From 792b295a235d706e216d5b6f0e2970a7801d8a07 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Mon, 11 Mar 2024 15:16:37 -0600 Subject: [PATCH 1/4] Update slots.yaml --- modules/slots.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/modules/slots.yaml b/modules/slots.yaml index 702e724..a5853b2 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 From 72c2db96901291487716074bd20fd558ef924843 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Mon, 11 Mar 2024 15:19:49 -0600 Subject: [PATCH 2/4] Update Demographics.yaml --- modules/enums/Demographics.yaml | 7 +++++++ 1 file changed, 7 insertions(+) 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: From 1cc3580ae8573026a750cbfff6243133a3daf1fe Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Mon, 11 Mar 2024 15:24:12 -0600 Subject: [PATCH 3/4] Update slots.yaml --- modules/slots.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/slots.yaml b/modules/slots.yaml index a5853b2..7cf4540 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -418,13 +418,13 @@ slots: ClassBRCA1: title: BRCA1 Classification required: false - 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). + 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: BRCA2 Classification required: false - 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). + 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: From 0b5dd459ee2e8d6a576060cb4ea9d5e6d15977d3 Mon Sep 17 00:00:00 2001 From: gf-dcc-service Date: Mon, 11 Mar 2024 21:24:35 +0000 Subject: [PATCH 4/4] Build jsonld --- GF.jsonld | 64 ++++++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 52 insertions(+), 12 deletions(-) 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",