diff --git a/src/data/schematic/include_schematic_linkml.jsonld b/src/data/schematic/include_schematic_linkml.jsonld index 85e70d88..ecd2f2d6 100644 --- a/src/data/schematic/include_schematic_linkml.jsonld +++ b/src/data/schematic/include_schematic_linkml.jsonld @@ -20,7 +20,7 @@ { "@id": "include:Study", "@type": "rdfs:Class", - "rdfs:comment": "A Study", + "rdfs:comment": "General information about the study", "rdfs:label": "Study", "rdfs:subClassOf": [ { @@ -63,7 +63,7 @@ { "@id": "include:Participant", "@type": "rdfs:Class", - "rdfs:comment": "A Participant in a Study", + "rdfs:comment": "Demographic and clinical information about the participant", "rdfs:label": "Participant", "rdfs:subClassOf": [ { @@ -84,6 +84,9 @@ } ], "sms:requiresDependency": [ + { + "@id": "include:studyCode" + }, { "@id": "include:participantId" }, @@ -134,9 +137,6 @@ }, { "@id": "include:ageAtLastVitalStatus" - }, - { - "@id": "include:studyCode" } ], "sms:validationRules": [] @@ -144,7 +144,7 @@ { "@id": "include:Condition", "@type": "rdfs:Class", - "rdfs:comment": "A Condition of a Participant", + "rdfs:comment": "Co-occurring conditions and other observations for the participant", "rdfs:label": "Condition", "rdfs:subClassOf": [ { @@ -157,6 +157,9 @@ "sms:displayName": "Condition", "sms:required": "sms:false", "sms:requiresDependency": [ + { + "@id": "include:participantId" + }, { "@id": "include:eventId" }, @@ -244,6 +247,12 @@ } ], "sms:requiresDependency": [ + { + "@id": "include:studyCode" + }, + { + "@id": "include:participantId" + }, { "@id": "include:sampleId" }, @@ -282,12 +291,6 @@ }, { "@id": "include:sampleAvailability" - }, - { - "@id": "include:participantId" - }, - { - "@id": "include:studyCode" } ], "sms:validationRules": [] @@ -319,6 +322,15 @@ } ], "sms:requiresDependency": [ + { + "@id": "include:studyCode" + }, + { + "@id": "include:participantId" + }, + { + "@id": "include:sampleId" + }, { "@id": "include:fileId" }, @@ -357,15 +369,6 @@ }, { "@id": "include:publicationDoi" - }, - { - "@id": "include:sampleId" - }, - { - "@id": "include:participantId" - }, - { - "@id": "include:studyCode" } ], "sms:validationRules": [] @@ -786,6 +789,22 @@ "sms:displayName": "KF", "sms:required": "sms:false" }, + { + "@id": "include:control_only", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "control_only", + "rdfs:subClassOf": [ + { + "@id": "include:familyType" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Control-only", + "sms:required": "sms:false" + }, { "@id": "include:duo", "@type": "rdfs:Class", @@ -866,6 +885,102 @@ "sms:displayName": "Trio+", "sms:required": "sms:false" }, + { + "@id": "include:proband", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "proband", + "rdfs:subClassOf": [ + { + "@id": "include:familyRelationship" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Proband", + "sms:required": "sms:false" + }, + { + "@id": "include:father", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "father", + "rdfs:subClassOf": [ + { + "@id": "include:familyRelationship" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Father", + "sms:required": "sms:false" + }, + { + "@id": "include:mother", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "mother", + "rdfs:subClassOf": [ + { + "@id": "include:familyRelationship" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Mother", + "sms:required": "sms:false" + }, + { + "@id": "include:sibling", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "sibling", + "rdfs:subClassOf": [ + { + "@id": "include:familyRelationship" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Sibling", + "sms:required": "sms:false" + }, + { + "@id": "include:other_relative", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "other_relative", + "rdfs:subClassOf": [ + { + "@id": "include:familyRelationship" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Other