Patch/classbrca (#91)

* Update slots.yaml * Update Demographics.yaml * Update slots.yaml * Build jsonld --------- Co-authored-by: gf-dcc-service <[email protected]>
gf-dcc · Mar 12, 2024 · 913583d · 913583d
1 parent de46d22
commit 913583d
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Showing 3 changed files with 65 additions and 16 deletions.
diff --git 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
@@ -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
@@ -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