatment_status", - "restrictions": { - "codeList": [ - "Treated and resolved", - "Under treatment", - "Untreated", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown", - "Not applicable" - ] - }, - "valueType": "string" - }, - { - "description": "Indicate the current state or activity of the comorbid condition.", - "meta": { - "displayName": "comorbidity_status", - "exact_mappings": { - "FHIR.v5.0.0": "Condition.clinicalStatus" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.clinicalStatus" - ] - }, - "name": "comorbidity_status", - "restrictions": { - "codeList": [ - "Active", - "In Remission", - "Resolved", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown", - "Not applicable" - ] - }, - "valueType": "string" - } + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "submitter_treatment_id", + "exact_mappings": { + "FHIR.v5.0.0": "Procedure.identifier" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" ], - "name": "comorbidity", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Capture information about external factors, agents, or conditions an individual has encountered that may influence health or disease outcomes.", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized codes from SNOMED CT, ExO, LOINC to represent the type of exposure.\nProvide code in Compact URI (CURIE) pattern.\n", - "meta": { - "displayName": "exposure_code", - "examples": [ - "LOINC:43164-0" - ] - }, - "name": "exposure_code", - "restrictions": { - "regex": "^snomedct:(\\w+)?\\d+$|^ExO:\\d{7}$|^LOINC:[0-9]{1,5}-[0-9]$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the exposure_code", - "meta": { - "displayName": "exposure_term", - "examples": [ - "Alcohol use" - ] - }, - "name": "exposure_term", - "valueType": "string" - }, - { - "description": "Provide the status of the exposure", - "meta": { - "displayName": "exposure_status" - }, - "name": "exposure_status", - "restrictions": { - "codeList": [ - "Current", - "Former", - "Never", - "Exposed - Current Unknown", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown", - "Not applicable" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Age (in days) when the participant was exposed (or first exposed) ", - "meta": { - "displayName": "age_at_exposure" - }, - "name": "age_at_exposure", - "valueType": "integer" - }, - { - "description": "Duration of exposure period in days", - "meta": { - "displayName": "exposure_duration" - }, - "name": "exposure_duration", - "valueType": "integer" - }, - { - "description": "Provide intensity, quantity or frequency of the exposure", - "meta": { - "displayName": "exposure_amount" - }, - "name": "exposure_amount", - "valueType": "number" - }, - { - "description": "Unit associated with exposure_amount", - "meta": { - "displayName": "exposure_unit", - "examples": [ - "drinks/day" - ] - }, - "name": "exposure_unit", - "valueType": "string" - } + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_treatment_id", + "description": "Unique identifier of the treatment, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "treatment_type" + }, + "name": "treatment_type", + "description": "The category or method of treatment administered", + "restrictions": { + "required": true, + "codeList": [ + "Medication", + "Procedure", + "Radiation therapy", + "Other" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_treatment", + "related_mappings": { + "ARGO.v1.34": "treatment.treatment_start_interval+donor.age_at_diagnosis", + "FHIR.v5.0.0": "Procedure.occurrenceDateTime-Patient.birthDate", + "MOHCCN.v3.1": "Systemic_therapy.start_date-Donor.date_of_birth", + "Phenopackets.v2.0": "TherapeuticRegimen.end_time-Individual.date_of_birth" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.occurrence_x_", + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" + ] + }, + "name": "age_at_treatment", + "description": "Age (in days) of the participant at the time the treatment was administered.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "treatment_duration", + "exact_mappings": { + "ARGO.v1.34": "treatment.treatment_duration", + "FHIR.v5.0.0": "Procedure.occurrencePeriod" + }, + "related_mappings": { + "MOHCCN.v3.1": "Systemic_therapy.start_date-Systemic_therapy.end_date", + "Phenopackets.v2.0": "TreatmentRegimen.end_time-TreatmentRegimen.start_time" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.occurrence_x_" + ] + }, + "name": "treatment_duration", + "description": "The length of time (in days) over which the treatment was administered.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "treatment_intent", + "exact_mappings": { + "ARGO.v1.34": "treatment.treatment_intent", + "MOHCCN.v3.1": "Treatment.treatment_intent" + } + }, + "name": "treatment_intent", + "description": "The purpose of the treatment or the desired effect or outcome resulting from the treatment.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Curative", + "Diagnostic", + "Forensic", + "Guidance", + "Palliative", + "Preventative", + "Screening", + "Supportive", + "Other", + "Missing - Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Not applicable" + ] + } + }, + { + "meta": { + "displayName": "treatment_response", + "exact_mappings": { + "ARGO.v1.34": "treatment.response_to_treatment", + "CQDG": "treatment_response", + "MOHCCN.v3.1": "Treatment.response_to_treatment" + } + }, + "name": "treatment_response", + "description": "The outcome of the treatment, indicating how the patient responded to the intervention", + "valueType": "string", + "restrictions": { + "codeList": [ + "Clinical remission", + "Disease Progression", + "Improvement of symptoms", + "No improvement of symptoms", + "No sign of disease", + "Partial Response", + "Stable Disease", + "Treatment cessation due to toxicity", + "Worsening of symptoms", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown", + "Not applicable" + ] + } + }, + { + "meta": { + "displayName": "treatment_status", + "exact_mappings": { + "ARGO.v1.34": "treatment.outcome_of_treatment", + "MOHCCN.v3.1": "Treatment.status_of_treatment" + } + }, + "name": "treatment_status", + "description": "Indicate the participant's status of the prescribed treatment.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Other", + "Patient choice (stopped or interrupted treatment)", + "Physician decision (stopped or interrupted treatment)", + "Treatment completed as prescribed", + "Treatment incomplete because patient died", + "Treatment incomplete due to technical or organizational problems", + "Treatment ongoing", + "Treatment stopped due to acute toxicity", + "Treatment stopped due to lack of efficacy (disease progression)", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown", + "Not applicable" + ] + } + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "diagnosis", + "mappings": [ + { + "local": "submitter_diagnosis_id", + "foreign": "submitter_diagnosis_id" + } + ] + }, + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "follow_up", + "description": "Any point of contact with a patient after primary diagnosis. ", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" ], - "name": "exposure", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Any material sample taken from a biological entity, living or dead, from physical object or the environment", - "fields": [ - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}", - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the specimen within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_specimen_id", - "exact_mappings": { - "ARGO.v1.34": "specimen.submitter_specimen_id", - "Beacon.v2.2.0": "biosample.id", - "CQDG": "submitter_biospecimen_id", - "FHIR.v5.0.0": "Specimen.identifier", - "MOHCCN.v3.1": "specimen.submitter_specimen_id", - "Phenopackets.v2.0": "Biosample.derived_from_id", - "mCODE.v4.0.0": "Specimen.identifier" - }, - "examples": [ - "LAML_PO", - "00445", - "THY_099-tumour" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier" - ] - }, - "name": "submitter_specimen_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Indicate the tissue source of the specimen from which a biopsy or other tissue specimen was obtained using codes from NCIt (NCI Thesaurus).\nProvide code in Compact URI (CURIE) pattern.", - "meta": { - "displayName": "specimen_tissue_source_code", - "exact_mappings": { - "ARGO.v1.34": "sample_registration.specimen_tissue_source", - "Beacon.v2.2.0": "biosample.sampleOriginType", - "CQDG": "biospecimen_tissue_source", - "Phenopackets.v2.0": "Biosample.sampled_tissue", - "mCODE.v4.0.0": "Specimen.type" - }, - "examples": [ - "NCIT:C12434" - ], - "related_mappings": { - "FHIR.v5.0.0": "Specimen.type.coding.system:Specimen.type.coding.code" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.type" - ] - }, - "name": "specimen_tissue_source_code", - "restrictions": { - "regex": "^NCIT:C[0-9]+$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the specimen tissue source code.", - "meta": { - "displayName": "specimen_tissue_source_term", - "exact_mappings": { - "ARGO.v1.34": "sample_registration.specimen_tissue_source", - "FHIR.v5.0.0": "Specimen.type.coding.display", - "MOHCCN.v3.1": "Specimen.specimen_tissue_source" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.type" - ] - }, - "name": "specimen_tissue_source_term", - "valueType": "string" - }, - { - "description": "Indicate the method of long term storage for specimen that were not extracted freshly or immediately cultured.", - "meta": { - "displayName": "specimen_storage", - "exact_mappings": { - "ARGO.v1.34": "specimen.specimen_storage", - "Beacon.v2.2.0": "biosample.sampleStorage", - "MOHCCN.v3.1": "specimen.specimen_storage", - "Phenopackets.v2.0": "Biosample.sample_storage" - } - }, - "name": "specimen_storage", - "restrictions": { - "codeList": [ - "Cut slide", - "Frozen in -70 freezer", - "Frozen in liquid nitrogen", - "Frozen in vapour phase", - "Not applicable", - "Other", - "Paraffin block", - "RNA later frozen", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown" - ] - }, - "valueType": "string" - }, - { - "description": "Indicate the technique used to process specimen.", - "meta": { - "displayName": "specimen_processing", - "exact_mappings": { - "ARGO.v1.34": "specimen.specimen_processing", - "Beacon.v2.2.0": "biosample.sampleProcessing", - "MOHCCN.v3.1": "Specimen.specimen_processing", - "Phenopackets.v2.0": "Biosample.sample_processing" - } - }, - "name": "specimen_processing", - "restrictions": { - "codeList": [ - "Cryopreservation - other", - "Cryopreservation in dry ice (dead tissue)", - "Cryopreservation in liquid nitrogen (dead tissue)", - "Cryopreservation of live cells in liquid nitrogen", - "Formalin fixed & paraffin embedded", - "Formalin fixed - buffered", - "Formalin fixed - unbuffered", - "Fresh", - "Other", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown", - "Not applicable" - ] - }, - "valueType": "string" - }, - { - "description": "Indicate participant's age( in days) when specimen was collected.", - "meta": { - "displayName": "age_at_specimen_collection", - "exact_mappings": { - "Phenopackets.v2.0": "Biosample.time_of_collection" - }, - "related_mappings": { - "ARGO.v1.34": "donor.age_at_diagnosis+specimen.specimen_acquisition_interval", - "FHIR.v5.0.0": "Specimen.collectedDateTime-Patient.dateBirth", - "MOHCCN.v3.1": "Specimen.specimen_collection_date-Donor.date_of_birth", - "mCODE.v4.0.0": "Specimen.collectedDateTime-Patient.dateBirth" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.collection.collected_x_", - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" - ] - }, - "name": "age_at_specimen_collection", - "valueType": "integer" - }, - { - "description": "Indicate the ICD-O-3 topography code or UBERON code for the anatomic location of a specimen when it was collected. Please use C80.9 if the anatomic location of a specimen is Unknown.\nProvide code in Compact URI (CURIE) pattern.\nRefer to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3) manual for guidelines at https://apps.who.int/iris/handle/10665/42344\nUBERON URL: http://purl.obolibrary.org/obo/UBERON_{code}", - "meta": { - "comments": [ - "Refer to the International Classification of Diseases for Oncology, 3rd Edition" - ], - "displayName": "specimen_anatomic_location_code", - "exact_mappings": { - "ARGO.v1.34": "specimen.specimen_anatomic_location", - "MOHCCN.v3.1": "Specimen.specimen_anatomic_location" - }, - "examples": [ - "UBERON:8600019" - ], - "related_mappings": { - "FHIR.v5.0.0": "Specimen.collection.bodySite.coding.system:Specimen.collection.bodySite.coding.code", - "mCODE.v4.0.0": "Specimen.collection.bodySite.coding.system:Specimen.collection.bodySite.coding.code" - }, - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.collection.bodySite" - ] - }, - "name": "specimen_anatomic_location_code", - "restrictions": { - "regex": "^ICDO3:[C][0-9]{2}(.[0-9]{1})?$|^UBERON:\\d{7,}$" - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the specimen anatomic location code.", - "meta": { - "displayName": "specimen_anatomic_location_term", - "exact_mappings": { - "FHIR.v5.0.0": "Specimen.collection.bodySite.coding.display", - "mCODE.v4.0.0": "Specimen.collection.bodySite.coding.display" - }, - "examples": [ - "placental basal plate" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.collection.bodySite" - ] - }, - "name": "specimen_anatomic_location_term", - "valueType": "string" - }, - { - "description": "For disease in a paired organ, indicate the side on which the specimen was obtained.", - "meta": { - "comments": [ - "Reference caDSR CDE ID 2007875 https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2007875&version=2.0" - ], - "displayName": "specimen_laterality", - "exact_mappings": { - "ARGO.v1.34": "specimen.specimen.laterality", - "MOHCCN.v3.1": "specimen.specimen.laterality", - "mCODE.v4.0.0": "Specimen.collection.bodySite.extension.lateralityQualifier" - } - }, - "name": "specimen_laterality", - "restrictions": { - "codeList": [ - "Left", - "Right", - "Missing - Not collected", - "Missing - Not provided", - "Missing - Restricted access", - "Missing - Unknown", - "Not applicable" - ] - }, - "valueType": "string" - } + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "disease_status_at_followup", + "exact_mappings": { + "ARGO.v1.34": "follow_up.disease_status_at_followup", + "MOHCCN.v3.1": "Follow_up.disease_status_at_followup" + } + }, + "name": "disease_status_at_followup", + "description": "Indicate the participant's disease status at time of follow-up", + "restrictions": { + "required": true, + "codeList": [ + "Complete remission", + "Distant progression", + "Loco-regional progression", + "No evidence of disease", + "Partial remission", + "Progression NOS", + "Relapse or recurrence", + "Stable" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_followup", + "related_mappings": { + "ARGO.v1.34": "primary_diagnosis.age_at_diagnosis+followup.interval_of_followup", + "FHIR.v5.0.0": "Observation.effectiveDateTime-Patient.birthDate", + "MOHCCN.v3.1": "Follow_up.date_of_followup-Donor.date_of_birth" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_", + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" + ] + }, + "name": "age_at_followup", + "description": "Participant's age (in days) at time of the follow up event", + "valueType": "integer" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "procedure", + "description": "A clinical procedure performed on a subject. For example a surgical or diagnostic procedure such as a biopsy.", + "fields": [ + { + "meta": { + "displayName": "submitter_treatment_id", + "exact_mappings": { + "FHIR.v5.0.0": "Procedure.identifier" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" ], - "name": "specimen", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - } - ] - } - }, - { - "description": "Refers to the molecular material (e.g., DNA, RNA, protein) extracted from the specimen and used for experiments or analysis.", - "fields": [ - { - "description": "Unique identifier of the sample within the study, assigned by the data provider.