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Switch to new JSON-LD context file for identifiers #194

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Jun 26, 2018
Merged

Switch to new JSON-LD context file for identifiers #194

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654c4df
Switching to using go_context / identifiers.org URIs
cmungall Apr 27, 2018
b22e285
Minerva changes in prep for switch of URIs, see https://github.com/ge…
cmungall May 18, 2018
9a6cd5a
Fix tests.
balhoff May 18, 2018
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4 changes: 4 additions & 0 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# See: https://github.com/geneontology/go-site/issues/617
# Note: we will later switch to doing this as part of the GO release
minerva-core/src/main/resources/go_context.jsonld:
wget --no-check-certificate https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/go_context.jsonld -O $@
5 changes: 3 additions & 2 deletions ...ter/src/test/java/org/geneontology/minerva/legacy/LegoToGeneAnnotationTranslatorTest.java
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Expand Up @@ -56,9 +56,9 @@ public static void beforeClass() throws Exception {
public void testZfinExample() throws Exception {
OWLOntology model = loadModel("gomodel-1.owl");
List<LookupEntry> entities = new ArrayList<>();
entities.add(new LookupEntry(IRI.create("http://zfin.org/ZDB-GENE-991124-7"), "tbx5a", "gene", "NCBITaxon:7955"));
entities.add(new LookupEntry(IRI.create("http://identifiers.org/zfin/ZDB-GENE-991124-7"), "tbx5a", "gene", "NCBITaxon:7955"));
// is actually a gene, but made a protein for this test case
entities.add(new LookupEntry(IRI.create("http://zfin.org/ZDB-GENE-040426-2843"), "kctd10", "protein", "NCBITaxon:7955"));
entities.add(new LookupEntry(IRI.create("http://identifiers.org/zfin/ZDB-GENE-040426-2843"), "kctd10", "protein", "NCBITaxon:7955"));
GafDocument gafDocument = translate(model, "gomodel-1", entities);
List<GeneAnnotation> allAnnotations = gafDocument.getGeneAnnotations();
assertFalse(allAnnotations.isEmpty());
Expand Down Expand Up @@ -96,6 +96,7 @@ else if (shortEvidence == null) {
List<Bioentity> noSymbol = new ArrayList<>();

for (Bioentity entity : bioentities) {
System.out.println("ENTITY: " + entity);
if (entity.getNcbiTaxonId() == null) {
noTaxon.add(entity);
}
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2 changes: 1 addition & 1 deletion minerva-converter/src/test/resources/catalog-v001.xml
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@@ -1,4 +1,4 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri name="http://purl.obolibrary.org/obo/go/extensions/go-lego.owl" uri="go-lego-module.omn.gz"/>
<uri name="http://purl.obolibrary.org/obo/go/extensions/go-lego.owl" uri="go-lego-module.omn"/>
</catalog>
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