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@allenbaron allenbaron released this 31 Jul 18:27
· 332 commits to main since this release
v2024-07-31
36309d8

This release of the Human Disease Ontology includes 11,612 disease classes, 9,280 with textual definitions (79.9%). Diseases that have been revised and/or expanded include CAMRQ syndrome, mosaic variegated aneuploidy syndromes, Fanconi anemia complementation groups, mal de Meleda, common cold, scarlet fever, Machado-Joseph disease, hematopoietic system disease, palmoplantar keratosis, glucose metabolism diseases, and polycystic liver diseases.

Additionally, synonyms that are considered acronyms, including initialisms & alphebetisms as defined in the new OBO Metadata Ontology acronym (OMO:0003012) annotation property, have been annotated as such. All acronyms remain synonyms with no change to their synonym type relationships (exact, broad, narrow, related). Instead, an additional annotation has been applied to the disease-synonym type-synonym triples as an owl:Axiom.

Examples of acronym annotations & how to access them

OBO format (e.g. doid.obo)

'Lambert-Eaton myasthenic syndrome' (DOID:0050214) 'LEMS' acronym

[Term]
...
synonym: "Lambert-Eaton syndrome" EXACT []
synonym: "LEMS" EXACT OMO:0003012 []
...

RDF/XML (e.g. doid.owl)

'drug-induced lupus erythematosus' (DOID:0040093) 'DILE' acronym

    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/DOID_0040093"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
        <owl:annotatedTarget xml:lang="en">DILE</owl:annotatedTarget>
        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/OMO_0003012"/>
    </owl:Axiom>

OWL Functional Syntax (e.g. doid-edit.owl)

'Polyomavirus-associated nephropathy' (DOID:0040086) 'PVAN' acronym

AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003012) oboInOwl:hasExactSynonym obo:DOID_0040086 "PVAN"@en)

Extracting acronyms with SPARQL

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>

SELECT ?class ?label ?synonym_type ?acronym
WHERE {
  VALUES ?synonym_type {
    oboInOwl:hasExactSynonym oboInOwl:hasBroadSynonym
        oboInOwl:hasNarrowSynonym oboInOwl:hasRelatedSynonym
  }

  ?class a owl:Class ;
    rdfs:label ?label ;
    ?synonym_type ?acronym .

  [] a owl:Axiom ;
    owl:annotatedSource ?class ;
    owl:annotatedProperty ?synonym_type ;
    owl:annotatedTarget ?acronym ;
    oboInOwl:hasSynonymType obo:OMO_0003012 .
}

Additional SPARQL queries for extracting acronyms can be found at https://github.com/DiseaseOntology/SPARQLqueries/tree/main/Datasets/Synonyms.

Full Changelog: v2024-06-28...v2024-07-31

Discussion regarding how acronyms are to be annotated across OBO ontologies can be found at information-artifact-ontology/ontology-metadata#135.

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