relative", + "sms:required": "sms:false" + }, + { + "@id": "include:unrelated_control", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "unrelated_control", + "rdfs:subClassOf": [ + { + "@id": "include:familyRelationship" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Unrelated control", + "sms:required": "sms:false" + }, { "@id": "include:female", "@type": "rdfs:Class", @@ -1027,19 +1142,67 @@ "sms:required": "sms:false" }, { - "@id": "include:asked_but_unknown", + "@id": "include:east_asian", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "asked_but_unknown", + "rdfs:label": "east_asian", "rdfs:subClassOf": [ { - "@id": "include:ethnicity" + "@id": "include:race" } ], "schema:isPartOf": { "@id": "https://w3id.org/include" }, - "sms:displayName": "Asked but unknown", + "sms:displayName": "East Asian", + "sms:required": "sms:false" + }, + { + "@id": "include:latin_american", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "latin_american", + "rdfs:subClassOf": [ + { + "@id": "include:race" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Latin American", + "sms:required": "sms:false" + }, + { + "@id": "include:middle_eastern_or_north_african", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "middle_eastern_or_north_african", + "rdfs:subClassOf": [ + { + "@id": "include:race" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "Middle Eastern or North African", + "sms:required": "sms:false" + }, + { + "@id": "include:south_asian", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "south_asian", + "rdfs:subClassOf": [ + { + "@id": "include:race" + } + ], + "schema:isPartOf": { + "@id": "https://w3id.org/include" + }, + "sms:displayName": "South Asian", "sms:required": "sms:false" }, { @@ -1151,7 +1314,7 @@ "schema:isPartOf": { "@id": "https://w3id.org/include" }, - "sms:displayName": "Unknown or Not Available", + "sms:displayName": "Unknown or not available", "sms:required": "sms:false" }, { @@ -1550,7 +1713,7 @@ { "@id": "include:familyType", "@type": "rdf:Property", - "rdfs:comment": "Structure of family members participating in the study (Proband-only = no family members participating; Duo = proband + parent; Trio = proband + 2 parents; Trio+ = proband + 2 parents + other relatives)", + "rdfs:comment": "Structure of family members participating in the study", "rdfs:label": "familyType", "schema:domainIncludes": [ { @@ -1561,6 +1724,9 @@ "@id": "https://w3id.org/include" }, "schema:rangeIncludes": [ + { + "@id": "include:control_only" + }, { "@id": "include:duo" }, @@ -1662,6 +1828,26 @@ "schema:isPartOf": { "@id": "https://w3id.org/include" }, + "schema:rangeIncludes": [ + { + "@id": "include:proband" + }, + { + "@id": "include:father" + }, + { + "@id": "include:mother" + }, + { + "@id": "include:sibling" + }, + { + "@id": "include:other_relative" + }, + { + "@id": "include:unrelated_control" + } + ], "sms:displayName": "Family Relationship", "sms:required": "sms:false", "sms:validationRules": [] @@ -1669,7 +1855,7 @@ { "@id": "include:sex", "@type": "rdf:Property", - "rdfs:comment": "sex of Participant", + "rdfs:comment": "Sex of Participant", "rdfs:label": "sex", "schema:domainIncludes": [ { @@ -1734,6 +1920,21 @@ }, { "@id": "include:prefer_not_to_answer" + }, + { + "@id": "include:unknown" + }, + { + "@id": "include:east_asian" + }, + { + "@id": "include:latin_american" + }, + { + "@id": "include:middle_eastern_or_north_african" + }, + { + "@id": "include:south_asian" } ], "sms:displayName": "Race", @@ -1754,9 +1955,6 @@ "@id": "https://w3id.org/include" }, "schema:rangeIncludes": [ - { - "@id": "include:asked_but_unknown" - }, { "@id": "include:hispanic_or_latino" }, @@ -1777,7 +1975,7 @@ { "@id": "include:downSyndromeStatus", "@type": "rdf:Property", - "rdfs:comment": "Down Syndrome status of participant (T21 = Trisomy 21; D21 = Disomy 21, euploid)", + "rdfs:comment": "Down Syndrome status of participant", "rdfs:label": "downSyndromeStatus", "schema:domainIncludes": [ { @@ -1977,7 +2175,7 @@ { "@id": "include:conditionInterpretation", "@type": "rdf:Property", - "rdfs:comment": "Whether condition was observed or not. \"Not Observed\" indicates participant was specifically examined for that condition, or health record specifically queried for that condition, and found to be negative.", + "rdfs:comment": "Whether condition was observed or not", "rdfs:label": "conditionInterpretation", "schema:domainIncludes": [ { @@ -2002,7 +2200,7 @@ { "@id": "include:conditionStatus", "@type": "rdf:Property", - "rdfs:comment": "Whether the Condition is ongoing (Current), has been resolved (Resolved), or a general history of the condition without known dates (History Of)", + "rdfs:comment": "Whether the Condition is ongoing, has been resolved, or this is a general history of the condition without known dates", "rdfs:label": "conditionStatus", "schema:domainIncludes": [ { @@ -2030,7 +2228,7 @@ { "@id": "include:conditionDataSource", "@type": "rdf:Property", - "rdfs:comment": "Whether condition information was obtained from medical records (Clinical) or reported by participant/family member (Self-Reported)", + "rdfs:comment": "Whether condition information was obtained from medical records or reported by participant/family member", "rdfs:label": "conditionDataSource", "schema:domainIncludes": [ { @@ -2491,6 +2689,9 @@ "rdfs:comment": "Link to a Participant", "rdfs:label": "hasParticipant", "schema:domainIncludes": [ + { + "@id": "include:Condition" + }, { "@id": "include:Biospecimen" }, diff --git a/src/linkml/include_assay.yaml b/src/linkml/include_assay.yaml index 1d47d898..dea44639 100644 --- a/src/linkml/include_assay.yaml +++ b/src/linkml/include_assay.yaml @@ -58,6 +58,8 @@ classes: name: Biospecimen title: Biospecimen slots: + - hasStudy + - hasParticipant - sampleId - sampleType - ageAtBiospecimenCollection @@ -72,8 +74,7 @@ classes: - biospecimenStorage - sampleAvailability # - hasDataFile - - hasParticipant - - hasStudy + # - hasAliquot DataFile: annotations: @@ -89,6 +90,9 @@ classes: name: DataFile title: Data File slots: + - hasStudy + - hasParticipant + - hasBiospecimen - fileId - fileName - fileHash @@ -102,9 +106,7 @@ classes: - fileSizeUnit - accessUrl - publicationDoi - - hasBiospecimen - - hasParticipant - - hasStudy + slots: sampleId: definition_uri: include:sampleId diff --git a/src/linkml/include_participant.yaml b/src/linkml/include_participant.yaml index df8a626c..ea0f60b4 100644 --- a/src/linkml/include_participant.yaml +++ b/src/linkml/include_participant.yaml @@ -6,7 +6,10 @@ prefixes: prefix_reference: https://w3id.org/include/ MONDO: prefix_prefix: MONDO - prefix_reference: http://purl.obolibrary.org/obo/ + prefix_reference: http://purl.obolibrary.org/obo/mondo + NCIT: + prefix_prefix: NCIT + prefix_reference: http://purl.obolibrary.org/obo/ncit linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ @@ -28,10 +31,11 @@ classes: requires_component: tag: requires_component value: Study,DataFile - description: A Participant in a Study + description: Demographic and clinical information about the participant title: Participant is_a: Thing slots: + - hasStudy - participantId - participantExternalId - familyId @@ -50,7 +54,6 @@ classes: - outcomesVitalStatus - ageAtLastVitalStatus # - hasCondition - - hasStudy # FamilyGroup: # name: FamilyGroup # definition_uri: include:FamilyGroup @@ -75,8 +78,9 @@ classes: value: 'False' definition_uri: include:Condition is_a: Thing - description: A Condition of a Participant + description: Co-occurring conditions and other observations for the participant slots: + - hasParticipant - eventId - eventType - conditionSourceText # will include DS Genetic Diagnosis @@ -116,7 +120,7 @@ slots: range: string familyType: definition_uri: include:familyType - description: Structure of family members participating in the study (Proband-only = no family members participating; Duo = proband + parent; Trio = proband + 2 parents; Trio+ = proband + 