From 2b1f4af484a59f88a92718a65f31f4439462f3d7 Mon Sep 17 00:00:00 2001 From: Becky Jackson Date: Fri, 27 Nov 2020 09:06:38 -0800 Subject: [PATCH] Add 'diagnositic interventions' (#37) --- Makefile | 2 +- gecko.owl | 15 ++++++++++++++- src/ontology/templates/gecko.tsv | 3 ++- src/ontology/templates/index.tsv | 1 + views/ihcc-gecko.csv | 1 + views/ihcc-gecko.owl | 14 +++++++++++++- 6 files changed, 32 insertions(+), 4 deletions(-) diff --git a/Makefile b/Makefile index 073b3d3..60bb4b0 100644 --- 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 index 5992193..49aff6a 100644 --- 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#"> - + An ontology to represent genomics cohort attributes. Genomics Cohorts Knowledge Ontology @@ -1170,6 +1170,19 @@ + + + + + non-pharmacological interventions + diagnostic interventions + A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease. + Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests. + diagnostic procedure history + + + + diff --git a/src/ontology/templates/gecko.tsv b/src/ontology/templates/gecko.tsv index 42cde64..ce7f3a6 100644 --- 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 index dbba932..51c9caa 100644 --- 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 index ecf1f92..c04e0f7 100644 --- 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 index a709bba..cc6dc47 100644 --- 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#"> - + @@ -951,6 +951,18 @@ + + + + + A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease. + diagnostic procedure history + Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests. + diagnostic interventions + + + +