diff --git a/src/data/schematic/include_schematic_linkml.Biospecimen.manifest.csv b/src/data/schematic/include_schematic_linkml.Biospecimen.manifest.csv index bb695254..89cebbcf 100644 --- a/src/data/schematic/include_schematic_linkml.Biospecimen.manifest.csv +++ b/src/data/schematic/include_schematic_linkml.Biospecimen.manifest.csv @@ -1 +1 @@ -Study Code,Participant External ID,Sample Global ID,Sample External ID,Sample Type,Age At Biospecimen Collection,Parent Sample Global Id,Parent Sample External Id,Parent Sample Type,Collection Global ID,Collection External ID,Collection Sample Type,Container Global ID,Container External ID,Volume,Volume Unit,Concentration,Concentration Unit,Laboratory Procedure,Biospecimen Storage,Sample Availability \ No newline at end of file +Study Code,Participant External ID,Sample Global ID,Sample External ID,Sample Type,Age At Biospecimen Collection,Parent Sample Global ID,Parent Sample External ID,Parent Sample Type,Collection Global ID,Collection External ID,Collection Sample Type,Container Global ID,Container External ID,Volume,Volume Unit,Concentration,Concentration Unit,Laboratory Procedure,Biospecimen Storage,Sample Availability \ No newline at end of file diff --git a/src/data/schematic/include_schematic_linkml.Biospecimen.schema.json b/src/data/schematic/include_schematic_linkml.Biospecimen.schema.json index 73bda559..ed2d4a8a 100644 --- a/src/data/schematic/include_schematic_linkml.Biospecimen.schema.json +++ b/src/data/schematic/include_schematic_linkml.Biospecimen.schema.json @@ -4,80 +4,80 @@ "title": "INCLUDE.Biospecimen.manifest", "type": "object", "properties": { - "Container Global ID": {}, - "Biospecimen Storage": {}, - "Sample Global ID": {}, - "Volume Unit": {}, "Concentration Unit": {}, + "Parent Sample Type": {}, + "Sample External ID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "Age At Biospecimen Collection": {}, + "Laboratory Procedure": {}, + "Sample Global ID": {}, + "Participant External ID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "Concentration": {}, + "Collection Sample Type": {}, + "Biospecimen Storage": {}, + "Parent Sample Global ID": {}, + "Container Global ID": {}, + "Parent Sample External ID": {}, + "Container External ID": {}, "Study Code": { "enum": [ - "DS-COG-ALL", - "DS-COG-AML", - "DSC", - "DS-Brain", + "DS-ISP", "DS-Sleep", + "DSC", + "ADS", + "ECODS", + "BRI-DSR", + "TRC-DS", + "CHARGE-DS", + "DS-COG-ALL", "DS-PCGC", - "DS-ISP", "DS360-CHD", + "HTP", + "DS-COG-AML", + "DS-Nexus", "BrainPower", - "BRI-DSR", + "DS-HSAT", + "DS-Brain", + "X01-Hakon", "DS-PALS", - "ECODS", + "AECOM-DS", "ExCEEDS", "ABC-DS", - "ADS", - "DS-DETERMINED", - "DS-HSAT", - "DS-Nexus", - "CHARGE-DS", - "TRC-DS", - "HTP", "X01-deSmith", - "X01-Hakon", - "AECOM-DS" + "DS-DETERMINED" ] }, - "Parent Sample Type": {}, - "Laboratory Procedure": {}, "Collection Global ID": {}, - "Parent Sample Global Id": {}, - "Collection External ID": {}, - "Volume": {}, - "Age At Biospecimen Collection": {}, - "Parent Sample External Id": {}, - "Sample Type": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "Container External ID": {}, - "Sample External ID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "Collection Sample Type": {}, "Sample Availability": { "enum": [ - "Unavailable", "Available", + "Unavailable", "" ] }, - "Participant External ID": { + "Volume": {}, + "Sample Type": { "not": { "type": "null" }, "minLength": 1 }, - "Concentration": {} + "Volume Unit": {}, + "Collection External ID": {} }, "required": [ - "Study Code", - "Sample Type", "Sample External ID", - "Participant External ID" + "Participant External ID", + "Study Code", + "Sample Type" ] } \ No newline at end of file diff --git a/src/data/schematic/include_schematic_linkml.Condition.manifest.csv b/src/data/schematic/include_schematic_linkml.Condition.manifest.csv index b237b262..045c41f7 100644 --- a/src/data/schematic/include_schematic_linkml.Condition.manifest.csv +++ b/src/data/schematic/include_schematic_linkml.Condition.manifest.csv @@ -1 +1 @@ -Participant External ID,Event Id,Event Type,Condition or Measure Source Text,Age At Condition or Measure Observation,Condition Interpretation,Condition Status,Condition Data Source,HPO Label,HPO Code,MONDO Label,MONDO Code,MAXO Label,MAXO Code,Other Label,Other Code,Measure Value,Measure Unit \ No newline at end of file +Participant External ID,Event ID,Event Type,Condition or Measure Source Text,Age At Condition or Measure Observation,Condition Interpretation,Condition Status,Condition Data Source,HPO Label,HPO Code,MONDO Label,MONDO Code,MAXO Label,MAXO Code,Other Label,Other Code,Measure Value,Measure Unit \ No newline at end of file diff --git a/src/data/schematic/include_schematic_linkml.Condition.schema.json b/src/data/schematic/include_schematic_linkml.Condition.schema.json index 837caed2..f2db0857 100644 --- a/src/data/schematic/include_schematic_linkml.Condition.schema.json +++ b/src/data/schematic/include_schematic_linkml.Condition.schema.json @@ -4,34 +4,22 @@ "title": "INCLUDE.Condition.manifest", "type": "object", "properties": { - "Age At Condition or Measure Observation": {}, - "Measure Unit": {}, - "Event Id": {}, - "Condition Status": { - "enum": [ - "Resolved", - "Current", - "History Of", - "" - ] - }, - "MONDO Code": {}, - "Other Label": {}, - "MAXO Label": {}, - "Condition or Measure Source Text": {}, "Condition Data Source": { "enum": [ - "Self-reported", "Clinical", + "Self-reported", "" ] }, - "MAXO Code": {}, - "HPO Label": {}, - "Measure Value": {}, - "MONDO Label": {}, + "Condition or Measure Source Text": {}, "Other Code": {}, "HPO Code": {}, + "MONDO Label": {}, + "MONDO Code": {}, + "Event Type": {}, + "MAXO Code": {}, + "MAXO Label": {}, + "Event ID": {}, "Condition Interpretation": { "enum": [ "Observed", @@ -39,13 +27,25 @@ "" ] }, + "Other Label": {}, + "Measure Value": {}, + "Measure Unit": {}, + "HPO Label": {}, + "Age At Condition or Measure Observation": {}, + "Condition Status": { + "enum": [ + "Resolved", + "Current", + "History Of", + "" + ] + }, "Participant External ID": { "not": { "type": "null" }, "minLength": 1 - }, - "Event Type": {} + } }, "required": [ "Participant External ID" diff --git a/src/data/schematic/include_schematic_linkml.DataFile.schema.json b/src/data/schematic/include_schematic_linkml.DataFile.schema.json index e4bf8e19..546714be 100644 --- a/src/data/schematic/include_schematic_linkml.DataFile.schema.json +++ b/src/data/schematic/include_schematic_linkml.DataFile.schema.json @@ -4,95 +4,95 @@ "title": "INCLUDE.DataFile.manifest", "type": "object", "properties": { - "Data Category": { + "File Hash": {}, + "Publication DOI": {}, + "Data Type": {}, + "File External ID": { "not": { "type": "null" }, "minLength": 1 }, "File Global ID": {}, - "Experimental Strategy": {}, - "File Size": {}, - "File Size Unit": {}, - "Access URL": {}, - "Study Code": { + "Data Access": { "enum": [ - "DS-COG-ALL", - "DS-COG-AML", - "DSC", - "DS-Brain", - "DS-Sleep", - "DS-PCGC", - "DS-ISP", - "DS360-CHD", - "BrainPower", - "BRI-DSR", - "DS-PALS", - "ECODS", - "ExCEEDS", - "ABC-DS", - "ADS", - "DS-DETERMINED", - "DS-HSAT", - "DS-Nexus", - "CHARGE-DS", - "TRC-DS", - "HTP", - "X01-deSmith", - "X01-Hakon", - "AECOM-DS" + "Controlled", + "Registered", + "Open", + "" ] }, - "File External ID": { + "File Size Unit": {}, + "Access URL": {}, + "Data Category": { "not": { "type": "null" }, "minLength": 1 }, - "File Name": { + "File Size": {}, + "File Format": { "not": { "type": "null" }, "minLength": 1 }, + "Experimental Strategy": {}, + "Experimental Platform": {}, "Sample External ID": { "not": { "type": "null" }, "minLength": 1 }, - "Data Type": {}, - "File Hash": {}, - "Experimental Platform": {}, - "File Format": { + "Study Code": { + "enum": [ + "DS-ISP", + "DS-Sleep", + "DSC", + "ADS", + "ECODS", + "BRI-DSR", + "TRC-DS", + "CHARGE-DS", + "DS-COG-ALL", + "DS-PCGC", + "DS360-CHD", + "HTP", + "DS-COG-AML", + "DS-Nexus", + "BrainPower", + "DS-HSAT", + "DS-Brain", + "X01-Hakon", + "DS-PALS", + "AECOM-DS", + "ExCEEDS", + "ABC-DS", + "X01-deSmith", + "DS-DETERMINED" + ] + }, + "File