diff --git a/GF.jsonld b/GF.jsonld index 3606aa1..3d56a10 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -822,6 +822,17 @@ }, "sms:displayName" : "TseriesEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:BRCAClassificationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BRCAClassificationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BRCAClassificationEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:DissociationMethodEnum", "@type" : "rdfs:Class", @@ -3398,16 +3409,25 @@ "sms:displayName" : "CellBarcodeLength", "sms:required" : "sms:false" }, { - "@id" : "bts:ClassBRCA1", - "@type" : "rdfs:Class", - "rdfs:comment" : "BRCA1 grouping.", - "rdfs:label" : "ClassBRCA1", "rdfs:subClassOf" : [ ], + "@id" : "bts:ClassBRCA1", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ClassBRCA1", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Pathogenic" + }, { + "@id" : "bts:LikelyPathogenic" + }, { + "@id" : "bts:VUS" + }, { + "@id" : "bts:Negative" + } ], + "rdfs:label" : "ClassBRCA1", + "rdfs:comment" : "The BRCA1 classification categorizes genetic test results for the BRCA1 gene into four options, pathogenic (mutation known to increase cancer risk), likely pathogenic (mutation probably increases cancer risk), variant of uncertain significance (VUS, unclear impact on cancer risk), and negative (no harmful mutations detected).", + "@type" : "rdfs:Class", + "sms:displayName" : "ClassBRCA1" }, { "@id" : "bts:SectionNumberinSequence", "@type" : "rdfs:Class", @@ -10544,16 +10564,25 @@ "sms:displayName" : "RRIDidentifier", "sms:required" : "sms:false" }, { - "@id" : "bts:ClassBRCA2", - "@type" : "rdfs:Class", - "rdfs:comment" : "BRCA2 grouping.", - "rdfs:label" : "ClassBRCA2", "rdfs:subClassOf" : [ ], + "@id" : "bts:ClassBRCA2", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ClassBRCA2", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Pathogenic" + }, { + "@id" : "bts:LikelyPathogenic" + }, { + "@id" : "bts:VUS" + }, { + "@id" : "bts:Negative" + } ], + "rdfs:label" : "ClassBRCA2", + "rdfs:comment" : "The BRCA2 classification refers to the categorization of genetic test results for the BRCA2 gene into four options, pathogenic (mutation known to significantly increase cancer risk), likely pathogenic (mutation likely increases cancer risk), variant of uncertain significance (VUS, unclear impact on cancer risk), and negative (no harmful mutations detected).", + "@type" : "rdfs:Class", + "sms:displayName" : "ClassBRCA2" }, { "@id" : "bts:WhitelistCellBarcodeFileLink", "@type" : "rdfs:Class", @@ -13709,6 +13738,17 @@ }, "sms:displayName" : "Hereditary renal oncocytoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:VUS", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "VUS", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "VUS", + "sms:required" : "sms:false" }, { "@id" : "bts:Radicalmastectomy", "@type" : "rdfs:Class", diff --git a/modules/enums/Demographics.yaml b/modules/enums/Demographics.yaml index aaf4b2a..db87b0f 100644 --- a/modules/enums/Demographics.yaml +++ b/modules/enums/Demographics.yaml @@ -1,4 +1,11 @@ enums: + BRCAClassificationEnum: + permissible_values: + Pathogenic: + Likely Pathogenic: + VUS: + Negative: + SexEnum: permissible_values: Female: diff --git a/modules/slots.yaml b/modules/slots.yaml index 702e724..7cf4540 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -416,15 +416,17 @@ slots: description: The average number of cigarettes smoked per day. annotations: ClassBRCA1: - title: Class BRCA1 + title: BRCA1 Classification required: false - description: BRCA1 grouping. + description: 'The BRCA1 classification categorizes genetic test results for the BRCA1 gene into four options, pathogenic (mutation known to increase cancer risk), likely pathogenic (mutation probably increases cancer risk), variant of uncertain significance (VUS, unclear impact on cancer risk), and negative (no harmful mutations detected).' annotations: + range: BRCAClassificationEnum ClassBRCA2: - title: Class BRCA2 + title: BRCA2 Classification required: false - description: BRCA2 grouping. + description: 'The BRCA2 classification refers to the categorization of genetic test results for the BRCA2 gene into four options, pathogenic (mutation known to significantly increase cancer risk), likely pathogenic (mutation likely increases cancer risk), variant of uncertain significance (VUS, unclear impact on cancer risk), and negative (no harmful mutations detected).' annotations: + range: BRCAClassificationEnum ClinicalBiospecimenType: title: Clinical Biospecimen Type required: false