2 parents + other relatives) + description: Structure of family members participating in the study title: Family Type range: enum_familyType required: true @@ -144,10 +148,10 @@ slots: definition_uri: include:familyRelationship description: Relationship of Participant to proband title: Family Relationship - range: string + range: enum_familyRelationship sex: definition_uri: include:sex - description: sex of Participant + description: Sex of Participant title: sex range: enum_sex required: true @@ -165,7 +169,7 @@ slots: required: true downSyndromeStatus: definition_uri: include:downSyndromeStatus - description: Down Syndrome status of participant (T21 = Trisomy 21; D21 = Disomy 21, euploid) + description: Down Syndrome status of participant title: Down Syndrome Status range: enum_downSyndromeStatus required: true @@ -219,17 +223,17 @@ slots: range: integer conditionInterpretation: definition_uri: include:conditionInterpretation - description: Whether condition was observed or not. "Not Observed" indicates participant was specifically examined for that condition, or health record specifically queried for that condition, and found to be negative. + description: Whether condition was observed or not title: Condition Interpretation range: enum_conditionInterpretation conditionStatus: definition_uri: include:conditionStatus - description: Whether the Condition is ongoing (Current), has been resolved (Resolved), or a general history of the condition without known dates (History Of) + description: Whether the Condition is ongoing, has been resolved, or this is a general history of the condition without known dates title: Condition Status range: enum_conditionStatus conditionDataSource: definition_uri: include:conditionDataSource - description: Whether condition information was obtained from medical records (Clinical) or reported by participant/family member (Self-Reported) + description: Whether condition information was obtained from medical records or reported by participant/family member title: Condition Data Source range: enum_conditionDataSource hpoLabel: @@ -300,30 +304,37 @@ enums: observed: text: observed title: Observed + description: Condition was observed or reported (this will be the case for most conditions) not_observed: text: not_observed title: Not Observed + description: Participant was specifically examined or medical record queried for condition and found to be negative enum_conditionDataSource: name: enum_conditionDataSource permissible_values: clinical: text: clinical title: Clinical + description: Information about condition was obtained from medical records or reported by investigator self_reported: text: self_reported title: Self-reported + description: Information about condition was reported by participant or family member enum_conditionStatus: name: enum_conditionStatus permissible_values: current: text: current title: Current + description: Condition is ongoing resolved: text: resolved title: Resolved + description: Condition has been resolved history_of: text: history_of title: History Of + description: This is a general history of the condition, without known dates enum_downSyndromeStatus: name: enum_downSyndromeStatus definition_uri: include:enum_downSyndromeStatus @@ -331,77 +342,152 @@ enums: d21: text: d21 title: D21 + description: Disomy 21 (euploid) t21: text: t21 meaning: MONDO:0008608 title: T21 + description: Trisomy 21 (Down syndrome) enum_ethnicity: name: enum_ethnicity definition_uri: include:enum_ethnicity permissible_values: - asked_but_unknown: - text: asked_but_unknown - title: Asked but unknown + # asked_but_unknown: + # text: asked_but_unknown + # title: Asked but unknown hispanic_or_latino: text: hispanic_or_latino title: Hispanic or Latino + meaning: NCIT:C17459 not_hispanic_or_latino: text: not_hispanic_or_latino title: Not Hispanic or Latino + meaning: NCIT:C41222 prefer_not_to_answer: text: prefer_not_to_answer title: Prefer not to answer + meaning: NCIT:C132222 unknown: text: unknown title: Unknown + meaning: NCIT:C17998 + enum_familyRelationship: + name: enum_familyRelationship + definition_uri: include:enum_familyRelationship + permissible_values: + proband: + text: proband + title: Proband + meaning: NCIT:C64435 + description: The first affected family member to join the study + father: + text: father + title: Father + meaning: NCIT:C25174 + mother: + text: mother + title: Mother + meaning: NCIT:C25189 + sibling: + text: sibling + title: Sibling + meaning: NCIT:C25204 + other_relative: + text: other_relative + title: Other relative + meaning: NCIT:C21480 + unrelated_control: + text: unrelated_control + title: Unrelated control + meaning: NCIT:C25328 enum_familyType: name: enum_familyType definition_uri: include:enum_familyType permissible_values: + control_only: + text: control_only + title: Control-only + description: Unrelated control, no Down syndrome family members duo: text: duo title: Duo + description: Proband + one parent other: text: other title: Other + description: Other family structure, e.g. one parent + twins proband_only: text: proband_only title: Proband-only + description: Proband only, no family members participating in study trio: text: trio title: Trio + description: Proband + two parents trio_plus: text: trio_plus title: Trio+ + description: Proband + two parents + other relatives enum_race: name: enum_race definition_uri: include:enum_race - title: Unknown permissible_values: american_indian_or_alaskan_native: text: american_indian_or_alaskan_native title: American Indian or Alaska Native + meaning: NCIT:C41259 asian: text: asian title: Asian + meaning: NCIT:C41260 black_or_african_american: text: black_or_african_american title: Black or African American + meaning: NCIT:C16352 more_than_one_race: text: more_than_one_race title: More than one race + meaning: NCIT:C67109 native_hawaiian_or_other_pacific_islander: text: native_hawaiian_or_other_pacific_islander title: Native Hawaiian or Other Pacific Islander + meaning: NCIT:C41219 other: text: other title: Other + meaning: NCIT:C17649 white: text: white title: White + meaning: NCIT:C41261 prefer_not_to_answer: text: prefer_not_to_answer title: Prefer not to answer + meaning: NCIT:C132222 + unknown: + text: unknown + title: Unknown + meaning: NCIT:C17998 + east_asian: + text: east_asian + title: East Asian + meaning: NCIT:C161419 + description: UK only; do not use for US data + latin_american: + text: latin_american + title: Latin American + meaning: NCIT:C126531 + description: UK only; do not use for US data + middle_eastern_or_north_african: + text: middle_eastern_or_north_african + title: Middle Eastern or North African + meaning: NCIT:C43866 + description: UK only; do not use for US data + south_asian: + text: south_asian + title: South Asian + meaning: NCIT:C41263 + description: UK only; do not use for US data enum_sex: name: enum_sex definition_uri: include:enum_sex @@ -409,15 +495,19 @@ enums: female: text: female title: Female + meaning: NCIT:C16576 male: text: male title: Male + meaning: NCIT:C20197 other: text: other title: Other + meaning: NCIT:C17649 unknown: text: unknown title: Unknown + meaning: NCIT:C17998 enum_vital_status: name: enum_vital_status definition_uri: include:vital_status @@ -425,9 +515,12 @@ enums: dead: text: dead title: Dead + meaning: NCIT:C28554 alive: text: alive title: Alive + meaning: NCIT:C37987 unknown_or_not_available: text: unknown_or_not_available - title: Unknown or Not Available + title: Unknown or not available + meaning: NCIT:C17998 diff --git a/src/linkml/include_study.yaml b/src/linkml/include_study.yaml index c24c4967..7e7b5cb9 100644 --- a/src/linkml/include_study.yaml +++ b/src/linkml/include_study.yaml @@ -20,7 +20,7 @@ classes: required: tag: required value: 'True' - description: A Study + description: General information about the study title: Study is_a: Thing slots: