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Replace CARO anatomical entity with Uberon. #515

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Jul 31, 2023
Merged

Replace CARO anatomical entity with Uberon. #515

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1 change: 1 addition & 0 deletions minerva-core/src/main/java/org/geneontology/minerva/BlazegraphOntologyManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@ public class BlazegraphOntologyManager {
root_types.add("http://purl.obolibrary.org/obo/UBERON_0001062"); //anatomical entity
root_types.add("http://purl.obolibrary.org/obo/GO_0110165"); //cellular anatomical entity
root_types.add("http://purl.obolibrary.org/obo/CARO_0000000"); // root root anatomical entity
root_types.add("http://purl.obolibrary.org/obo/UBERON_0001062"); // anatomical entity
root_types.add("http://purl.obolibrary.org/obo/UBERON_0000105"); // life cycle stage
root_types.add("http://purl.obolibrary.org/obo/PO_0009012"); // plant structure development stage
root_types.add("http://purl.obolibrary.org/obo/GO_0044848"); // biological phase
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4 changes: 2 additions & 2 deletions minerva-core/src/test/java/org/geneontology/minerva/BlazegraphOntologyManagerTest.java
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Expand Up @@ -161,7 +161,7 @@ public void testGetSuperClasses() throws IOException {
//GO native cell - used a lot in shex
assertTrue("WBbt_0005753 not subclass of CL_0000003", supers.contains("http://purl.obolibrary.org/obo/CL_0000003"));
//anatomy - also used a lot in shex
assertTrue("WBbt_0005753 not subclass of CARO_0000000", supers.contains("http://purl.obolibrary.org/obo/CARO_0000000"));
assertTrue("WBbt_0005753 not subclass of UBERON_0001062", supers.contains("http://purl.obolibrary.org/obo/UBERON_0001062"));
//Cell component
uri = "http://purl.obolibrary.org/obo/GO_0000776";
supers = onto_repo.getAllSuperClasses(uri);
Expand Down Expand Up @@ -227,7 +227,7 @@ public void testGetUpperTypes() throws IOException {
//GO native cell - used a lot in shex
//assertTrue("WBbt_0005753 not subclass of CL_0000003", supers.contains("http://purl.obolibrary.org/obo/CL_0000003"));
//anatomy - also used a lot in shex
assertTrue("WBbt_0005753 not subclass of CARO_0000000", supers.contains("http://purl.obolibrary.org/obo/CARO_0000000"));
assertTrue("WBbt_0005753 not subclass of UBERON_0001062", supers.contains("http://purl.obolibrary.org/obo/UBERON_0001062"));
//Cell component
supers = uri_roots.get(cc);
assertTrue("GO_0000776 not subclass of GO_0110165 'cellular anatomical entity'", supers.contains("http://purl.obolibrary.org/obo/GO_0110165"));
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