\n", - "meta": { - "displayName": "submitter_sample_id", - "exact_mappings": { - "ARGO.v1.34": "sample_registration.submitter_sample_id", - "MOHCCN.v3.1": "Sample_registration.submitter_sample_id", - "Phenopackets.v2.0": "Biosample.id" - }, - "examples": [ - "hnc_12", - "CCG_34_94583", - "BRCA47832-3239" - ] - }, - "name": "submitter_sample_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Unique identifier of the specimen within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_specimen_id", - "exact_mappings": { - "ARGO.v1.34": "specimen.submitter_specimen_id", - "Beacon.v2.2.0": "biosample.id", - "CQDG": "submitter_biospecimen_id", - "FHIR.v5.0.0": "Specimen.identifier", - "MOHCCN.v3.1": "specimen.submitter_specimen_id", - "Phenopackets.v2.0": "Biosample.derived_from_id", - "mCODE.v4.0.0": "Specimen.identifier" - }, - "examples": [ - "LAML_PO", - "00445", - "THY_099-tumour" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier" - ] - }, - "name": "submitter_specimen_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate NCIT or SO code to denote the type of source material used for sequencing and analysis.\nProvide code in Compact URI (CURIE) pattern.", - "meta": { - "displayName": "molecule_type_code", - "exact_mappings": { - "Beacon.v2.2.0": "biosample.sample_type", - "CQDG": "sample_type", - "GA4GH.Experiment.Metadata.Checklist": "molecule_type", - "Phenopackets.v2.0": "sample_type" - }, - "examples": [ - "NCIT:C449", - "NCIT:C812", - "NCIT:C80376", - "SO:0000991", - "SO:0000234", - "SO:0001877" - ] - }, - "name": "molecule_type_code", - "restrictions": { - "regex": "^NCIT:C[0-9]+$|^SO:\\d{7}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with molecule type code.", - "meta": { - "displayName": "molecule_type_term", - "examples": [ - "DNA" - ] - }, - "name": "molecule_type_term", - "valueType": "string" - }, - { - "description": "Indicate the status of the sample for data analysis.\nCase sample refers to a sample that meets the disease or exposure criteria under investigation.\nControl sample refers to of the same type that does not meet the criteria, representing a normal or baseline state for comparison.", - "meta": { - "displayName": "sample_status" - }, - "name": "sample_status", - "restrictions": { - "codeList": [ - "Case", - "Control", - "Not applicable" - ], - "required": true - }, - "valueType": "string" - } + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_treatment_id", + "description": "Unique identifier of the treatment, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "procedure_body_site_code", + "exact_mappings": { + "ARGO.v1.34": "surgery.surgery_site", + "FHIR.v5.0.0": "Procedure.bodySite.coding.code", + "mCODE.v4.0.0": "Specimen.collection.bodySite", + "MOHCCN.v3.1": "Surgery.surgery_site", + "Phenopackets.v2.0": "Procedure.body_site.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.bodySite" ], - "name": "sample", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_specimen_id", - "local": "submitter_specimen_id" - } - ], - "schema": "specimen" - } - ] - } - }, - { - "description": "Contains information about the experimental design of the sequencing", - "fields": [ - { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_experiment_id", - "exact_mappings": { - "ARGO.v1.34": "experiment.submitter_sequencing_experiment_id" - } - }, - "name": "submitter_experiment_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Unique identifier of the sample within the study, assigned by the data provider.\n", - "meta": { - "displayName": "submitter_sample_id", - "exact_mappings": { - "ARGO.v1.34": "sample_registration.submitter_sample_id", - "MOHCCN.v3.1": "Sample_registration.submitter_sample_id", - "Phenopackets.v2.0": "Biosample.id" - }, - "examples": [ - "hnc_12", - "CCG_34_94583", - "BRCA47832-3239" - ] - }, - "name": "submitter_sample_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate NCIt (NCI Thesaurus) code and term to denote the broad type of sequencing experiment performed. A mixture of library strategy and source.", - "meta": { - "displayName": "experiment_type", - "exact_mappings": { - "GA4GHExperimentMetadataChecklist": "experiment_type" - } - }, - "name": "experiment_type", - "restrictions": { - "codeList": [ - "NCIT:C84343 (Genomics)", - "NCIT:C153189 (Transcriptomics)", - "NCIT:C20085 (Proteomics)", - "NCIT:C153191 (Metagenomics)", - "NCIT:C153190 (Epigenomics)" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "The high-level experiment design including layout, protocol.", - "meta": { - "displayName": "experiment_design", - "exact_mappings": { - "GA4GH.Experiment.Metadata.Checklist": "design_description" - } - }, - "name": "experiment_design", - "valueType": "string" - }, - { - "description": "Indicate OBI code to provide the sequencing technique intended for the library for sequencing data.\nProvide code in Compact URI (CURIE) pattern.", - "meta": { - "displayName": "assay_type_code", - "exact_mappings": { - "Beacon.v2.2.0": "runs.libraryStrategy", - "GA4GH.Experiment.Metadata.Checklist": "assay_type" - }, - "examples": [ - "OBI:0002117" - ] - }, - "name": "assay_type_code", - "restrictions": { - "regex": "^OBI:\\d{7}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide the standardized and human readable term derived from the coding system associated with the assay type code.", - "meta": { - "displayName": "assay_type_term", - "examples": [ - "whole genome sequencing assay" - ] - }, - "name": "assay_type_term", - "valueType": "string" - }, - { - "description": "The sequencing platform type used in data generation.", - "meta": { - "displayName": "platform", - "exact_mappings": { - "ARGO.v1.34": "experiment.platform", - "Beacon.v2.2.0": "runs.platform" - } - }, - "name": "platform", - "restrictions": { - "codeList": [ - "CAPILLARY", - "DNBSEQ", - "ELEMENT", - "HELICOS", - "ILLUMINA", - "IONTORRENT", - "LS454", - "ONT", - "PACBIO", - "SINGULAR", - "SOLID", - "ULTIMA" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Provide detailed information about the sequencing platform or technology used, including the name and/or model number of the specific instrument. Whenever possible, specify the exact model or revision rather than the general manufacturer name. It is recommended to use standardized terminology by including the appropriate OBI (Ontology for Biomedical Investigations) code and term to ensure precision.\n\nUse the format: OBI code in CURIE format (OBI term) ", - "meta": { - "displayName": "instrument", - "exact_mappings": { - "GA4GH.Experiment.Metadata.Checklist": "instrument" - }, - "examples": [ - "OBI:0002752 (Oxford Nanopore PromethION)", - "OBI:0000759 (Illumina)", - "OBI:0002630 (Illumina NovaSeq 6000)", - "OBI:0002012 (PacBio RS II)" - ] - }, - "name": "instrument", - "restrictions": { - "regex": "^OBI:\\d{7} \\(.*\\)$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Captures metadata about sequencing instrument usage (e.g. instruments parameters and usage conditions)", - "meta": { - "displayName": "instrument_metadata", - "exact_mappings": { - "GA4GH.Experiment.Metadata.Checklist": "instrument_metadata" - } - }, - "name": "instrument_metadata", - "valueType": "string" - }, - { - "description": "Set of rules which guides how the sequencing protocol was followed. Change-tracking services such as Protocol.io or GitHub are encouraged instead of dumping free text in this field.\nE.g, https://www.protocols.io/view/environmental-dna-edna-metabarcoding-protocol-for-rm7vzy3q2lx1/v1", - "meta": { - "displayName": "sequencing_protocol", - "exact_mappings": { - "GA4GH.Experiment.Metadata.Checklist": "sequencing_protocol" - } - }, - "name": "sequencing_protocol", - "valueType": "string" - } + "examples": [ + "C50.1", + "C18" + ] + }, + "name": "procedure_body_site_code", + "description": "Indicate the ICD-O-3 topography code or UBERON code for the anatomic location of a specimen when it was collected. Please use C80.9 if the anatomic location of a specimen is Unknown.", + "restrictions": { + "required": true, + "regex": "^ICDO3:[C][0-9]{2}(.[0-9]{1})?$|^UBERON:\\d{7,}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "procedure_code", + "exact_mappings": { + "Phenopackets.v2.0": "Procedure.code.id" + }, + "related_mappings": { + "FHIR.v5.0.0": "Procedure.code.coding.system:Procedure.code" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" ], - "name": "experiment", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_sample_id", - "local": "submitter_sample_id" - } - ], - "schema": "sample" - } - ] - } - }, - { - "description": "Holds the read group information about the raw reads generated in a run of sequencing", - "fields": [ - { - "description": "The identifier of a read group; must be unique within each payload.", - "meta": { - "displayName": "submitter_read_group_id", - "exact_mappings": { - "ARGO.v1.34": "read_groups.submitter_read_group_id", - "Beacon.v2.2.0": "runs.id" - } - }, - "name": "submitter_read_group_id", - "restrictions": { - "regex": "^[a-zA-Z0-9\\-_:\\.']+$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_experiment_id", - "exact_mappings": { - "ARGO.v1.34": "experiment.submitter_sequencing_experiment_id" - } - }, - "name": "submitter_experiment_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "Name of the sequencing file containing reads from the first end of a sequencing run.", - "meta": { - "displayName": "file_r1", - "exact_mappings": { - "ARGO": "read_groups.file_r1" - } - }, - "name": "file_r1", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "Name of the sequencing file containing reads from the second end of a paired-end sequencing run. Required if and only if paired-end sequencing was done.", - "meta": { - "displayName": "file_r2", - "exact_mappings": { - "ARGO": "read_groups.file_r2" - } - }, - "name": "file_r2", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "all", - "fields": [ - "library_layout" - ], - "match": { - "value": "OBI:0000722 (paired-end library)" - } - } - ] - }, - "then": { - "required": true - } - }, - "valueType": "string" - }, - { - "description": "Name of a sequencing library made from a molecular sample or a sample pool (multiplex sequencing).", - "meta": { - "displayName": "library_name", - "exact_mappings": { - "ARGO": "read_groups.library_name", - "GA4GH.Experiment.Metadata.Checklist": "library_extra_id" - } - }, - "name": "library_name", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicate whether the library was built as paired-end or single-end if applicable.", - "meta": { - "displayName": "library_layout", - "exact_mappings": { - "Beacon.v2.2.0": "runs.libraryLayout", - "GA4GH.Experiment.Metadata.Checklist": "library_layout" - } - }, - "name": "library_layout", - "restrictions": { - "codeList": [ - "OBI:0000722 (paired-end library)", - "OBI:0000736 (single fragment library)", - "Not applicable" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier for each read group. For example, Illumina has format {FLOWCELL_BARCODE}.{LANE}.{SAMPLE_BARCODE}. The {FLOWCELL_BARCODE} refers to the unique identifier for a particular flow cell. The {LANE} indicates the lane of the flow cell and the {SAMPLE_BARCODE} is a sample/library-specific identifier. For non-multiplex sequencing, platform unit and read group have a one-to-one relationship.", - "meta": { - "displayName": "platform_unit", - "exact_mappings": { - "ARGO": "read_groups.platform_unit" - } - }, - "name": "platform_unit", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "Description of the nucleotide sequencing library, including targeting information, spot, gap descriptors, and any other information relevant to its construction", - "meta": { - "displayName": "library_description", - "exact_mappings": { - "GA4GH.Experiment.Metadata.Checklist": "library_description" - } - }, - "name": "library_description", - "valueType": "string" - }, - { - "description": "Optional field indicating the @RD ID in the BAM. If submitted, this will be used to map the @RG ID in the BAM header to the submitter_read_group_id in the payload. After submission, the @RG ID in the payload will be used for all future headers. This cannot be submitted for FASTQ files.", - "meta": { - "displayName": "read_group_id_in_bam", - "exact_mappings": { - "ARGO": "read_groups.read_group_id_in_bam" - } - }, - "name": "read_group_id_in_bam", - "restrictions": { - "regex": "^[a-zA-Z0-9\\-_:\\.']+$" - }, - "valueType": "string" - }, - { - "description": "Length of sequencing reads in file_r1; this corresponds to the number of sequencing cycles of the first end.", - "meta": { - "displayName": "read_length_r1", - "exact_mappings": { - "ARGO": "read_groups.read_length_r1" - } - }, - "name": "read_length_r1", - "restrictions": { - "range": { - "min": 20 - } - }, - "valueType": "integer" - }, - { - "description": "Length of sequencing reads in file_r2; this corresponds to the number of sequencing cycles of the second end.", - "meta": { - "displayName": "read_length_r2", - "exact_mappings": { - "ARGO": "read_groups.read_length_r2" - } - }, - "name": "read_length_r2", - "restrictions": { - "range": { - "min": 20 - } - }, - "valueType": "integer" - }, - { - "description": "For paired-end sequencing, the average size of sequences between two sequencing ends. Required only for paired-end sequencing.", - "meta": { - "displayName": "insert_size", - "exact_mappings": { - "ARGO": "read_groups.insert_size", - "GA4GH.Experiment.Metadata.Checklist": "insert_size" - } - }, - "name": "insert_size", - "restrictions": { - "range": { - "min": 0 - } - }, - "valueType": "integer" - } + "comments": [ + "Provide code in Compact URI (CURIE) pattern. NCIt URL: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C\n SNOMED-CT URL: http://snomed.info/id/\n UMLS URL: https://uts.nlm.nih.gov/uts/umls/concept/ CCI URL:https://www.cihi.ca/en/cci-coding-structure" ], - "name": "read_group", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_experiment_id", - "local": "submitter_experiment_id" - } - ], - "schema": "experiment" - } - ] - } - }, - { - "description": "This entity is intended to contain metadata about a detailed examination of data (mainly data processing protocols) in order to come to some conclusion. It can be of different types (e.g. sequence variation, sequence alignment, phenotype characterization, gene expression, etc.) that will mainly differ in the protocols used to achieve the processed data of the analysis.", - "fields": [ - { - "description": "Unique identifier of the study.", - "meta": { - "displayName": "studyId", - "exact_mappings": { - "ARGO.v1.34": "program_id", - "CQDG": "study_id" - } - }, - "name": "studyId", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the analysis within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_analysis_id", - "exact_mappings": { - "Beacon.v2.2.0": "analyses.id", - "EGA": "ANALYSIS_ALIAS" - }, - "examples": [ - "hnc_12", - "CCG_34_94583", - "BRCA47832-3239" - ] - }, - "name": "submitter_analysis_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "unique": true, - "valueType": "string" - }, - { - "description": "Overall type of the analysis. Term chosen from a controlled vocabulary (CV) list.", - "meta": { - "displayName": "analysisType", - "exact_mappings": { - "ARGO": "analysisType", - "EGA": "ANALYSIS/ANALYSIS_TYPE" - } - }, - "name": "analysisType", - "restrictions": { - "codeList": [ - "sequenceExperiment", - "sequenceAlignment", - "variantCall", - "variantAnnotation" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the participant within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_participant_id", - "exact_mappings": { - "ARGO.v1.34": "donor.submitter_donor_id", - "Beacon.v2.2.0": "individual.id", - "CQDG": "submitter_participant_id", - "FHIR.v5.0.0": "Patient.identifier", - "MOHCCN.v3.1": "Donor.submitter_donor_id", - "Phenopackets.v2.0": "Individual.id", - "mCODE.v4.0.0": "Patient.identifier" - }, - "examples": [ - "90234", - "BLD_donor_89", - "AML-90" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" - ] - }, - "name": "submitter_participant_id", - "restrictions": { - "else": { - "required": true - }, - "if": { - "conditions": [ - { - "case": "any", - "fields": [ - "submitter_experiment_id", - "submitter_sample_id", - "submitter_specimen_id" - ], - "match": { - "exists": true - } - } - ] - }, - "then": { - "empty": true, - "required": false - } - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the specimen within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_specimen_id", - "exact_mappings": { - "ARGO.v1.34": "specimen.submitter_specimen_id", - "Beacon.v2.2.0": "biosample.id", - "CQDG": "submitter_biospecimen_id", - "FHIR.v5.0.0": "Specimen.identifier", - "MOHCCN.v3.1": "specimen.submitter_specimen_id", - "Phenopackets.v2.0": "Biosample.derived_from_id", - "mCODE.v4.0.0": "Specimen.identifier" - }, - "examples": [ - "LAML_PO", - "00445", - "THY_099-tumour" - ], - "specifications": [ - "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier" - ] - }, - "name": "submitter_specimen_id", - "restrictions": { - "else": { - "required": true - }, - "if": { - "conditions": [ - { - "case": "any", - "fields": [ - "submitter_participant_id", - "submitter_experiment_id", - "submitter_sample_id" - ], - "match": { - "exists": true - } - } - ] - }, - "then": { - "empty": true, - "required": false - } - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the sample within the study, assigned by the data provider.\n", - "meta": { - "displayName": "submitter_sample_id", - "exact_mappings": { - "ARGO.v1.34": "sample_registration.submitter_sample_id", - "MOHCCN.v3.1": "Sample_registration.submitter_sample_id", - "Phenopackets.v2.0": "Biosample.id" - }, - "examples": [ - "hnc_12", - "CCG_34_94583", - "BRCA47832-3239" - ] - }, - "name": "submitter_sample_id", - "restrictions": { - "else": { - "required": true - }, - "if": { - "conditions": [ - { - "case": "any", - "fields": [ - "submitter_participant_id", - "submitter_experiment_id", - "submitter_specimen_id" - ], - "match": { - "exists": true - } - } - ] - }, - "then": { - "empty": true, - "required": false - } - }, - "valueType": "string" - }, - { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_experiment_id", - "exact_mappings": { - "ARGO.v1.34": "experiment.submitter_sequencing_experiment_id" - } - }, - "name": "submitter_experiment_id", - "restrictions": { - "else": { - "empty": true, - "required": false - }, - "if": { - "conditions": [ - { - "case": "any", - "fields": [ - "analysisType" - ], - "match": { - "codeList": [ - "sequenceExperiment", - "sequenceAlignment", - "variantCall" - ] - } - } - ] - }, - "then": { - "required": true - } - }, - "valueType": "string" - }, - { - "description": "Indicate the category of data produced as outputs from the analysis. ", - "meta": { - "displayName": "data_category" - }, - "name": "data_category", - "restrictions": { - "codeList": [ - "Genomics", - "Transcriptomics", - "Proteomics", - "Epigenomics", - "Imaging", - "Reference" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicates whether the called variants are germline, somatic, or of uncertain classification.", - "meta": { - "displayName": "variant_class" - }, - "name": "variant_class", - "restrictions": { - "codeList": [ - "Germline", - "Somatic", - "Unknown" - ] - }, - "valueType": "string" - }, - { - "description": "Indicate the approach used to identify genetic variants from sequencing data, based on the availability of reference samples (e.g., matched normal) and the study design.", - "meta": { - "displayName": "variant_calling_strategy" - }, - "name": "variant_calling_strategy", - "restrictions": { - "codeList": [ - "Tumour only", - "Tumour normal", - "Single sample", - "Family based", - "RNA based", - "Joint calling" - ] - }, - "valueType": "string" - }, - { - "description": "The reference genome build that is used in the workflow. ", - "meta": { - "displayName": "genome_build" - }, - "name": "genome_build", - "restrictions": { - "codeList": [ - "GRCh38", - "GRCh37" - ] - }, - "valueType": "string" - }, - { - "description": "Indicates which genome annotation build or version was used in the analysis (e.g., Ensembl release, RefSeq release, etc.).", - "meta": { - "displayName": "genome_annotation" - }, - "name": "genome_annotation", - "restrictions": { - "regex": "^(?:Ensembl \\d{1,5}|RefSeq \\d{1,5}|Gencode v\\d{1,5})$" - }, - "valueType": "string" - } + "examples": [ + "NCIT:C51894", + "snomedct:284196006", + "umls:C2584994", + "CCI:1CA14STCDR" + ] + }, + "name": "procedure_code", + "description": "Use code from NCIt, SNOMED-CT, UMLS or CCI to represent the procedure performed. Provide code in Compact URI (CURIE) pattern.\n\nNCIt URL:\nhttp://purl.obolibrary.org/obo/NCIT_{code}\nSNOMED-CT URL:\nhttp://snomed.info/id/{code}\nUMLS URL:\nhttps://uts.nlm.nih.gov/uts/umls/concept/{code}\nCCI URL:\nhttps://www.cihi.ca/en/cci-coding-structure", + "restrictions": { + "required": true, + "regex": "^NCIT:C\\d+$|^snomedct:(\\w+)?\\d+$|^umls:C\\d+$|^CCI:[A-Z0-9]([0-9]{2}|[A-Z]{2}){3}(([0-9]{2}|[A-Z]{2})[A-Z0-9]?)?$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "procedure_body_site_term", + "exact_mappings": { + "FHIR.v5.0.0": "Procedure.bodySite.coding.display", + "Phenopackets.v2.0": "Procedure.body_site.label" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.bodySite" + ] + }, + "name": "procedure_body_site_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the procedure_body_site_code", + "valueType": "string" + }, + { + "meta": { + "displayName": "procedure_term", + "exact_mappings": { + "FHIR.v5.0.0": "Procedure.code.display", + "Phenopackets.v2.0": "Procedure.code.label" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" + ] + }, + "name": "procedure_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the procedure_code", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "treatment", + "mappings": [ + { + "local": "submitter_treatment_id", + "foreign": "submitter_treatment_id" + } + ] + } + ] + } + }, + { + "name": "medication", + "description": "An agent such as a drug (pharmaceutical agent), broadly defined as prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies.", + "fields": [ + { + "meta": { + "displayName": "submitter_treatment_id", + "exact_mappings": { + "FHIR.v5.0.0": "Procedure.identifier" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" ], - "name": "analysis", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_experiment_id", - "local": "submitter_experiment_id" - } - ], - "schema": "experiment" - }, - { - "mappings": [ - { - "foreign": "submitter_participant_id", - "local": "submitter_participant_id" - } - ], - "schema": "participant" - }, - { - "mappings": [ - { - "foreign": "submitter_sample_id", - "local": "submitter_sample_id" - } - ], - "schema": "sample" - }, - { - "mappings": [ - { - "foreign": "submitter_specimen_id", - "local": "submitter_specimen_id" - } - ], - "schema": "specimen" - } - ] - } - }, - { - "description": "Contains information about the analysis workflow generating the analysis", - "fields": [ - { - "description": "Indicate the unique identifier of the data processing workflow used in the analysis.", - "meta": { - "displayName": "submitter_workflow_id" - }, - "name": "submitter_workflow_id", - "unique": true, - "valueType": "string" - }, - { - "description": "Unique identifier of the analysis within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_analysis_id", - "exact_mappings": { - "Beacon.v2.2.0": "analyses.id", - "EGA": "ANALYSIS_ALIAS" - }, - "examples": [ - "hnc_12", - "CCG_34_94583", - "BRCA47832-3239" - ] - }, - "name": "submitter_analysis_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "The name of the genomic data processing workflow used for data analysis.", - "meta": { - "displayName": "workflow_name" - }, - "name": "workflow_name", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "The version of the workflow or pipeline being used. ", - "meta": { - "displayName": "workflow_version" - }, - "name": "workflow_version", - "valueType": "string" - }, - { - "description": "A URL linking to the workflow's repository or documentation. This could be a reference to a GitHub repository, a website where the workflow is described, or documentation on how to run the workflow.", - "meta": { - "displayName": "workflow_url" - }, - "name": "workflow_url", - "valueType": "string" + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_treatment_id", + "description": "Unique identifier of the treatment, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "drug_code", + "related_mappings": { + "ARGO.v1.34": "chemotherapy.drug_database:chemotherapy.drug_rxnormcui,chemotherapy.drug_id,hormone_therapy.drug_database:hormone_therapy.drug_rxnormcui,hormone_therapy.drug_id,immunotherapy.drug_database:immunotherapy.drug_rxnormcui,immunotherapy.drug_id", + "FHIR.v5.0.0": "MedicationAdministration.medication.code.coding.system:MedicationAdministration.medication.code.coding.code", + "MOHCCN.v3.1": "Systemic_therapy.drug_reference_database:Systemic_therapy.drug_reference_identifier" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/medicationadministration-definitions.html#MedicationAdministration.medication" + ], + "comments": [ + "Provide code in Compact URI (CURIE) pattern. RxNorm URL: https://rxnav.nlm.nih.gov/REST/rxcui/{code} KEGG URL: https://www.kegg.jp/entry/{code} PubChem URL: https://pubchem.ncbi.nlm.nih.gov/compound/{code} NCIt URL: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C{code}" + ], + "examples": [ + "rxnorm:221058", + "kegg.drug:D00123", + "pubchem.compound:100101", + "NCIT:C138986" + ] + }, + "name": "drug_code", + "description": "Provide the standardized code from RxNorm, KEGG drug database, PubChem Compound or NCIt to represent the drug.\nProvide code in Compact URI (CURIE) pattern.