Name": { "not": { "type": "null" }, "minLength": 1 }, - "Publication DOI": {}, "Participant External ID": { "not": { "type": "null" }, "minLength": 1 - }, - "Data Access": { - "enum": [ - "Open", - "Controlled", - "Registered", - "" - ] } }, "required": [ + "File External ID", "Data Category", + "File Format", + "Sample External ID", "Study Code", - "File External ID", "File Name", - "Sample External ID", - "File Format", "Participant External ID" ] } \ No newline at end of file diff --git a/src/data/schematic/include_schematic_linkml.Participant.schema.json b/src/data/schematic/include_schematic_linkml.Participant.schema.json index 90f4050f..9c1310a9 100644 --- a/src/data/schematic/include_schematic_linkml.Participant.schema.json +++ b/src/data/schematic/include_schematic_linkml.Participant.schema.json @@ -4,137 +4,137 @@ "title": "INCLUDE.Participant.manifest", "type": "object", "properties": { - "Age at Last Vital Status": {}, + "Sibling ID": {}, "Family Type": { "enum": [ + "Duo", "Other", - "Control-only", "Trio+", - "Duo", - "Trio", - "Proband-only" + "Control-only", + "Proband-only", + "Trio" + ] + }, + "Down Syndrome Status": { + "enum": [ + "T21", + "D21" ] }, - "Other Family Member ID": {}, "Sex": { "enum": [ - "Female", - "Other", "Male", - "Unknown" + "Unknown", + "Female", + "Other" + ] + }, + "First Patient Engagement Event": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "Outcomes Vital Status": { + "enum": [ + "Dead", + "Unknown or not available", + "Alive", + "" ] }, - "Father ID": {}, - "Sibling ID": {}, "Participant Global ID": {}, - "Family ID": {}, + "Age at Last Vital Status": {}, "Race": { "enum": [ + "American Indian or Alaska Native", "Asian", + "Prefer not to answer", "Other", - "American Indian or Alaska Native", + "More than one race", + "Middle Eastern or North African", "East Asian", "Latin American", - "South Asian", - "Middle Eastern or North African", "Unknown", "Black or African American", - "More than one race", + "South Asian", + "White", + "Native Hawaiian or Other Pacific Islander" + ] + }, + "Family ID": {}, + "Father ID": {}, + "Mother ID": {}, + "Ethnicity": { + "enum": [ + "Hispanic or Latino", + "Unknown", "Prefer not to answer", - "Native Hawaiian or Other Pacific Islander", - "White" + "Not Hispanic or Latino" ] }, + "Age at First Patient Engagement": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "Other Family Member ID": {}, "Study Code": { "enum": [ - "DS-COG-ALL", - "DS-COG-AML", - "DSC", - "DS-Brain", + "DS-ISP", "DS-Sleep", + "DSC", + "ADS", + "ECODS", + "BRI-DSR", + "TRC-DS", + "CHARGE-DS", + "DS-COG-ALL", "DS-PCGC", - "DS-ISP", "DS360-CHD", + "HTP", + "DS-COG-AML", + "DS-Nexus", "BrainPower", - "BRI-DSR", + "DS-HSAT", + "DS-Brain", + "X01-Hakon", "DS-PALS", - "ECODS", + "AECOM-DS", "ExCEEDS", "ABC-DS", - "ADS", - "DS-DETERMINED", - "DS-HSAT", - "DS-Nexus", - "CHARGE-DS", - "TRC-DS", - "HTP", "X01-deSmith", - "X01-Hakon", - "AECOM-DS" - ] - }, - "First Patient Engagement Event": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "Ethnicity": { - "enum": [ - "Hispanic or Latino", - "Not Hispanic or Latino", - "Prefer not to answer", - "Unknown" + "DS-DETERMINED" ] }, - "Participant External ID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "Family Relationship": { "enum": [ - "Father", - "Unrelated control", + "Sibling", "Proband", + "Unrelated control", + "Father", "Mother", - "Sibling", "Other relative", "" ] }, - "Age at First Patient Engagement": { + "Participant External ID": { "not": { "type": "null" }, "minLength": 1 - }, - "Down Syndrome Status": { - "enum": [ - "T21", - "D21" - ] - }, - "Mother ID": {}, - "Outcomes Vital Status": { - "enum": [ - "Dead", - "Alive", - "Unknown or not available", - "" - ] } }, "required": [ "Family Type", + "Down Syndrome Status", "Sex", - "Race", - "Study Code", "First Patient Engagement Event", + "Race", "Ethnicity", - "Participant