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updated SNOMED CT functionality to current URI standard, 2nd attempt #3

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updated SNOMED CT functionality to current URI standard, 2nd attempt #3

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ea20b7d
updated SNOMED CT functionality to current URI standard
Jul 6, 2016
818bb9a
added trim() to URI string
Jul 6, 2016
815ff58
added trim() to URI string
Jul 6, 2016
7cd6680
fixed rolegroup
Aug 19, 2016
a1e14fb
added .gitigonre
Aug 19, 2016
b6f976c
removed build folder
Aug 19, 2016
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
build
11 changes: 11 additions & 0 deletions .project
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>module-extractor_dk</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
</buildSpec>
<natures>
</natures>
</projectDescription>
Binary file added owl-me.jar
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15 changes: 7 additions & 8 deletions src/uk/ac/manchester/cs/modularity/owlme/ModuleExtractor.java
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Expand Up @@ -49,17 +49,16 @@ public static Set<OWLEntity> getSignature(OWLOntology ontology, BufferedReader f
// Check entity IRIs for Snomed concepts
loopClasses:
for(OWLClass c : ontology.getClassesInSignature()) {
if(c.getIRI().toString().contains("www.ihtsdo.org")) {
if(c.getIRI().toString().contains("snomed.info")) {
snomed = true;
termsIri += c.getIRI().toString();
termsIri = termsIri.substring(0, termsIri.indexOf(".org/")+5);
termsIri = "http://snomed.info/id/";
break loopClasses;
}
}

if(ontIri.toString().contains("www.ihtsdo.org")) {
if(ontIri.toString().contains("snomed.info")) {
snomed = true;
termsIri = ontIri.toString().substring(0, ontIri.toString().indexOf(".org/")+5);
termsIri = "http://snomed.info/id/";
}

if(snomed) {
Expand All @@ -69,7 +68,7 @@ public static Set<OWLEntity> getSignature(OWLOntology ontology, BufferedReader f
int pos = s.indexOf("|");
if(pos < 0) throw new RuntimeException("There is no '|' in: ");

s = "SCT_" + s.substring(0,pos);
s = s.substring(0,pos).trim();
IRI iri = IRI.create(termsIri + s);
OWLClass cls = df.getOWLClass(iri);
if (ontology.containsClassInSignature(iri)) {
Expand All @@ -82,7 +81,7 @@ public static Set<OWLEntity> getSignature(OWLOntology ontology, BufferedReader f
}
}

IRI roleGroupIRI = IRI.create(ontology.getOntologyID().getOntologyIRI() + "RoleGroup");
IRI roleGroupIRI = IRI.create(termsIri + "609096000");
OWLObjectProperty roleGroup = df.getOWLObjectProperty(roleGroupIRI);

if (ontology.containsObjectPropertyInSignature(roleGroupIRI)) {
Expand Down Expand Up @@ -167,4 +166,4 @@ private static String getManchesterSyntax(OWLObject obj) {
String str = wr.getBuffer().toString();
return str;
}
}
}
2 changes: 1 addition & 1 deletion src/uk/ac/manchester/cs/modularity/owlme/ModuleExtractorView.java
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Expand Up @@ -450,7 +450,7 @@ else if(loaded && !ontUriChanged && currentOntology != null)
OWLOntology mod = null;
publish("\n" + prefix("EXTRACTING MODULE ..."));

String moduleName = currentOntology.getOntologyID().getOntologyIRI().toString();
String moduleName = currentOntology.getOntologyID().getOntologyIRI().get().toString();
if(moduleName.contains(".owl"))
moduleName = moduleName.substring(0, moduleName.indexOf(".owl")) + "_module" + modCounter + ".owl";
else
Expand Down