\nRxNorm URL:\nhttps://rxnav.nlm.nih.gov/REST/rxcui/{code}\nKEGG URL:\nhttps://www.kegg.jp/entry/{code}\nPubChem URL:\nhttps://pubchem.ncbi.nlm.nih.gov/compound/{code}\nNCIt URL:\nhttps://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C{code}'", + "restrictions": { + "required": true, + "regex": "^rxnorm:\\d{1,8}$|^kegg\\.drug:D\\d+$|^pubchem\\.chem:\\d+$|^NCIT:C\\d{1,7}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "actual_cumulative_drug_dose", + "exact_mappings": { + "MOHCCN.v3.1": "Systemic_therapy.actual_cumulative_drug_dose" + }, + "related_mappings": { + "ARGO.v1.34": "chemotherapy.actual_cumulative_drug_dose,hormone_therapy.actual_cumulative_drug_dose,immunotherapy.actual_cumulative_drug_dose" + } + }, + "name": "actual_cumulative_drug_dose", + "description": "Indicate the total actual cumulative drug dose in the same units specified in drug_dose_units.", + "valueType": "number" + }, + { + "meta": { + "displayName": "drug_dose_units", + "exact_mappings": { + "MOHCCN.v3.1": "Systemic_therapy.drug_dose_units" + }, + "related_mappings": { + "ARGO.v1.34": "chemotherapy.chemotherapy_drug_dose_units,hormone_therapy.hormone_drug_dose_units,immunotherapy.immunotherapy_drug_dose_units" + } + }, + "name": "drug_dose_units", + "description": "Provide the ontology of standardized units to indicate units used to record drug dose.", + "valueType": "string", + "restrictions": { + "regex": "^UO:\\d{7}$" + } + }, + { + "meta": { + "displayName": "drug_term", + "exact_mappings": { + "MOHCCN.v3.1": "Systemic_therapy.drug_name" + }, + "related_mappings": { + "ARGO.v1.34": "chemotherapy.drug_name,hormone_therapy.drug_name,immunotherapy.drug_name" + } + }, + "name": "drug_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the drug_code", + "valueType": "string" + }, + { + "meta": { + "displayName": "prescribed_cumulative_drug_dose", + "exact_mappings": { + "FHIR": "MedicationAdministration.medication.code.coding.display", + "MOHCCN.v3.1": "Systemic_therapy.prescribed_cumulative_drug_dose" + }, + "related_mappings": { + "ARGO.v1.34": "chemotherapy.prescribed_cumulative_drug_dose,hormone_therapy.prescribed_cumulative_drug_dose,immunotherapy.prescribed_cumulative_drug_dose" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/medicationadministration-definitions.html#MedicationAdministration.medication" + ] + }, + "name": "prescribed_cumulative_drug_dose", + "description": "Indicate the total prescribed cumulative drug dose in the same units specified in drug_dose_units.", + "valueType": "number" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "treatment", + "mappings": [ + { + "local": "submitter_treatment_id", + "foreign": "submitter_treatment_id" + } + ] + } + ] + } + }, + { + "name": "radiation", + "description": "Uses ionizing radiation, generally as part of cancer treatment to control or kill malignant cells.", + "fields": [ + { + "meta": { + "displayName": "submitter_treatment_id", + "exact_mappings": { + "FHIR.v5.0.0": "Procedure.identifier" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.identifier" + ], + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_treatment_id", + "description": "Unique identifier of the treatment, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "anatomical_site_irradiated_code", + "exact_mappings": { + "ARGO.v1.34": "radiation.anatomical_site_irradiated_code", + "FHIR.v5.0.0": "Procedure.bodySite", + "mCODE.v4.0.0": "Specimen.collection.bodySite", + "MOHCCN.v3.1": "Radiation.anatomical_site_irradiated_code", + "Phenopackets.v2.0": "RadiationTherapy.body_site" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.bodySite" + ], + "comments": [ + "Refer to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3) manual for guidelines at https://apps.who.int/iris/handle/10665/42344" + ], + "examples": [ + "C50.1", + "C18" + ] + }, + "name": "anatomical_site_irradiated_code", + "description": "Indicate the ICD-O-3 topography code or UBERON code for the anatomic location where radiation therapy was administered.\n Please use C80.9 if the anatomic location is Unknown. Provide code in Compact URI (CURIE) pattern.\n\n Refer to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3) manual for guidelines at https://apps.who.int/iris/handle/10665/42344\n\n UBERON URL: http://purl.obolibrary.org/obo/UBERON_{code}", + "restrictions": { + "required": true, + "regex": "^ICDO3:[C][0-9]{2}(.[0-9]{1})?$|^UBERON:\\d{7,}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "radiation_modality_code", + "exact_mappings": { + "Phenopackets.v2.0": "RadiationTherapy.modality" + }, + "related_mappings": { + "FHIR.v5.0.0": "Procedure.code.coding.system:Procedure.code" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" + ], + "examples": [ + "NCIT:C28039" + ] + }, + "name": "radiation_modality_code", + "description": "Indicate NCIt code to denote the modality of radiation therapy.\nProvide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^NCIT:C\\d+$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "anatomical_site_irradiated_term" + }, + "name": "anatomical_site_irradiated_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the anatomical_site_irradiated_code", + "valueType": "string" + }, + { + "meta": { + "displayName": "radiation_dosage", + "exact_mappings": { + "ARGO.v1.34": "radiation.radiation_therapy_dosage", + "MOHCCN.v3.1": "Radiation.radiation_therapy_dosage", + "Phenopackets.v2.0": "RadiationTherapy.dosage" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_", + "FHIRSpec.v5.0.0:http://hl7.org/fhir/observation-definitions.html#Observation.partOf" + ], + "comments": [ + "For FHIR.v5.0.0 mapping:Observation.valueQuantity and link Observation to radiation therapy Procedure using Observation.partOf -> Procedure" + ] + }, + "name": "radiation_dosage", + "description": "Indicate the total dose given in units of Gray (Gy).", + "valueType": "integer" + }, + { + "meta": { + "displayName": "radiation_fractions", + "exact_mappings": { + "ARGO.v1.34": "radiation.radiation_therapy_fractions", + "MOHCCN.v3.1": "Radiation.radiation_therapy_fractions", + "Phenopackets.v2.0": "RadiationTherapy.fractions" + } + }, + "name": "radiation_fractions", + "description": "Indicate the total number of fractions delivered as part of treatment.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "radiation_modality_term", + "exact_mappings": { + "FHIR.v5.0.0": "Procedure.code.coding.display" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/procedure-definitions.html#Procedure.code" + ], + "examples": [ + "Electron Beam" + ] + }, + "name": "radiation_modality_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the radiation modality code.", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "treatment", + "mappings": [ + { + "local": "submitter_treatment_id", + "foreign": "submitter_treatment_id" + } + ] + } + ] + } + }, + { + "name": "measurement", + "description": "Record individual measurements to capture quantitative, ordinal (e.g., absent/present), or categorical measurements.", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" + ], + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "measurement_code", + "exact_mappings": { + "Phenopackets.v2.0": "Measurement.assay.id" + }, + "related_mappings": { + "FHIR.v5.0.0": "Observation.code.coding.system:Observation.code.coding.code" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" + ], + "comments": [ + "Provide code in Compact URI (CURIE) pattern. LOINC URL: https://loinc.org/{code}" + ] + }, + "name": "measurement_code", + "description": "Use standardized LOINC (Logical Observation Identifiers Names and Codes) code to represent quantitative, ordinal, or categorical measurements.\nProvide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^LOINC:[0-9]{1,5}-[0-9]$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_measurement", + "exact_mappings": { + "Phenopackets.v2.0": "Measurement.timeObserved.timeElement.age" + }, + "related_mappings": { + "FHIR.v5.0.0": "Observation.effectiveDateTime-Patient.birthDate" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_", + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" + ] + }, + "name": "age_at_measurement", + "description": "Age (in days) of the participant at the time the lab test or measurement was conducted.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "measurement_result_categorical", + "exact_mappings": { + "FHIR.v5.0.0": "Observation.value.valueCodeableConcept", + "Phenopackets.v2.0": "Measurement.measurement.value.quantity.value" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_" + ] + }, + "name": "measurement_result_categorical", + "description": "The categorical result of the lab test or measurement.", + "valueType": "string" + }, + { + "meta": { + "displayName": "measurement_result_numeric", + "exact_mappings": { + "FHIR.v5.0.0": "Observation.value.valueQuantity.value", + "Phenopackets.v2.0": "Measurement.measurement.value.quantity.value" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_" + ] + }, + "name": "measurement_result_numeric", + "description": "The numeric result of the lab test or measurement.", + "valueType": "number" + }, + { + "meta": { + "displayName": "measurement_term", + "exact_mappings": { + "FHIR.v5.0.0": "Observation.code.coding.display", + "Phenopackets.v2.0": "Measurement.assay.label" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" + ] + }, + "name": "measurement_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the measurement_code", + "valueType": "string" + }, + { + "meta": { + "displayName": "measurement_unit", + "exact_mappings": { + "FHIR.v5.0.0": "Observation.value.valueQuantity.unit", + "Phenopackets.v2.0": "Measurement.measurement.value.quantity.unit" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.value_x_" + ] + }, + "name": "measurement_unit", + "description": "Provide the ontology of standardized units to indicate units used to record measurement result. Provide code in Compact URI (CURIE) pattern. UO URL: http://purl.obolibrary.org/obo/UO_{code}", + "valueType": "string", + "restrictions": { + "regex": "^UO:\\d{7}$" + } + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "phenotype", + "description": "Individual phenotypic features, observed as either present or absent (excluded), with possible onset, modifiers and frequency", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" + ], + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "phenotype_code", + "exact_mappings": { + "FHIR.v5.0.0": "Observation.code.coding.code", + "Phenopackets.v2.0": "PhenotypicFeature.type.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" + ], + "comments": [ + "Provide code in Compact URI (CURIE) pattern. HPO URL: https://hpo.jax.org/app/browse/term/HP:" + ] + }, + "name": "phenotype_code", + "description": "Use standardized HPO (Human Phenotype Ontology) codes to represent the phenotype.\nProvide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^HP:[0-9]{7}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "phenotype_observed" + }, + "name": "phenotype_observed", + "description": "Indicate whether the phenotype was observed in the participant.", + "restrictions": { + "required": true, + "codeList": [ + "No", + "Unknown", + "Yes" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_phenotype", + "exact_mappings": { + "Phenopackets.v2.0": "PhenotypicFeature.onset" + }, + "related_mappings": { + "FHIR.v5.0.0": "Observation.effectiveDateTime-Patient.birthDate" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_", + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" + ], + "comments": [ + "EDI indicator" + ] + }, + "name": "age_at_phenotype", + "description": "Participant's age (in days) when phenotype was observed", + "valueType": "integer" + }, + { + "meta": { + "displayName": "phenotype_duration", + "exact_mappings": { + "FHIR.v5.0.0": "Observation.effectivePeriod" + }, + "related_mappings": { + "Phenopackets.v2.0": "PhenotypicFeature.resolution-PhenotypicFeature.onset" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.effective_x_" + ] + }, + "name": "phenotype_duration", + "description": "Indicate the length of time (in days) over which the phenotype was observed in the participant.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "phenotype_severity", + "exact_mappings": { + "Phenopackets.v2.0": "PhenotypicFeature.severity" + }, + "comments": [ + "Permissible values from https://hpo.jax.org/browse/term/HP:0012824" + ] + }, + "name": "phenotype_severity", + "description": "The degree or severity of the observed phenotype.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Borderline", + "Mild", + "Moderate", + "Profound", + "Severe" + ] + } + }, + { + "meta": { + "displayName": "phenotype_term", + "exact_mappings": { + "FHIR.v5.0.0": "Observation.code.coding.display", + "Phenopackets.v2.0": "PhenotypicFeature.type.label" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/observation-definitions.html#Observation.code" + ] + }, + "name": "phenotype_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the phenotype_code.", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "comorbidity", + "description": "Any medical conditions (e.g diabetes, prior cancer malignancies) that have existed or may occur during the clinical course of the participant who has the index disease under study.", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" + ], + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "comorbidity_code", + "exact_mappings": { + "ARGO.v1.34": "Comorbidity.comorbidity_type_code", + "FHIR.v.5.0.0": "Condition.code.coding.code", + "MOHCCN.v3.1": "Comorbidity.comorbidity_type_code" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" + ], + "comments": [ + "Provide code in Compact URI (CURIE) pattern. ICD-10 code: refer to https://icd.who.int/browse10/2019/en MONDO code: refer to https://www.ebi.ac.uk/ols/ontologies/mondo" + ], + "examples": [ + "MONDO:0000001", + "icd10:C34" + ] + }, + "name": "comorbidity_code", + "description": "Use ICD-10 code or Mondo code to indicate the comorbidity diagnosed. Provide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^icd10:[A-Z][0-9][A-Z0-9](\\.[A-Z0-9]{1,4})?$|^MONDO:\\d{7}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_comorbidity_diagnosis", + "exact_mappings": { + "ARGO.v1.34": "Comorbidity.age_at_comorbidity_diagnosis", + "MOHCCN.v3.1": "Comorbidity.age_at_comorbidity_diagnosis" + }, + "related_mappings": { + "FHIR.v5.0.0": "Condition.onsetDateTime-Patient.birthDate" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.onset_x_", + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" + ] + }, + "name": "age_at_comorbidity_diagnosis", + "description": "Indicate the age (in days) of comorbidity diagnosis.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "comorbidity_status", + "exact_mappings": { + "FHIR.v5.0.0": "Condition.clinicalStatus" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.clinicalStatus" + ] + }, + "name": "comorbidity_status", + "description": "Indicate the current state or activity of the comorbid condition.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Active", + "In Remission", + "Resolved", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown", + "Not applicable" + ] + } + }, + { + "meta": { + "displayName": "comorbidity_term", + "exact_mappings": { + "FHIR.v5.0.0": "Condition.code.coding.display", + "mCODE.v4.0.0": "condition.code.coding.display", + "Phenopackets.v2.0": "Disease.term" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/condition-definitions.html#Condition.code" + ] + }, + "name": "comorbidity_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the comorbidity_code", + "valueType": "string" + }, + { + "meta": { + "displayName": "comorbidity_treatment_status" + }, + "name": "comorbidity_treatment_status", + "description": "Indicate whether the comorbid condition is currently being treated or not.