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Update curie formation logic #750

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Update curie formation logic #750

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3422b93
- Update curie formation logic
haideriqbal Oct 1, 2024
4eb0e5f
- Improve code logic
haideriqbal Oct 1, 2024
5e161a1
- Improve code logic to handle edge cases
haideriqbal Oct 2, 2024
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11 changes: 8 additions & 3 deletions dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,16 +36,21 @@ public static void annotateShortForms(OntologyGraph graph) {
}

String shortForm = extractShortForm(graph, ontologyBaseUris, preferredPrefix, c.uri);
String curie = shortForm.replaceFirst("_", ":");

/*
CURIEs are formed by following rules:
If there is only one underscore "_" AND the characters after the underscore are numbers then replace the underscore with colon ":"
If there is only one underscore "_" and the characters after the underscore are not just numbers then just keep the curie same as shortform
If there are multiple underscore but has only digits after the last underscore then the code replaces the last underscore with a colon
*/

String curie = shortForm.replaceFirst("_(\\d+)$", ":$1");
c.properties.addProperty("shortForm", PropertyValueLiteral.fromString(shortForm));
c.properties.addProperty("curie", PropertyValueLiteral.fromString(curie));
}
}
long endTime3 = System.nanoTime();
logger.info("annotate short forms: {}", ((endTime3 - startTime3) / 1000 / 1000 / 1000));


}

private static String extractShortForm(OntologyGraph graph, Set<String> ontologyBaseUris, String preferredPrefix,
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