External ID", "Age at First Patient Engagement", - "Down Syndrome Status" + "Study Code", + "Participant External ID" ] } \ No newline at end of file diff --git a/src/data/schematic/include_schematic_linkml.Study.schema.json b/src/data/schematic/include_schematic_linkml.Study.schema.json index a502066f..2510c79f 100644 --- a/src/data/schematic/include_schematic_linkml.Study.schema.json +++ b/src/data/schematic/include_schematic_linkml.Study.schema.json @@ -4,52 +4,52 @@ "title": "INCLUDE.Study.manifest", "type": "object", "properties": { - "Study Code": { - "enum": [ - "DS-COG-ALL", - "DS-COG-AML", - "DSC", - "DS-Brain", - "DS-Sleep", - "DS-PCGC", - "DS-ISP", - "DS360-CHD", - "BrainPower", - "BRI-DSR", - "DS-PALS", - "ECODS", - "ExCEEDS", - "ABC-DS", - "ADS", - "DS-DETERMINED", - "DS-HSAT", - "DS-Nexus", - "CHARGE-DS", - "TRC-DS", - "HTP", - "X01-deSmith", - "X01-Hakon", - "AECOM-DS" - ] - }, + "dbGaP": {}, "Program": { "enum": [ "KF", "INCLUDE" ] }, - "Virtual Biorepository Contact": {}, "Study Name": { "not": { "type": "null" }, "minLength": 1 }, - "dbGaP": {} + "Virtual Biorepository Contact": {}, + "Study Code": { + "enum": [ + "DS-ISP", + "DS-Sleep", + "DSC", + "ADS", + "ECODS", + "BRI-DSR", + "TRC-DS", + "CHARGE-DS", + "DS-COG-ALL", + "DS-PCGC", + "DS360-CHD", + "HTP", + "DS-COG-AML", + "DS-Nexus", + "BrainPower", + "DS-HSAT", + "DS-Brain", + "X01-Hakon", + "DS-PALS", + "AECOM-DS", + "ExCEEDS", + "ABC-DS", + "X01-deSmith", + "DS-DETERMINED" + ] + } }, "required": [ - "Study Code", "Program", - "Study Name" + "Study Name", + "Study Code" ] } \ No newline at end of file diff --git a/src/data/schematic/include_schematic_linkml.jsonld b/src/data/schematic/include_schematic_linkml.jsonld index 937e37c4..e4877650 100644 --- a/src/data/schematic/include_schematic_linkml.jsonld +++ b/src/data/schematic/include_schematic_linkml.jsonld @@ -2152,7 +2152,7 @@ "schema:isPartOf": { "@id": "https://w3id.org/include" }, - "sms:displayName": "Event Id", + "sms:displayName": "Event ID", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2536,7 +2536,7 @@ "schema:isPartOf": { "@id": "https://w3id.org/include" }, - "sms:displayName": "Parent Sample Global Id", + "sms:displayName": "Parent Sample Global ID", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2553,7 +2553,7 @@ "schema:isPartOf": { "@id": "https://w3id.org/include" }, - "sms:displayName": "Parent Sample External Id", + "sms:displayName": "Parent Sample External ID", "sms:required": "sms:false", "sms:validationRules": [] }, diff --git a/src/linkml/include_assay.yaml b/src/linkml/include_assay.yaml index 0afbec78..74829e94 100644 --- a/src/linkml/include_assay.yaml +++ b/src/linkml/include_assay.yaml @@ -142,13 +142,13 @@ slots: parentSampleGlobalId: definition_uri: include:parentSampleGlobalId description: INCLUDE global identifier for the direct parent from which Sample was derived, assigned by DCC - title: Parent Sample Global Id + title: Parent Sample Global ID range: string parentSampleExternalId: definition_uri: include:parentSampleExternalId description: Identifier for the direct parent from which Sample was derived, processed, pooled, etc. (if applicable); assigned by data contributor - title: Parent Sample External Id + title: Parent Sample External ID range: string parentSampleType: definition_uri: include:parentSampleType diff --git a/src/linkml/include_participant.yaml b/src/linkml/include_participant.yaml index 237db8db..b2f00b54 100644 --- a/src/linkml/include_participant.yaml +++ b/src/linkml/include_participant.yaml @@ -205,7 +205,7 @@ slots: eventId: definition_uri: include:eventId description: Identifier for event (Visit, Survey completion, Sample collection, etc.) to which the Condition data are linked, if applicable. There may be multiple events linked to a Participant. - title: Event Id + title: Event ID eventType: definition_uri: include:eventType description: Type of event for which Event ID is given (Visit, Survey completion, Sample collection, etc.)