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Treated and resolved", + "Under treatment", + "Untreated", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown", + "Not applicable" + ] + } + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "exposure", + "description": "Capture information about external factors, agents, or conditions an individual has encountered that may influence health or disease outcomes.", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" + ], + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "exposure_code", + "examples": [ + "LOINC:43164-0" + ] + }, + "name": "exposure_code", + "description": "Provide the standardized codes from SNOMED CT, ExO, LOINC to represent the type of exposure.\nProvide code in Compact URI (CURIE) pattern.\n", + "restrictions": { + "required": true, + "regex": "^snomedct:(\\w+)?\\d+$|^ExO:\\d{7}$|^LOINC:[0-9]{1,5}-[0-9]$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "exposure_status" + }, + "name": "exposure_status", + "description": "Provide the status of the exposure", + "restrictions": { + "required": true, + "codeList": [ + "Current", + "Former", + "Never", + "Exposed - Current Unknown", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown", + "Not applicable" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_exposure" + }, + "name": "age_at_exposure", + "description": "Age (in days) when the participant was exposed (or first exposed) ", + "valueType": "integer" + }, + { + "meta": { + "displayName": "exposure_amount" + }, + "name": "exposure_amount", + "description": "Provide intensity, quantity or frequency of the exposure", + "valueType": "number" + }, + { + "meta": { + "displayName": "exposure_duration" + }, + "name": "exposure_duration", + "description": "Duration of exposure period in days", + "valueType": "integer" + }, + { + "meta": { + "displayName": "exposure_term", + "examples": [ + "Alcohol use" + ] + }, + "name": "exposure_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the exposure_code", + "valueType": "string" + }, + { + "meta": { + "displayName": "exposure_unit", + "examples": [ + "drinks/day" + ] + }, + "name": "exposure_unit", + "description": "Unit associated with exposure_amount", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "specimen", + "description": "Any material sample taken from a biological entity, living or dead, from physical object or the environment", + "fields": [ + { + "meta": { + "displayName": "submitter_participant_id", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" + ], + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_id", + "description": "Unique identifier of the participant within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "submitter_specimen_id", + "exact_mappings": { + "ARGO.v1.34": "specimen.submitter_specimen_id", + "Beacon.v2.2.0": "biosample.id", + "CQDG": "submitter_biospecimen_id", + "FHIR.v5.0.0": "Specimen.identifier", + "mCODE.v4.0.0": "Specimen.identifier", + "MOHCCN.v3.1": "specimen.submitter_specimen_id", + "Phenopackets.v2.0": "Biosample.derived_from_id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier" + ], + "examples": [ + "LAML_PO", + "00445", + "THY_099-tumour" + ] + }, + "name": "submitter_specimen_id", + "description": "Unique identifier of the specimen within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "specimen_tissue_source_code", + "exact_mappings": { + "ARGO.v1.34": "sample_registration.specimen_tissue_source", + "Beacon.v2.2.0": "biosample.sampleOriginType", + "CQDG": "biospecimen_tissue_source", + "mCODE.v4.0.0": "Specimen.type", + "Phenopackets.v2.0": "Biosample.sampled_tissue" + }, + "related_mappings": { + "FHIR.v5.0.0": "Specimen.type.coding.system:Specimen.type.coding.code" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.type" + ], + "examples": [ + "NCIT:C12434" + ] + }, + "name": "specimen_tissue_source_code", + "description": "Indicate the tissue source of the specimen from which a biopsy or other tissue specimen was obtained using codes from NCIt (NCI Thesaurus).\nProvide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^NCIT:C[0-9]+$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "age_at_specimen_collection", + "exact_mappings": { + "Phenopackets.v2.0": "Biosample.time_of_collection" + }, + "related_mappings": { + "ARGO.v1.34": "donor.age_at_diagnosis+specimen.specimen_acquisition_interval", + "FHIR.v5.0.0": "Specimen.collectedDateTime-Patient.dateBirth", + "mCODE.v4.0.0": "Specimen.collectedDateTime-Patient.dateBirth", + "MOHCCN.v3.1": "Specimen.specimen_collection_date-Donor.date_of_birth" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.collection.collected_x_", + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.birthDate" + ] + }, + "name": "age_at_specimen_collection", + "description": "Indicate participant's age( in days) when specimen was collected.", + "valueType": "integer" + }, + { + "meta": { + "displayName": "specimen_anatomic_location_code", + "exact_mappings": { + "ARGO.v1.34": "specimen.specimen_anatomic_location", + "MOHCCN.v3.1": "Specimen.specimen_anatomic_location" + }, + "related_mappings": { + "FHIR.v5.0.0": "Specimen.collection.bodySite.coding.system:Specimen.collection.bodySite.coding.code", + "mCODE.v4.0.0": "Specimen.collection.bodySite.coding.system:Specimen.collection.bodySite.coding.code" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.collection.bodySite" + ], + "comments": [ + "Refer to the International Classification of Diseases for Oncology, 3rd Edition" + ], + "examples": [ + "UBERON:8600019" + ] + }, + "name": "specimen_anatomic_location_code", + "description": "Indicate the ICD-O-3 topography code or UBERON code for the anatomic location of a specimen when it was collected. Please use C80.9 if the anatomic location of a specimen is Unknown.\nProvide code in Compact URI (CURIE) pattern.\nRefer to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3) manual for guidelines at https://apps.who.int/iris/handle/10665/42344\nUBERON URL: http://purl.obolibrary.org/obo/UBERON_{code}", + "valueType": "string", + "restrictions": { + "regex": "^ICDO3:[C][0-9]{2}(.[0-9]{1})?$|^UBERON:\\d{7,}$" + } + }, + { + "meta": { + "displayName": "specimen_anatomic_location_term", + "exact_mappings": { + "FHIR.v5.0.0": "Specimen.collection.bodySite.coding.display", + "mCODE.v4.0.0": "Specimen.collection.bodySite.coding.display" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.collection.bodySite" + ], + "examples": [ + "placental basal plate" + ] + }, + "name": "specimen_anatomic_location_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the specimen anatomic location code.", + "valueType": "string" + }, + { + "meta": { + "displayName": "specimen_laterality", + "exact_mappings": { + "ARGO.v1.34": "specimen.specimen.laterality", + "mCODE.v4.0.0": "Specimen.collection.bodySite.extension.lateralityQualifier", + "MOHCCN.v3.1": "specimen.specimen.laterality" + }, + "comments": [ + "Reference caDSR CDE ID 2007875 https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2007875&version=2.0" + ] + }, + "name": "specimen_laterality", + "description": "For disease in a paired organ, indicate the side on which the specimen was obtained.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Left", + "Right", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown", + "Not applicable" + ] + } + }, + { + "meta": { + "displayName": "specimen_processing", + "exact_mappings": { + "ARGO.v1.34": "specimen.specimen_processing", + "Beacon.v2.2.0": "biosample.sampleProcessing", + "MOHCCN.v3.1": "Specimen.specimen_processing", + "Phenopackets.v2.0": "Biosample.sample_processing" + } + }, + "name": "specimen_processing", + "description": "Indicate the technique used to process specimen.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Cryopreservation - other", + "Cryopreservation in dry ice (dead tissue)", + "Cryopreservation in liquid nitrogen (dead tissue)", + "Cryopreservation of live cells in liquid nitrogen", + "Formalin fixed & paraffin embedded", + "Formalin fixed - buffered", + "Formalin fixed - unbuffered", + "Fresh", + "Other", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown", + "Not applicable" + ] + } + }, + { + "meta": { + "displayName": "specimen_storage", + "exact_mappings": { + "ARGO.v1.34": "specimen.specimen_storage", + "Beacon.v2.2.0": "biosample.sampleStorage", + "MOHCCN.v3.1": "specimen.specimen_storage", + "Phenopackets.v2.0": "Biosample.sample_storage" + } + }, + "name": "specimen_storage", + "description": "Indicate the method of long term storage for specimen that were not extracted freshly or immediately cultured.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Cut slide", + "Frozen in -70 freezer", + "Frozen in liquid nitrogen", + "Frozen in vapour phase", + "Not applicable", + "Other", + "Paraffin block", + "RNA later frozen", + "Missing - Not collected", + "Missing - Not provided", + "Missing - Restricted access", + "Missing - Unknown" + ] + } + }, + { + "meta": { + "displayName": "specimen_tissue_source_term", + "exact_mappings": { + "ARGO.v1.34": "sample_registration.specimen_tissue_source", + "FHIR.v5.0.0": "Specimen.type.coding.display", + "MOHCCN.v3.1": "Specimen.specimen_tissue_source" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.type" + ] + }, + "name": "specimen_tissue_source_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the specimen tissue source code.", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "participant", + "mappings": [ + { + "local": "submitter_participant_id", + "foreign": "submitter_participant_id" + } + ] + } + ] + } + }, + { + "name": "sample", + "description": "Refers to the molecular material (e.g., DNA, RNA, protein) extracted from the specimen and used for experiments or analysis.", + "fields": [ + { + "meta": { + "displayName": "submitter_sample_id", + "exact_mappings": { + "ARGO.v1.34": "sample_registration.submitter_sample_id", + "MOHCCN.v3.1": "Sample_registration.submitter_sample_id", + "Phenopackets.v2.0": "Biosample.id" + }, + "examples": [ + "hnc_12", + "CCG_34_94583", + "BRCA47832-3239" + ] + }, + "name": "submitter_sample_id", + "description": "Unique identifier of the sample within the study, assigned by the data provider.\n", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "submitter_specimen_id", + "exact_mappings": { + "ARGO.v1.34": "specimen.submitter_specimen_id", + "Beacon.v2.2.0": "biosample.id", + "CQDG": "submitter_biospecimen_id", + "FHIR.v5.0.0": "Specimen.identifier", + "mCODE.v4.0.0": "Specimen.identifier", + "MOHCCN.v3.1": "specimen.submitter_specimen_id", + "Phenopackets.v2.0": "Biosample.derived_from_id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier" + ], + "examples": [ + "LAML_PO", + "00445", + "THY_099-tumour" + ] + }, + "name": "submitter_specimen_id", + "description": "Unique identifier of the specimen within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "molecule_type_code", + "exact_mappings": { + "Beacon.v2.2.0": "biosample.sample_type", + "CQDG": "sample_type", + "GA4GH.Experiment.Metadata.Checklist": "molecule_type", + "Phenopackets.v2.0": "sample_type" + }, + "examples": [ + "NCIT:C449", + "NCIT:C812", + "NCIT:C80376", + "SO:0000991", + "SO:0000234", + "SO:0001877" + ] + }, + "name": "molecule_type_code", + "description": "Indicate NCIT or SO code to denote the type of source material used for sequencing and analysis.\nProvide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^NCIT:C[0-9]+$|^SO:\\d{7}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "sample_status" + }, + "name": "sample_status", + "description": "Indicate the status of the sample for data analysis.\nCase sample refers to a sample that meets the disease or exposure criteria under investigation.\nControl sample refers to of the same type that does not meet the criteria, representing a normal or baseline state for comparison.", + "restrictions": { + "required": true, + "codeList": [ + "Case", + "Control", + "Not applicable" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "molecule_type_term", + "examples": [ + "DNA" + ] + }, + "name": "molecule_type_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with molecule type code.", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "specimen", + "mappings": [ + { + "local": "submitter_specimen_id", + "foreign": "submitter_specimen_id" + } + ] + } + ] + } + }, + { + "name": "experiment", + "description": "Contains information about the experimental design of the sequencing", + "fields": [ + { + "meta": { + "displayName": "submitter_experiment_id", + "exact_mappings": { + "ARGO.v1.34": "experiment.submitter_sequencing_experiment_id" + } + }, + "name": "submitter_experiment_id", + "description": "Unique identifier of the experiment within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "submitter_sample_id", + "exact_mappings": { + "ARGO.v1.34": "sample_registration.submitter_sample_id", + "MOHCCN.v3.1": "Sample_registration.submitter_sample_id", + "Phenopackets.v2.0": "Biosample.id" + }, + "examples": [ + "hnc_12", + "CCG_34_94583", + "BRCA47832-3239" + ] + }, + "name": "submitter_sample_id", + "description": "Unique identifier of the sample within the study, assigned by the data provider.\n", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "assay_type_code", + "exact_mappings": { + "Beacon.v2.2.0": "runs.libraryStrategy", + "GA4GH.Experiment.Metadata.Checklist": "assay_type" + }, + "examples": [ + "OBI:0002117" + ] + }, + "name": "assay_type_code", + "description": "Indicate OBI code to provide the sequencing technique intended for the library for sequencing data.\nProvide code in Compact URI (CURIE) pattern.", + "restrictions": { + "required": true, + "regex": "^OBI:\\d{7}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "experiment_type", + "exact_mappings": { + "GA4GHExperimentMetadataChecklist": "experiment_type" + } + }, + "name": "experiment_type", + "description": "Indicate NCIt (NCI Thesaurus) code and term to denote the broad type of sequencing experiment performed. A mixture of library strategy and source.", + "restrictions": { + "required": true, + "codeList": [ + "NCIT:C84343 (Genomics)", + "NCIT:C153189 (Transcriptomics)", + "NCIT:C20085 (Proteomics)", + "NCIT:C153191 (Metagenomics)", + "NCIT:C153190 (Epigenomics)" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "instrument", + "exact_mappings": { + "GA4GH.Experiment.Metadata.Checklist": "instrument" + }, + "examples": [ + "OBI:0002752 (Oxford Nanopore PromethION)", + "OBI:0000759 (Illumina)", + "OBI:0002630 (Illumina NovaSeq 6000)", + "OBI:0002012 (PacBio RS II)" + ] + }, + "name": "instrument", + "description": "Provide detailed information about the sequencing platform or technology used, including the name and/or model number of the specific instrument. Whenever possible, specify the exact model or revision rather than the general manufacturer name. It is recommended to use standardized terminology by including the appropriate OBI (Ontology for Biomedical Investigations) code and term to ensure precision.\n\nUse the format: OBI code in CURIE format (OBI term) ", + "restrictions": { + "required": true, + "regex": "^OBI:\\d{7} \\(.*\\)$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "platform", + "exact_mappings": { + "ARGO.v1.34": "experiment.platform", + "Beacon.v2.2.0": "runs.platform" + } + }, + "name": "platform", + "description": "The sequencing platform type used in data generation.", + "restrictions": { + "required": true, + "codeList": [ + "CAPILLARY", + "DNBSEQ", + "ELEMENT", + "HELICOS", + "ILLUMINA", + "IONTORRENT", + "LS454", + "ONT", + "PACBIO", + "SINGULAR", + "SOLID", + "ULTIMA" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "assay_type_term", + "examples": [ + "whole genome sequencing assay" + ] + }, + "name": "assay_type_term", + "description": "Provide the standardized and human readable term derived from the coding system associated with the assay type code.", + "valueType": "string" + }, + { + "meta": { + "displayName": "experiment_design", + "exact_mappings": { + "GA4GH.Experiment.Metadata.Checklist": "design_description" + } + }, + "name": "experiment_design", + "description": "The high-level experiment design including layout, protocol.", + "valueType": "string" + }, + { + "meta": { + "displayName": "instrument_metadata", + "exact_mappings": { + "GA4GH.Experiment.Metadata.Checklist": "instrument_metadata" + } + }, + "name": "instrument_metadata", + "description": "Captures metadata about sequencing instrument usage (e.g. instruments parameters and usage conditions)", + "valueType": "string" + }, + { + "meta": { + "displayName": "sequencing_protocol", + "exact_mappings": { + "GA4GH.Experiment.Metadata.Checklist": "sequencing_protocol" + } + }, + "name": "sequencing_protocol", + "description": "Set of rules which guides how the sequencing protocol was followed. Change-tracking services such as Protocol.io or GitHub are encouraged instead of dumping free text in this field.\nE.g, https://www.protocols.io/view/environmental-dna-edna-metabarcoding-protocol-for-rm7vzy3q2lx1/v1", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "sample", + "mappings": [ + { + "local": "submitter_sample_id", + "foreign": "submitter_sample_id" + } + ] + } + ] + } + }, + { + "name": "read_group", + "description": "Holds the read group information about the raw reads generated in a run of sequencing", + "fields": [ + { + "meta": { + "displayName": "submitter_experiment_id", + "exact_mappings": { + "ARGO.v1.34": "experiment.submitter_sequencing_experiment_id" + } + }, + "name": "submitter_experiment_id", + "description": "Unique identifier of the experiment within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "submitter_read_group_id", + "exact_mappings": { + "ARGO.v1.34": "read_groups.submitter_read_group_id", + "Beacon.v2.2.0": "runs.id" + } + }, + "name": "submitter_read_group_id", + "description": "The identifier of a read group; must be unique within each payload.", + "restrictions": { + "required": true, + "regex": "^[a-zA-Z0-9\\-_:\\.']+$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "file_r1", + "exact_mappings": { + "ARGO": "read_groups.file_r1" + } + }, + "name": "file_r1", + "description": "Name of the sequencing file containing reads from the first end of a sequencing run.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "library_layout", + "exact_mappings": { + "Beacon.v2.2.0": "runs.libraryLayout", + "GA4GH.Experiment.Metadata.Checklist": "library_layout" + } + }, + "name": "library_layout", + "description": "Indicate whether the library was built as paired-end or single-end if applicable.", + "restrictions": { + "required": true, + "codeList": [ + "OBI:0000722 (paired-end library)", + "OBI:0000736 (single fragment library)", + "Not applicable" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "library_name", + "exact_mappings": { + "ARGO": "read_groups.library_name", + "GA4GH.Experiment.Metadata.Checklist": "library_extra_id" + } + }, + "name": "library_name", + "description": "Name of a sequencing library made from a molecular sample or a sample pool (multiplex sequencing).", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "platform_unit", + "exact_mappings": { + "ARGO": "read_groups.platform_unit" + } + }, + "name": "platform_unit", + "description": "Unique identifier for each read group. For example, Illumina has format {FLOWCELL_BARCODE}.{LANE}.{SAMPLE_BARCODE}. The {FLOWCELL_BARCODE} refers to the unique identifier for a particular flow cell. The {LANE} indicates the lane of the flow cell and the {SAMPLE_BARCODE} is a sample/library-specific identifier. For non-multiplex sequencing, platform unit and read group have a one-to-one relationship.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "file_r2", + "exact_mappings": { + "ARGO": "read_groups.file_r2" + } + }, + "name": "file_r2", + "description": "Name of the sequencing file containing reads from the second end of a paired-end sequencing run. Required if and only if paired-end sequencing was done.", + "valueType": "string", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "library_layout" + ], + "match": { + "value": "OBI:0000722 (paired-end library)" + }, + "case": "all" } + ] + }, + "then": { + "required": true + }, + "else": { + "required": false, + "empty": true + } + } + }, + { + "meta": { + "displayName": "insert_size", + "exact_mappings": { + "ARGO": "read_groups.insert_size", + "GA4GH.Experiment.Metadata.Checklist": "insert_size" + } + }, + "name": "insert_size", + "description": "For paired-end sequencing, the average size of sequences between two sequencing ends. Required only for paired-end sequencing.", + "valueType": "integer", + "restrictions": { + "range": { + "min": 0 + } + } + }, + { + "meta": { + "displayName": "library_description", + "exact_mappings": { + "GA4GH.Experiment.Metadata.Checklist": "library_description" + } + }, + "name": "library_description", + "description": "Description of the nucleotide sequencing library, including targeting information, spot, gap descriptors, and any other information relevant to its construction", + "valueType": "string" + }, + { + "meta": { + "displayName": "read_group_id_in_bam", + "exact_mappings": { + "ARGO": "read_groups.read_group_id_in_bam" + } + }, + "name": "read_group_id_in_bam", + "description": "Optional field indicating the @RD ID in the BAM. If submitted, this will be used to map the @RG ID in the BAM header to the submitter_read_group_id in the payload. After submission, the @RG ID in the payload will be used for all future headers. This cannot be submitted for FASTQ files.", + "valueType": "string", + "restrictions": { + "regex": "^[a-zA-Z0-9\\-_:\\.']+$" + } + }, + { + "meta": { + "displayName": "read_length_r1", + "exact_mappings": { + "ARGO": "read_groups.read_length_r1" + } + }, + "name": "read_length_r1", + "description": "Length of sequencing reads in file_r1; this corresponds to the number of sequencing cycles of the first end.", + "valueType": "integer", + "restrictions": { + "range": { + "min": 20 + } + } + }, + { + "meta": { + "displayName": "read_length_r2", + "exact_mappings": { + "ARGO": "read_groups.read_length_r2" + } + }, + "name": "read_length_r2", + "description": "Length of sequencing reads in file_r2; this corresponds to the number of sequencing cycles of the second end.", + "valueType": "integer", + "restrictions": { + "range": { + "min": 20 + } + } + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "experiment", + "mappings": [ + { + "local": "submitter_experiment_id", + "foreign": "submitter_experiment_id" + } + ] + } + ] + } + }, + { + "name": "analysis", + "description": "This entity is intended to contain metadata about a detailed examination of data (mainly data processing protocols) in order to come to some conclusion. It can be of different types (e.g. sequence variation, sequence alignment, phenotype characterization, gene expression, etc.) that will mainly differ in the protocols used to achieve the processed data of the analysis.", + "fields": [ + { + "meta": { + "displayName": "submitter_analysis_id", + "exact_mappings": { + "Beacon.v2.2.0": "analyses.id", + "EGA": "ANALYSIS_ALIAS" + }, + "examples": [ + "hnc_12", + "CCG_34_94583", + "BRCA47832-3239" + ] + }, + "name": "submitter_analysis_id", + "description": "Unique identifier of the analysis within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "analysisType", + "exact_mappings": { + "ARGO": "analysisType", + "EGA": "ANALYSIS/ANALYSIS_TYPE" + } + }, + "name": "analysisType", + "description": "Overall type of the analysis. Term chosen from a controlled vocabulary (CV) list.", + "restrictions": { + "required": true, + "codeList": [ + "sequenceExperiment", + "sequenceAlignment", + "variantCall", + "variantAnnotation" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "data_category" + }, + "name": "data_category", + "description": "Indicate the category of data produced as outputs from the analysis. ", + "restrictions": { + "required": true, + "codeList": [ + "Genomics", + "Transcriptomics", + "Proteomics", + "Epigenomics", + "Imaging", + "Reference" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "studyId", + "exact_mappings": { + "ARGO.v1.34": "program_id", + "CQDG": "study_id" + } + }, + "name": "studyId", + "description": "Unique identifier of the study.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "submitter_experiment_ids", + "exact_mappings": { + "ARGO.v1.34": "experiment.submitter_sequencing_experiment_id" + } + }, + "name": "submitter_experiment_ids", + "description": "A list of Unique identifiers (min 1) for experiments within the study, assigned by the data provider.", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "analysisType" + ], + "match": { + "codeList": [ + "sequenceExperiment", + "sequenceAlignment", + "variantCall" + ] + }, + "case": "any" + } + ] + }, + "then": { + "required": true + }, + "else": { + "required": false, + "empty": true + } + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "submitter_participant_ids", + "exact_mappings": { + "ARGO.v1.34": "donor.submitter_donor_id", + "Beacon.v2.2.0": "individual.id", + "CQDG": "submitter_participant_id", + "FHIR.v5.0.0": "Patient.identifier", + "mCODE.v4.0.0": "Patient.identifier", + "MOHCCN.v3.1": "Donor.submitter_donor_id", + "Phenopackets.v2.0": "Individual.id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/patient-definitions.html#Patient.identifier" ], - "name": "workflow", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_analysis_id", - "local": "submitter_analysis_id" - } - ], - "schema": "analysis" - } - ] - } - }, - { - "description": "Contains information about the files generated from a run of sequencing or data analysis", - "fields": [ - { - "description": "Unique identifier of the analysis within the study, assigned by the data provider.", - "meta": { - "displayName": "submitter_analysis_id", - "exact_mappings": { - "Beacon.v2.2.0": "analyses.id", - "EGA": "ANALYSIS_ALIAS" - }, - "examples": [ - "hnc_12", - "CCG_34_94583", - "BRCA47832-3239" - ] - }, - "name": "submitter_analysis_id", - "restrictions": { - "regex": "^[A-Za-z0-9\\-\\._]{1,64}$", - "required": true - }, - "valueType": "string" - }, - { - "description": "File name, subdirectory-relative path, or absolute path of the data file. For more details see https://github.com/Pan-Canadian-Genome-Library/molecular-data-submission-workflow/blob/main/docs/input.md.", - "meta": { - "displayName": "fileName", - "exact_mappings": { - "ARGO": "fileName" - } - }, - "name": "fileName", - "restrictions": { - "regex": "^[A-Za-z0-9_\\.\\-\\[\\]\\(\\)]+$.", - "required": true - }, - "valueType": "string" - }, - { - "description": "Size of the file, in bytes. If not provided, will be populated by molecular submission workflow.", - "meta": { - "displayName": "fileSize", - "exact_mappings": { - "ARGO": "files.size" - } - }, - "name": "fileSize", - "valueType": "integer" - }, - { - "description": "Computed md5sum of the file. If not provided, will be populated by molecular submission workflow.", - "meta": { - "displayName": "fileMd5sum", - "exact_mappings": { - "ARGO": "files.md5sum" - } - }, - "name": "fileMd5sum", - "restrictions": { - "regex": "^[a-fA-F0-9]{32}$" - }, - "valueType": "string" - }, - { - "description": "Data format of files.", - "meta": { - "displayName": "fileType", - "exact_mappings": { - "ARGO": "files.format", - "EGA": "ANALYSIS/FILES/FILE@filetype" - } - }, - "name": "fileType", - "restrictions": { - "required": true - }, - "valueType": "string" - }, - { - "description": "The permission level of a file for public access.", - "meta": { - "displayName": "fileAccess", - "exact_mappings": { - "ARGO": "fileAccess" - } - }, - "name": "fileAccess", - "restrictions": { - "codeList": [ - "open", - "controlled" - ], - "required": true - }, - "valueType": "string" - }, - { - "description": "Indicates the type of data produced as outputs from the analysis. ", - "meta": { - "displayName": "dataType" - }, - "name": "dataType", - "restrictions": { - "codeList": [ - "Raw Sequencing Reads", - "Aligned Reads", - "Aligned Reads Index", - "Single Nucleotide Variants (SNVs)", - "Insertions and Deletions (InDels)", - "Structural Variations (SVs)", - "Copy Number Variations (CNVs)", - "Variant Calls Index", - "Quality Control Metrics", - "Gene Fusions", - "Alternative Splicing", - "Gene Expression Quantification", - "Transcript Expression Quantification", - "Single-Cell Expression Matrices", - "Splicing Junctions", - "Differential Expression Analysis" - ], - "required": true - }, - "valueType": "string" + "examples": [ + "90234", + "BLD_donor_89", + "AML-90" + ] + }, + "name": "submitter_participant_ids", + "description": "A list of Unique identifiers (min 1) for participants within the study, assigned by the data provider.", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "submitter_experiment_ids", + "submitter_sample_ids", + "submitter_specimen_ids" + ], + "match": { + "exists": true + }, + "case": "any" } + ] + }, + "then": { + "required": false, + "empty": true + }, + "else": { + "required": true + } + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "submitter_sample_ids", + "exact_mappings": { + "ARGO.v1.34": "sample_registration.submitter_sample_id", + "MOHCCN.v3.1": "Sample_registration.submitter_sample_id", + "Phenopackets.v2.0": "Biosample.id" + }, + "examples": [ + "hnc_12", + "CCG_34_94583", + "BRCA47832-3239" + ] + }, + "name": "submitter_sample_ids", + "description": "List of Unique identifiers (min 1) for samples within the study, assigned by the data provider.