Add 'diagnositic interventions' (#37)

IHCC-cohorts · Nov 27, 2020 · 2b1f4af · 2b1f4af
1 parent e5875d5
commit 2b1f4af
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Showing 6 changed files with 32 additions and 4 deletions.
diff --git a/Makefile b/Makefile
@@ -132,7 +132,7 @@ build/annotations.txt: src/ontology/templates/properties.tsv
 	grep 'owl:AnnotationProperty$$' $< | grep -v '^GECKO' | cut -f1 > $@
 
 build/imports/%.ttl: build/imports/%.db build/imports/%.txt build/annotations.txt
-	python3 -m gizmos.extract -d $< -T $(word 2,$^) -A $(word 3,$^) -n > $@
+	python3 -m gizmos.extract -d $< -T $(word 2,$^) -P $(word 3,$^) -n > $@
 
 src/ontology/annotations.owl: $(IMPORT_MODS) src/queries/fix_annotations.rq build/properties.ttl  | build/robot.jar
 	$(ROBOT) merge \

diff --git a/gecko.owl b/gecko.owl
@@ -11,7 +11,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/gecko.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/gecko/releases/2020-11-24/gecko.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/gecko/releases/2020-11-27/gecko.owl"/>
         <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An ontology to represent genomics cohort attributes.</dc:description>
         <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genomics Cohorts Knowledge Ontology</dc:title>
         <terms:license rdf:resource="https://creativecommons.org/licenses/by/4.0/"/>
@@ -1170,6 +1170,19 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/GECKO_0000133 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GECKO_0000133">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GECKO_0000091"/>
+        <obo:GECKO_9000000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">non-pharmacological interventions</obo:GECKO_9000000>
+        <obo:GECKO_9000001 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">diagnostic interventions</obo:GECKO_9000001>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease.</obo:IAO_0000115>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests.</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">diagnostic procedure history</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/GO_0008150 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0008150">

diff --git a/src/ontology/templates/gecko.tsv b/src/ontology/templates/gecko.tsv
@@ -55,4 +55,5 @@ information on functional limitations	functional limitations	information content
 information on use of assistive devices	use of assistive devices	information content entity	Information about an individual's use of assistive devices in performing daily activities.	Maelstrom:Use_devices	perception of health and quality of life					
 religious affiliation	religion	information content entity	Information about an individual's association with a religion, denomiation, or sub- or non-denominational religious group.	url:http://archive.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/religious-affiliation/definition.aspx	socio-demographic and economic characteristics					
 human social environment	social environment	immaterial entity	An immaterial entity that encompasses the domain made up of interactions between the individual's physical environment, social processes, and relationships with other individuals and groups.	PMID:10352860	other questionnaire/survey data					
-family history of disease	family history of disease	clinical history	A clinical history that is about any family history of disease.		other questionnaire/survey data					
+family history of disease	family history of disease	clinical history	A clinical history that is about any family history of disease.		other questionnaire/survey data	
+diagnostic procedure history	diagnostic interventions	non-pharmacological treatment history	A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease.		non-pharmacological interventions					Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests.				
diff --git a/src/ontology/templates/index.tsv b/src/ontology/templates/index.tsv
@@ -76,6 +76,7 @@ GECKO:0000129	information on use of assistive devices
 GECKO:0000130	religious affiliation
 GECKO:0000131	human social environment
 GECKO:0000132	family history of disease
+GECKO:0000133	diagnostic procedure history
 GO:0008150	biological_process
 IAO:0000005	objective specification
 IAO:0000027	data item

diff --git a/views/ihcc-gecko.csv b/views/ihcc-gecko.csv
@@ -67,6 +67,7 @@ non-pharmacological interventions,GECKO:0000092,surgical interventions,A clinica
 non-pharmacological interventions,GECKO:0000123,psychological interventions,A non-pharmacological treatment history that is about psychological treatments such as counselling.
 non-pharmacological interventions,GECKO:0000124,radiological interventions,"A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom."
 non-pharmacological interventions,GECKO:0000125,physical therapy interventions,A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation.
+non-pharmacological interventions,GECKO:0000133,diagnostic interventions,A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease.
 questionnaire/survey data,GECKO:0000093,medication,A clinical history that is about the prescription drugs taken by an individual.
 medication,GECKO:0000094,associated disease(s),Information that is about the disease treated by a drug prescribed to an individual.
 medication,GECKO:0000096,drug response(s),A biological process that results from a drug stimulus.

diff --git a/views/ihcc-gecko.owl b/views/ihcc-gecko.owl
@@ -9,7 +9,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/gecko/ihcc-gecko.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/gecko/releases/2020-11-24/views/ihcc-gecko.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/gecko/releases/2020-11-27/views/ihcc-gecko.owl"/>
     </owl:Ontology>
 
 
@@ -951,6 +951,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/GECKO_0000133 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GECKO_0000133">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GECKO_0000091"/>
+        <obo:IAO_0000115>A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease.</obo:IAO_0000115>
+        <oboInOwl:hasExactSynonym>diagnostic procedure history</oboInOwl:hasExactSynonym>
+        <rdfs:comment>Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests.</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">diagnostic interventions</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/IAO_0000005 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000005">