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  1. NIF
  2. NIF-11715

Return source of graph edges in OQ queries

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    • NIF

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      Currently it is possible to query graph edges in OQ. The resulting structure is a list of XML elements with name "relationship" with sub-elements: subject, property, object.

      Many ontologies in the Monarch chain have axiom annotations. For example

      SubClassOf( Annotation(dc:source "PMID:1234") ClassA ClassB)

      See Uberon in particular. Future iterations of the merged disease ontology will also include these.

      We need to be able to show the provenance of every assertion in our web interface, so OQ should return axiom annotations along with each edge. This could be done by adding an extra sub-element for each annotation on the axiom.

      It would also be useful if we could also get the source ontology of the edge. Note here I mean ontology in the OWL sense, not the OQ sense of the parent of the import chain.

      Thus for example, if monarch.owl imports hp.owl, and hp.owl includes an annotation-free axiom

      SubClassOf(HP_1 HP_2)

      Then the resulting XML returned by OQ should be like the following:

      <relationship><subject=HP_1><property=subClassOf><object=HP_2><source=http://purl.obolibrary.org/obo/hp.owl></relationship>

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            agupta Amarnath Gupta (use this)
            cmungall Chris Mungall
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