\n", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "submitter_participant_ids", + "submitter_experiment_ids", + "submitter_specimen_ids" + ], + "match": { + "exists": true + }, + "case": "any" + } + ] + }, + "then": { + "required": false, + "empty": true + }, + "else": { + "required": true + } + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "submitter_specimen_ids", + "exact_mappings": { + "ARGO.v1.34": "specimen.submitter_specimen_id", + "Beacon.v2.2.0": "biosample.id", + "CQDG": "submitter_biospecimen_id", + "FHIR.v5.0.0": "Specimen.identifier", + "mCODE.v4.0.0": "Specimen.identifier", + "MOHCCN.v3.1": "specimen.submitter_specimen_id", + "Phenopackets.v2.0": "Biosample.derived_from_id" + }, + "specifications": [ + "FHIRSpec.v5.0.0:https://hl7.org/fhir/specimen-definitions.html#Specimen.identifier" ], - "name": "file", - "restrictions": { - "foreignKey": [ - { - "mappings": [ - { - "foreign": "submitter_analysis_id", - "local": "submitter_analysis_id" - } - ], - "schema": "analysis" - } - ] + "examples": [ + "LAML_PO", + "00445", + "THY_099-tumour" + ] + }, + "name": "submitter_specimen_ids", + "description": "List of Unique identifiers (min 1) for specimens within the study, assigned by the data provider.", + "restrictions": { + "if": { + "conditions": [ + { + "fields": [ + "submitter_participant_ids", + "submitter_experiment_ids", + "submitter_sample_ids" + ], + "match": { + "exists": true + }, + "case": "any" + } + ] + }, + "then": { + "required": false, + "empty": true + }, + "else": { + "required": true + } + }, + "valueType": "string", + "isArray": true, + "delimiter": "|" + }, + { + "meta": { + "displayName": "genome_annotation" + }, + "name": "genome_annotation", + "description": "Indicates which genome annotation build or version was used in the analysis (e.g., Ensembl release, RefSeq release, etc.).", + "valueType": "string", + "restrictions": { + "regex": "^(?:Ensembl \\d{1,5}|RefSeq \\d{1,5}|Gencode v\\d{1,5})$" + } + }, + { + "meta": { + "displayName": "genome_build" + }, + "name": "genome_build", + "description": "The reference genome build that is used in the workflow. ", + "valueType": "string", + "restrictions": { + "codeList": [ + "GRCh38", + "GRCh37" + ] + } + }, + { + "meta": { + "displayName": "variant_calling_strategy" + }, + "name": "variant_calling_strategy", + "description": "Indicate the approach used to identify genetic variants from sequencing data, based on the availability of reference samples (e.g., matched normal) and the study design.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Tumour only", + "Tumour normal", + "Single sample", + "Family based", + "RNA based", + "Joint calling" + ] + } + }, + { + "meta": { + "displayName": "variant_class" + }, + "name": "variant_class", + "description": "Indicates whether the called variants are germline, somatic, or of uncertain classification.", + "valueType": "string", + "restrictions": { + "codeList": [ + "Germline", + "Somatic", + "Unknown" + ] + } + } + ] + }, + { + "name": "workflow", + "description": "Contains information about the analysis workflow generating the analysis", + "fields": [ + { + "meta": { + "displayName": "submitter_analysis_id", + "exact_mappings": { + "Beacon.v2.2.0": "analyses.id", + "EGA": "ANALYSIS_ALIAS" + }, + "examples": [ + "hnc_12", + "CCG_34_94583", + "BRCA47832-3239" + ] + }, + "name": "submitter_analysis_id", + "description": "Unique identifier of the analysis within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "submitter_workflow_id" + }, + "name": "submitter_workflow_id", + "description": "Indicate the unique identifier of the data processing workflow used in the analysis.", + "valueType": "string", + "unique": true + }, + { + "meta": { + "displayName": "workflow_name" + }, + "name": "workflow_name", + "description": "The name of the genomic data processing workflow used for data analysis.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "workflow_url" + }, + "name": "workflow_url", + "description": "A URL linking to the workflow's repository or documentation. This could be a reference to a GitHub repository, a website where the workflow is described, or documentation on how to run the workflow.", + "valueType": "string" + }, + { + "meta": { + "displayName": "workflow_version" + }, + "name": "workflow_version", + "description": "The version of the workflow or pipeline being used. ", + "valueType": "string" + } + ], + "restrictions": { + "foreignKey": [ + { + "schema": "analysis", + "mappings": [ + { + "local": "submitter_analysis_id", + "foreign": "submitter_analysis_id" + } + ] + } + ] + } + }, + { + "name": "file", + "description": "Contains information about the files generated from a run of sequencing or data analysis", + "fields": [ + { + "meta": { + "displayName": "submitter_analysis_id", + "exact_mappings": { + "Beacon.v2.2.0": "analyses.id", + "EGA": "ANALYSIS_ALIAS" + }, + "examples": [ + "hnc_12", + "CCG_34_94583", + "BRCA47832-3239" + ] + }, + "name": "submitter_analysis_id", + "description": "Unique identifier of the analysis within the study, assigned by the data provider.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "dataType" + }, + "name": "dataType", + "description": "Indicates the type of data produced as outputs from the analysis. ", + "restrictions": { + "required": true, + "codeList": [ + "Raw Sequencing Reads", + "Aligned Reads", + "Aligned Reads Index", + "Single Nucleotide Variants (SNVs)", + "Insertions and Deletions (InDels)", + "Structural Variations (SVs)", + "Copy Number Variations (CNVs)", + "Variant Calls Index", + "Quality Control Metrics", + "Gene Fusions", + "Alternative Splicing", + "Gene Expression Quantification", + "Transcript Expression Quantification", + "Single-Cell Expression Matrices", + "Splicing Junctions", + "Differential Expression Analysis" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "fileAccess", + "exact_mappings": { + "ARGO": "fileAccess" + } + }, + "name": "fileAccess", + "description": "The permission level of a file for public access.", + "restrictions": { + "required": true, + "codeList": [ + "open", + "controlled" + ] + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "fileName", + "exact_mappings": { + "ARGO": "fileName" + } + }, + "name": "fileName", + "description": "File name, subdirectory-relative path, or absolute path of the data file. For more details see https://github.com/Pan-Canadian-Genome-Library/molecular-data-submission-workflow/blob/main/docs/input.md.", + "restrictions": { + "required": true, + "regex": "^[A-Za-z0-9_\\.\\-\\[\\]\\(\\)]+$." + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "fileType", + "exact_mappings": { + "ARGO": "files.format", + "EGA": "ANALYSIS/FILES/FILE@filetype" + } + }, + "name": "fileType", + "description": "Data format of files.", + "restrictions": { + "required": true + }, + "valueType": "string" + }, + { + "meta": { + "displayName": "fileMd5sum", + "exact_mappings": { + "ARGO": "files.md5sum" + } + }, + "name": "fileMd5sum", + "description": "Computed md5sum of the file. If not provided, will be populated by molecular submission workflow.", + "valueType": "string", + "restrictions": { + "regex": "^[a-fA-F0-9]{32}$" + } + }, + { + "meta": { + "displayName": "fileSize", + "exact_mappings": { + "ARGO": "files.size" } + }, + "name": "fileSize", + "description": "Size of the file, in bytes. If not provided, will be populated by molecular submission workflow.", + "valueType": "integer" } - ], - "version": "1.0" + ], + "restrictions": { + "foreignKey": [ + { + "schema": "analysis", + "mappings": [ + { + "local": "submitter_analysis_id", + "foreign": "submitter_analysis_id" + } + ] + } + ] + } + } + ] } \ No newline at end of file diff --git a/restrictions/pcgl/restrictions.json b/restrictions/pcgl/restrictions.json index dd43260..f6c39bc 100644 --- a/restrictions/pcgl/restrictions.json +++ b/restrictions/pcgl/restrictions.json @@ -169,8 +169,7 @@ "name": "analysis", "fields" : [ { - "name":"submitter_experiment_id", - "valueType": "string", + "name":"submitter_experiment_ids", "restrictions" : { "if":{ "conditions": [ @@ -192,13 +191,12 @@ } }, { - "name":"submitter_participant_id", - "valueType": "string", + "name":"submitter_participant_ids", "restrictions" : { "if":{ "conditions": [ { - "fields":["submitter_experiment_id","submitter_sample_id","submitter_specimen_id"], + "fields":["submitter_experiment_ids","submitter_sample_ids","submitter_specimen_ids"], "match":{"exists": true}, "case": "any" } @@ -210,13 +208,12 @@ } }, { - "name":"submitter_sample_id", - "valueType": "string", + "name":"submitter_sample_ids", "restrictions" : { "if":{ "conditions": [ { - "fields":["submitter_participant_id","submitter_experiment_id","submitter_specimen_id"], + "fields":["submitter_participant_ids","submitter_experiment_ids","submitter_specimen_ids"], "match":{"exists": true}, "case": "any" } @@ -228,13 +225,12 @@ } }, { - "name":"submitter_specimen_id", - "valueType": "string", + "name":"submitter_specimen_ids", "restrictions" : { "if":{ "conditions": [ { - "fields":["submitter_participant_id","submitter_experiment_id","submitter_sample_id"], + "fields":["submitter_participant_ids","submitter_experiment_ids","submitter_sample_ids"], "match":{"exists": true}, "case": "any" } diff --git a/scripts/gen_song_schema.py b/scripts/gen_song_schema.py index cdf32bf..a8c5d18 100644 --- a/scripts/gen_song_schema.py +++ b/scripts/gen_song_schema.py @@ -155,6 +155,19 @@ def update_schema(schema, top_class, file_type_enum, data_type_enum): schema['properties']['files']['items']['properties']['fileType']['enum'] = file_type_enum if 'dataType' in schema['properties']['files']['items']['properties']: schema['properties']['files']['items']['properties']['dataType']['enum'] = data_type_enum + # fileSize and fileMd5sum were made optional for data viewer and workflow but we want to make it mandatory on server side so add it back here. + if 'fileSize' in schema['properties']['files']['items']['properties']: + schema['properties']['files']['items']['properties']['fileSize']['type']="integer" + schema['properties']['files']['items']['required'].append('fileSize') if 'fileSize' not in schema['properties']['files']['items']['required'] else None + if 'fileMd5sum' in schema['properties']['files']['items']['properties']: + schema['properties']['files']['items']['properties']['fileMd5sum']['type']="string" + schema['properties']['files']['items']['required'].append('fileMd5sum') if 'fileMd5sum' not in schema['properties']['files']['items']['required'] else None + + # LinkML to JSON Schema misses converting `list_elements_unique: true` to `"uniqueItems": true`. Manually add + for property in schema['properties'].keys(): + if property.endswith("_ids"): + schema['properties'][property]['uniqueItems']=True + return schema def ensure_directory_exists(directory): diff --git a/song_schema/conf/options.json b/song_schema/conf/options.json index cb65747..0493ecd 100644 --- a/song_schema/conf/options.json +++ b/song_schema/conf/options.json @@ -5,7 +5,7 @@ "externalValidations":[ { "url": "http://submission.submission.svc.cluster.local/validator/entity/experiment/field/submitter_experiment_id/exists?study={study}&value={value}", - "jsonPath": "submitter_experiment_id" + "jsonPath": "submitter_experiment_ids" } ] }, @@ -18,7 +18,7 @@ "externalValidations":[ { "url": "http://submission.submission.svc.cluster.local/validator/entity/experiment/field/submitter_experiment_id/exists?study={study}&value={value}", - "jsonPath": "submitter_experiment_id" + "jsonPath": "submitter_experiment_ids" } ] }, @@ -32,7 +32,7 @@ "externalValidations":[ { "url": "http://submission.submission.svc.cluster.local/validator/entity/experiment/field/submitter_experiment_id/exists?study={study}&value={value}", - "jsonPath": "submitter_experiment_id" + "jsonPath": "submitter_experiment_ids" } ] }, diff --git a/song_schema/json-schema/dynamic/sequenceAlignment.json b/song_schema/json-schema/dynamic/sequenceAlignment.json index 653eb35..0191ac3 100644 --- a/song_schema/json-schema/dynamic/sequenceAlignment.json +++ b/song_schema/json-schema/dynamic/sequenceAlignment.json @@ -10,7 +10,7 @@ "externalValidations": [ { "url": "http://submission.submission.svc.cluster.local/validator/entity/experiment/field/submitter_experiment_id/exists?study={study}&value={value}", - "jsonPath": "submitter_experiment_id" + "jsonPath": "submitter_experiment_ids" } ] }, @@ -41,10 +41,15 @@ "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", "type": "string" }, - "submitter_experiment_id": { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", - "type": "string" + "submitter_experiment_ids": { + "description": "List of Unique identifier for experiments within the study, assigned by the data provider.", + "items": { + "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", + "type": "string" + }, + "minItems": 1, + "type": "array", + "uniqueItems": true }, "workflow": { "additionalProperties": false, @@ -81,7 +86,7 @@ } }, "required": [ - "submitter_experiment_id", + "submitter_experiment_ids", "workflow", "genome_build", "submitter_analysis_id", diff --git a/song_schema/json-schema/dynamic/sequenceExperiment.json b/song_schema/json-schema/dynamic/sequenceExperiment.json index 9dedbd5..0982cf3 100644 --- a/song_schema/json-schema/dynamic/sequenceExperiment.json +++ b/song_schema/json-schema/dynamic/sequenceExperiment.json @@ -8,7 +8,7 @@ "externalValidations": [ { "url": "http://submission.submission.svc.cluster.local/validator/entity/experiment/field/submitter_experiment_id/exists?study={study}&value={value}", - "jsonPath": "submitter_experiment_id" + "jsonPath": "submitter_experiment_ids" } ] }, @@ -31,14 +31,19 @@ "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", "type": "string" }, - "submitter_experiment_id": { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", - "type": "string" + "submitter_experiment_ids": { + "description": "List of Unique identifier for experiments within the study, assigned by the data provider.", + "items": { + "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", + "type": "string" + }, + "minItems": 1, + "type": "array", + "uniqueItems": true } }, "required": [ - "submitter_experiment_id", + "submitter_experiment_ids", "submitter_analysis_id", "data_category" ], diff --git a/song_schema/json-schema/dynamic/variantCall.json b/song_schema/json-schema/dynamic/variantCall.json index e98a67c..c1d13e8 100644 --- a/song_schema/json-schema/dynamic/variantCall.json +++ b/song_schema/json-schema/dynamic/variantCall.json @@ -8,7 +8,7 @@ "externalValidations": [ { "url": "http://submission.submission.svc.cluster.local/validator/entity/experiment/field/submitter_experiment_id/exists?study={study}&value={value}", - "jsonPath": "submitter_experiment_id" + "jsonPath": "submitter_experiment_ids" } ] }, @@ -27,7 +27,8 @@ "type": "string" }, "genome_annotation": { - "description": "Indicates which genome annotation build or version was used in the analysis (e.g., Ensembl release, RefSeq release, and Gencode release.).", + "description": "Indicates which genome annotation build or version was used in the analysis (e.g., Ensembl release, RefSeq release, etc.).", + "pattern": "^(?:Ensembl \\d{1,5}|RefSeq \\d{1,5}|Gencode v\\d{1,5})$", "type": [ "string", "null" @@ -46,10 +47,15 @@ "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", "type": "string" }, - "submitter_experiment_id": { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", - "type": "string" + "submitter_experiment_ids": { + "description": "List of Unique identifier for experiments within the study, assigned by the data provider.", + "items": { + "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", + "type": "string" + }, + "minItems": 1, + "type": "array", + "uniqueItems": true }, "variant_calling_strategy": { "description": "", @@ -107,7 +113,7 @@ } }, "required": [ - "submitter_experiment_id", + "submitter_experiment_ids", "variant_calling_strategy", "variant_class", "workflow", diff --git a/song_schema/json-schema/full/sequenceAlignment.json b/song_schema/json-schema/full/sequenceAlignment.json index e0aac1f..6f38df7 100644 --- a/song_schema/json-schema/full/sequenceAlignment.json +++ b/song_schema/json-schema/full/sequenceAlignment.json @@ -41,21 +41,25 @@ "type": "string" }, "fileAccess": { - "description": "The permission level of a file for public access.", + "description": "", + "enum": [ + "open", + "controlled" + ], "type": "string" }, "fileMd5sum": { - "description": "Computed md5sum of the file.", + "description": "Computed md5sum of the file. If not provided, will be populated by molecular submission workflow.", "pattern": "^[a-fA-F0-9]{32}$", "type": "string" }, "fileName": { - "description": "Name of the file.", + "description": "File name, subdirectory-relative path, or absolute path of the data file. For more details see https://github.com/Pan-Canadian-Genome-Library/molecular-data-submission-workflow/blob/main/docs/input.md.", "pattern": "^[A-Za-z0-9_\\.\\-\\[\\]\\(\\)]+$.", "type": "string" }, "fileSize": { - "description": "Size of the file, in bytes.", + "description": "Size of the file, in bytes. If not provided, will be populated by molecular submission workflow.", "type": "integer" }, "fileType": { @@ -72,10 +76,10 @@ "required": [ "dataType", "fileAccess", - "fileMd5sum", "fileName", + "fileType", "fileSize", - "fileType" + "fileMd5sum" ], "type": "object" }, @@ -98,10 +102,15 @@ "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", "type": "string" }, - "submitter_experiment_id": { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", - "type": "string" + "submitter_experiment_ids": { + "description": "List of Unique identifier for experiments within the study, assigned by the data provider.", + "items": { + "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", + "type": "string" + }, + "minItems": 1, + "type": "array", + "uniqueItems": true }, "workflow": { "additionalProperties": false, @@ -138,7 +147,7 @@ } }, "required": [ - "submitter_experiment_id", + "submitter_experiment_ids", "workflow", "genome_build", "studyId", diff --git a/song_schema/json-schema/full/sequenceExperiment.json b/song_schema/json-schema/full/sequenceExperiment.json index f5cb602..1e7822e 100644 --- a/song_schema/json-schema/full/sequenceExperiment.json +++ b/song_schema/json-schema/full/sequenceExperiment.json @@ -40,21 +40,25 @@ "type": "string" }, "fileAccess": { - "description": "The permission level of a file for public access.", + "description": "", + "enum": [ + "open", + "controlled" + ], "type": "string" }, "fileMd5sum": { - "description": "Computed md5sum of the file.", + "description": "Computed md5sum of the file. If not provided, will be populated by molecular submission workflow.", "pattern": "^[a-fA-F0-9]{32}$", "type": "string" }, "fileName": { - "description": "Name of the file.", + "description": "File name, subdirectory-relative path, or absolute path of the data file. For more details see https://github.com/Pan-Canadian-Genome-Library/molecular-data-submission-workflow/blob/main/docs/input.md.", "pattern": "^[A-Za-z0-9_\\.\\-\\[\\]\\(\\)]+$.", "type": "string" }, "fileSize": { - "description": "Size of the file, in bytes.", + "description": "Size of the file, in bytes. If not provided, will be populated by molecular submission workflow.", "type": "integer" }, "fileType": { @@ -69,10 +73,10 @@ "required": [ "dataType", "fileAccess", - "fileMd5sum", "fileName", + "fileType", "fileSize", - "fileType" + "fileMd5sum" ], "type": "object" }, @@ -87,14 +91,19 @@ "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", "type": "string" }, - "submitter_experiment_id": { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", - "type": "string" + "submitter_experiment_ids": { + "description": "List of Unique identifier for experiments within the study, assigned by the data provider.", + "items": { + "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", + "type": "string" + }, + "minItems": 1, + "type": "array", + "uniqueItems": true } }, "required": [ - "submitter_experiment_id", + "submitter_experiment_ids", "studyId", "analysisType", "submitter_analysis_id", diff --git a/song_schema/json-schema/full/variantCall.json b/song_schema/json-schema/full/variantCall.json index e3ab8bd..4eddb9f 100644 --- a/song_schema/json-schema/full/variantCall.json +++ b/song_schema/json-schema/full/variantCall.json @@ -44,21 +44,25 @@ "type": "string" }, "fileAccess": { - "description": "The permission level of a file for public access.", + "description": "", + "enum": [ + "open", + "controlled" + ], "type": "string" }, "fileMd5sum": { - "description": "Computed md5sum of the file.", + "description": "Computed md5sum of the file. If not provided, will be populated by molecular submission workflow.", "pattern": "^[a-fA-F0-9]{32}$", "type": "string" }, "fileName": { - "description": "Name of the file.", + "description": "File name, subdirectory-relative path, or absolute path of the data file. For more details see https://github.com/Pan-Canadian-Genome-Library/molecular-data-submission-workflow/blob/main/docs/input.md.", "pattern": "^[A-Za-z0-9_\\.\\-\\[\\]\\(\\)]+$.", "type": "string" }, "fileSize": { - "description": "Size of the file, in bytes.", + "description": "Size of the file, in bytes. If not provided, will be populated by molecular submission workflow.", "type": "integer" }, "fileType": { @@ -73,17 +77,18 @@ "required": [ "dataType", "fileAccess", - "fileMd5sum", "fileName", + "fileType", "fileSize", - "fileType" + "fileMd5sum" ], "type": "object" }, "type": "array" }, "genome_annotation": { - "description": "Indicates which genome annotation build or version was used in the analysis (e.g., Ensembl release, RefSeq release, and Gencode release.).", + "description": "Indicates which genome annotation build or version was used in the analysis (e.g., Ensembl release, RefSeq release, etc.).", + "pattern": "^(?:Ensembl \\d{1,5}|RefSeq \\d{1,5}|Gencode v\\d{1,5})$", "type": [ "string", "null" @@ -106,10 +111,15 @@ "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", "type": "string" }, - "submitter_experiment_id": { - "description": "Unique identifier of the experiment within the study, assigned by the data provider.", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", - "type": "string" + "submitter_experiment_ids": { + "description": "List of Unique identifier for experiments within the study, assigned by the data provider.", + "items": { + "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$", + "type": "string" + }, + "minItems": 1, + "type": "array", + "uniqueItems": true }, "variant_calling_strategy": { "description": "", @@ -167,7 +177,7 @@ } }, "required": [ - "submitter_experiment_id", + "submitter_experiment_ids", "variant_calling_strategy", "variant_class", "workflow", diff --git a/song_schema/json-schema/template/sequenceAlignment_template.json b/song_schema/json-schema/template/sequenceAlignment_template.json index 6702042..5f89d2d 100644 --- a/song_schema/json-schema/template/sequenceAlignment_template.json +++ b/song_schema/json-schema/template/sequenceAlignment_template.json @@ -16,7 +16,9 @@ "genome_build": "", "studyId": "", "submitter_analysis_id": "", - "submitter_experiment_id": "", + "submitter_experiment_ids": [ + {} + ], "workflow": { "submitter_workflow_id": "", "workflow_name": "", diff --git a/song_schema/json-schema/template/sequenceExperiment_template.json b/song_schema/json-schema/template/sequenceExperiment_template.json index 7d3226d..d4cdc6b 100644 --- a/song_schema/json-schema/template/sequenceExperiment_template.json +++ b/song_schema/json-schema/template/sequenceExperiment_template.json @@ -15,5 +15,7 @@ ], "studyId": "", "submitter_analysis_id": "", - "submitter_experiment_id": "" + "submitter_experiment_ids": [ + {} + ] } \ No newline at end of file diff --git a/song_schema/json-schema/template/variantCall_template.json b/song_schema/json-schema/template/variantCall_template.json index ef1d7a4..9066982 100644 --- a/song_schema/json-schema/template/variantCall_template.json +++ b/song_schema/json-schema/template/variantCall_template.json @@ -17,7 +17,9 @@ "genome_build": "", "studyId": "", "submitter_analysis_id": "", - "submitter_experiment_id": "", + "submitter_experiment_ids": [ + {} + ], "variant_calling_strategy": "", "variant_class": "", "workflow": { diff --git a/song_schema/linkml/pcgl_song_schema.yaml b/song_schema/linkml/pcgl_song_schema.yaml index cfb8f13..55d1b10 100644 --- a/song_schema/linkml/pcgl_song_schema.yaml +++ b/song_schema/linkml/pcgl_song_schema.yaml @@ -66,7 +66,7 @@ classes: title: Sequence Experiment is_a: Analysis slots: - - submitter_experiment_id + - submitter_experiment_ids slot_usage: submitter_experiment_id: required: true @@ -79,11 +79,11 @@ classes: title: Sequence Alignment is_a: Analysis slots: - - submitter_experiment_id + - submitter_experiment_ids - workflow - genome_build slot_usage: - submitter_experiment_id: + submitter_experiment_ids: required: true workflow: required: true @@ -98,14 +98,14 @@ classes: title: Variant Call is_a: Analysis slots: - - submitter_experiment_id + - submitter_experiment_ids - variant_calling_strategy - variant_class - workflow - genome_build - genome_annotation slot_usage: - submitter_experiment_id: + submitter_experiment_ids: required: true variant_calling_strategy: required: true diff --git a/test_data/molecular_data_submission/bam/sequenceExperimentPayload.json b/test_data/molecular_data_submission/bam/sequenceExperimentPayload.json index 2cc9ea6..97e6abe 100644 --- a/test_data/molecular_data_submission/bam/sequenceExperimentPayload.json +++ b/test_data/molecular_data_submission/bam/sequenceExperimentPayload.json @@ -15,5 +15,5 @@ ], "studyId": "test-001", "submitter_analysis_id": "analysis_002", - "submitter_experiment_id": "exp_002" + "submitter_experiment_id": ["exp_002"] } \ No newline at end of file diff --git a/test_data/molecular_data_submission/cram/sequenceAlignmentPayload.json b/test_data/molecular_data_submission/cram/sequenceAlignmentPayload.json index 6a5d3aa..e609004 100644 --- a/test_data/molecular_data_submission/cram/sequenceAlignmentPayload.json +++ b/test_data/molecular_data_submission/cram/sequenceAlignmentPayload.json @@ -24,7 +24,7 @@ "genome_build": "GRCh37", "studyId": "test-001", "submitter_analysis_id": "analysis_003", - "submitter_experiment_id": "exp_003", + "submitter_experiment_id": ["exp_003"], "workflow": { "submitter_workflow_id": "workflow_001", "workflow_name": "DNA Seq Alignment", diff --git a/test_data/molecular_data_submission/fastq/sequenceExperimentPayload.json b/test_data/molecular_data_submission/fastq/sequenceExperimentPayload.json index 06bad22..ac8d702 100644 --- a/test_data/molecular_data_submission/fastq/sequenceExperimentPayload.json +++ b/test_data/molecular_data_submission/fastq/sequenceExperimentPayload.json @@ -55,5 +55,5 @@ ], "studyId": "test-001", "submitter_analysis_id": "analysis_001", - "submitter_experiment_id": "exp_001" + "submitter_experiment_id": ["exp_001"] } \ No newline at end of file diff --git a/test_data/molecular_data_submission/multi_ids_validation/sequenceExperimentPayload.json b/test_data/molecular_data_submission/multi_ids_validation/sequenceExperimentPayload.json new file mode 100644 index 0000000..06a76d1 --- /dev/null +++ b/test_data/molecular_data_submission/multi_ids_validation/sequenceExperimentPayload.json @@ -0,0 +1,59 @@ +{ + "analysisType": { + "name": "sequenceExperiment" + }, + "data_category": "Genomics", + "files": [ + { + "fileName": "C0HVY.2_r1.fq.gz", + "fileSize": 2040, + "fileMd5sum": "64cf635dbc54f53cae2cb03ec8e8471b", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Raw Sequencing Reads" + }, + { + "fileName": "C0HVY.2_r2.fq.gz", + "fileSize": 2042, + "fileMd5sum": "ceb7e66d031cb894fa9d1d3f8da65fc7", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Raw Sequencing Reads" + }, + { + "fileName": "D0RE2.1_r1.fq.gz", + "fileSize": 2309, + "fileMd5sum": "44bea7aa32a1afb68eec24496b608545", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Raw Sequencing Reads" + }, + { + "fileName": "D0RE2.1_r2.fq.gz", + "fileSize": 2365, + "fileMd5sum": "d73b37eca9375258ab42905f7943b1b6", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Raw Sequencing Reads" + }, + { + "fileName": "D0RH0.2_r1.fq.gz", + "fileSize": 1872, + "fileMd5sum": "b90a3c9750db29406f31e9488d5b7e2b", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Raw Sequencing Reads" + }, + { + "fileName": "D0RH0.2_r2.fq.gz", + "fileSize": 1894, + "fileMd5sum": "a407247b584daa078114ab05e6e489be", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Raw Sequencing Reads" + } + ], + "studyId": "PCGLST0003", + "submitter_analysis_id": "analysis_001", + "submitter_experiment_id": ["EXP_001"] +} \ No newline at end of file