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phyloref / phyloref-ontology

Phyloreferencing Ontology and OWL DL reasoning with phyloreferences
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An object property for asserting that a phyloreference should resolve to a particular node in a phylogeny #26

Closed gaurav closed 5 years ago

gaurav commented 6 years ago

Proposed term: has_expected_resolution Definition: Identifies the Node that a particular phyloreference is expected to resolve to. Additional assertations may be used to clarify who has asserted this and what evidence they used. Domain: Phyloreference (phyloref:Phyloreference) Range: Node (obo:CDAO_0000140)

Competency questions:

We currently use text-based labels for this, but plan to replace them with IRIs (phyloref/curation-tool#65).

hlapp commented 6 years ago

Well, if we want provenance, then we should discuss what to stick the provenance on. It's quite awkward to stick assertions (or annotations) on a property (because then properties become the subject). So perhaps this should be a class instead, and then we can use prov:wasGeneratedBy, prov:wasDerivedFrom and prov:wasAttributedTo to track who or what process posited the resolution.

hlapp commented 5 years ago

In the revised Phyloref model proposed in #29, this is to be expressed with the following pattern:

rdf:type (obi:is_specified_output_of some 
    (obi:prediction and (obi:has_specified_input some <Phyloreference>))

where <Phyloreference> is the class for which the node instance is expected as the resolution.

In an example:

# Individual: :CLADO_00000062_node22 (Alligatoridae)
ClassAssertion(
    ObjectSomeValuesFrom(
        obo:OBI_0000312 ObjectIntersectionOf(
            obo:OBI_0302910 ObjectSomeValuesFrom(obo:OBI_0000293 :CLADO_00000010)))
    :CLADO_00000062_node22)
gaurav commented 5 years ago

Sounds good! This will be implemented in phyloref/phyx.js#4.