diff --git a/src/data/sheets/schemasheet.tsv b/src/data/sheets/schemasheet.tsv index 0988cca..5a24f03 100644 --- a/src/data/sheets/schemasheet.tsv +++ b/src/data/sheets/schemasheet.tsv @@ -1,6 +1,6 @@ class slot title description required range any_of minimum_value maximum_value multivalued enum permissible_value meaning >class slot title description required range any_of minimum_value maximum_value multivalued enum permissible_value meaning - studyCode Study Code Unique identifier for the study (generally a short acronym) true enum_studyCode + studyCode Study Code Unique short acronym for the study true enum_studyCode studyTitle Study Title Full title of the study true string program Program Funding source(s) for the study (pipe-separated if multiple) true enum_program true studyDescription Study Description Brief description of the study (2-4 sentences) true string @@ -8,7 +8,7 @@ class slot title description required range any_of minimum_value maximum_value m studyContactName Study Contact Name Name of contact person for this study; pipe-separated if multiple true string true studyContactInstitution Study Contact Institution Institution of contact person for this study; pipe-separated if multiple true string true studyContactEmail Study Contact Email Email address of contact person for this study; pipe-separated if multiple true string true - vbrEmail VBR Email Email address for Virtual Biorepository requests/inquiries, if participating string + vbrEmail VBR Email Email address for Virtual Biorepository requests/inquiries, if participating string true vbrUrl VBR URL Link to Virtual Biorepository request form, if participating uri vbrReadme VBR Readme Instructions for contacting or requesting samples from Virtual Biorepository, if participating string researchDomain Research Domain Main research domain(s) of the study, other than Down syndrome; pipe-separated if multiple true enum_researchDomain true @@ -38,13 +38,11 @@ class slot title description required range any_of minimum_value maximum_value m secondaryOutcomeMeasure Secondary Outcome Measure A description of each secondary outcome measure (title, description, and time point/duration of assessment). Multiple values should be pipe-separated. string true otherOutcomeMeasure Other Outcome Measure A description of other outcome measures (title, description, and time point/duration of assessment). Multiple values should be pipe-separated. string true datasetName Dataset Name Full name of the dataset, provided by contributor true string - datasetDescription Dataset Description Brief additional notes about the dataset (1-3 sentences) that are not already captured in the other fields string + datasetDescription Dataset Description Brief additional notes about the dataset (1-3 sentences) that are not already captured in the other fields true string datasetGlobalId Dataset Global ID Unique Global ID for dataset, generated by DCC false string datasetExternalId Dataset External ID Unique identifier or code for dataset, if provided by contributor string dataCollectionStartYear Data Collection Start Year Year that data collection started false string dataCollectionEndYear Data Collection End Year Year that data collection ended false string - accessLimitations Access Limitations Data access limitations, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) false string - accessRequirements Access Requirements Data access requirements, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) false string otherRepository Other Repository URL if dataset is already deposited in a public repository other than dbGaP (e.g. LONI, Metabolomics Workbench, etc.) uri true otherAccessAuthority Other Access Authority Email or URL for dataset's Access Authority, if not dbGaP string isHarmonized Is Harmonized All of the elements in this Dataset are harmonized and available in the INCLUDE Data Hub boolean @@ -136,11 +134,9 @@ DatasetManifest Dataset Manifest Mapping information for files in Dataset DatasetManifest studyCode Study DatasetManifest fileGlobalId DataFile DatasetManifest datasetGlobalId Dataset -ParticipantSampleDataFileManifest Participant-Sample-DataFile Manifest List of Participants and/or Samples in DataFiles with multiple Participants and/or Samples -ParticipantSampleDataFileManifest studyCode Study -ParticipantSampleDataFileManifest fileName DataFile -ParticipantSampleDataFileManifest participantExternalId Participant -ParticipantSampleDataFileManifest sampleExternalId Biospecimen +ParticipantDataFileManifest Participant-DataFile Manifest List of Participants in DataFiles with multiple Participants +ParticipantDataFileManifest fileName DataFile +ParticipantDataFileManifest participantExternalId Participant Participant Participant Demographic and clinical information about the participant Condition Condition Co-occurring conditions and other observations for the participant Condition studyCode Study @@ -181,6 +177,7 @@ DataFile sampleGlobalId Biospecimen DS-Nexus enum_studyCode ds_nexus DS-PALS enum_studyCode ds_pals DS-PCGC enum_studyCode ds_pcgc + DS-SAH enum_studyCode ds_sah DS-Sleep enum_studyCode ds_sleep DS-VitE enum_studyCode ds_vite DS360-CHD enum_studyCode ds360_chd @@ -210,6 +207,7 @@ DataFile sampleGlobalId Biospecimen Behavior and Behavior Mechanisms enum_researchDomain behavior_and_behavior_mechanisms mesh:D001520 Congenital Heart Defects enum_researchDomain congenital_heart_defects mesh:D006330 Embryonic and Fetal Development enum_researchDomain embryonic_and_fetal_development mesh:D005314 + Hearing Disorders enum_researchDomain hearing_disorders D006311 Immune System Diseases enum_researchDomain immune_system_diseases mesh:D007154 Hematologic Diseases enum_researchDomain hematologic_diseases mesh:D006402 Neurodevelopment enum_researchDomain neurodevelopment mesh:D065886 @@ -265,6 +263,7 @@ DataFile sampleGlobalId Biospecimen Physical Activity enum_dataCategory physical_activity Other enum_dataCategory other Sleep enum_dataCategory sleep_study + Speech/Language/Hearing enum_dataCategory speech_language_hearing enum_guidType NDAR GUID generated by NIMH Data Archive (NDA) GUID tool enum_guidType ndar Other GUID generated by other system enum_guidType other diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 830711d..3003a0f 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -31,6 +31,7 @@ classes: description: General information about the study title: Study slots: + # - studyGlobalId - studyCode - studyTitle - program @@ -109,8 +110,8 @@ classes: - experimentalStrategy - experimentalPlatform - publication - - accessLimitations - - accessRequirements +# - accessLimitations +# - accessRequirements - dbgap - otherRepository - otherAccessAuthority @@ -156,26 +157,22 @@ classes: range: DataFile datasetGlobalId: range: Dataset - ParticipantSampleDataFileManifest: - definition_uri: include:ParticipantSampleDataFileManifest - description: List of Participants and/or Samples in DataFiles with multiple Participants and/or Samples - title: Participant-Sample-DataFile Manifest + ParticipantDataFileManifest: + definition_uri: include:ParticipantDataFileManifest + description: List of Participants in DataFiles with multiple Participants + title: Participant-DataFile Manifest slots: - - studyCode - participantExternalId - - sampleExternalId + - participantGlobalId - fileName + - fileGlobalId #TODO: add Dictonary File Name & Global ID slot_usage: # Reference Slots - studyCode: - range: Study fileName: range: DataFile participantExternalId: range: Participant - sampleExternalId: - range: Biospecimen Participant: definition_uri: include:Participant description: Demographic and clinical information about the participant @@ -338,9 +335,14 @@ classes: #################################################################################################### slots: + # studyGlobalId: + # definition_uri: include:studyGlobalId + # description: Unique identifier for the study, assigned by DCC + # title: Study Global ID + # required: true studyCode: definition_uri: include:studyCode - description: Unique identifier for the study (generally a short acronym) + description: Unique short acronym for the study title: Study Code range: enum_studyCode required: true @@ -397,6 +399,7 @@ slots: description: Email address for Virtual Biorepository requests/inquiries, if participating title: VBR Email range: string + multivalued: true vbrUrl: definition_uri: include:vbrUrl description: Link to Virtual Biorepository request form, if participating @@ -606,6 +609,7 @@ slots: description: Brief additional notes about the dataset (1-3 sentences) that are not already captured in the other fields title: Dataset Description range: string + required: true datasetGlobalId: definition_uri: include:datasetGlobalId description: Unique Global ID for dataset, generated by DCC @@ -637,18 +641,18 @@ slots: range: string #pattern: "^1|2\\d(3)$|nan" required: false - accessLimitations: - definition_uri: include:accessLimitations - description: Data access limitations, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) - title: Access Limitations - range: string - required: false #make true when we have enums - accessRequirements: - definition_uri: include:accessRequirements - description: Data access requirements, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) - title: Access Requirements - range: string - required: false #make true when we have enums + # accessLimitations: + # definition_uri: include:accessLimitations + # description: Data access limitations, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) + # title: Access Limitations + # range: string + # required: false + # accessRequirements: + # definition_uri: include:accessRequirements + # description: Data access requirements, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) + # title: Access Requirements + # range: string + # required: false otherRepository: definition_uri: include:otherRepository description: URL if dataset is already deposited in a public repository other than dbGaP (e.g. LONI, Metabolomics Workbench, etc.) @@ -1121,6 +1125,8 @@ enums: title: DS-PALS ds_pcgc: title: DS-PCGC + ds_sah: + title: DS-SAH ds_sleep: title: DS-Sleep ds_vite: @@ -1186,6 +1192,9 @@ enums: embryonic_and_fetal_development: title: Embryonic and Fetal Development meaning: mesh:D005314 + hearing_disorders: + title: Hearing Disorders + meaning: D006311 immune_system_diseases: title: Immune System Diseases meaning: mesh:D007154 @@ -1289,8 +1298,10 @@ enums: permissible_values: demographic_clinical_data: title: Demographic/Clinical Data + #use for Study Expected Data Category unharmonized_demographic_clinical_data: title: Unharmonized Demographic/Clinical Data + #use for Dataset Data Category genomics: title: Genomics transcriptomics: @@ -1319,6 +1330,8 @@ enums: title: Other sleep_study: title: Sleep + speech_language_hearing: + title: Speech/Language/Hearing enum_guidType: definition_uri: include:enum_guidType permissible_values: