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monarch-initiative / monarch-phenote

stub for monarch phenote
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Fix OWL model of evidence to conform to standard #42

Open cmungall opened 8 years ago

cmungall commented 8 years ago

See: http://create.monarchinitiative.org/download/gomodel:5797c67200000003/owl

Individual: <http://model.geneontology.org/5797c67200000003/5797c67200000005>

    Annotations: 
******        <http://geneontology.org/lego/evidence> <http://model.geneontology.org/5797c67200000003/5797c67200000007>,
        <http://purl.org/dc/elements/1.1/date> "2016-07-26"^^xsd:string,
        <http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-6601-2165"^^xsd:string

    Types: 
        <http://purl.obolibrary.org/obo/HP_0001337>

    Facts:  

     Annotations: <http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-6601-2165"^^xsd:string, 
                 <http://purl.org/dc/elements/1.1/date> "2016-07-26"^^xsd:string

                 <http://purl.obolibrary.org/obo/RO_0002488>  <http://model.geneontology.org/5797c67200000003/5797c67200000008>

Note that 5797c67200000007 is the ECO instance.

Two issues:

  1. it's using the old vocabulary for evidence (not a big deal, we haven't switched in GO yet)
  2. structurally it's not correct. It's placing the evidence instance as an annotation on the phenotype instance. It should be putting it as an axiom annotation on the doid->hp OPA

https://github.com/geneontology/minerva/blob/master/specs/owl-model.md#axiom-annotations-and-evidence

cc @kltm @balhoff

mellybelly commented 8 years ago

@mbrush

On Jul 26, 2016, at 9:07 PM, Chris Mungall notifications@github.com<mailto:notifications@github.com> wrote:

See: http://create.monarchinitiative.org/download/gomodel:5797c67200000003/owl

Individual: http://model.geneontology.org/5797c67200000003/5797c67200000005

Annotations:

****\ http://geneontology.org/lego/evidence http://model.geneontology.org/5797c67200000003/5797c67200000007, http://purl.org/dc/elements/1.1/date "2016-07-26"^^xsd:string, http://purl.org/dc/elements/1.1/contributor "http://orcid.org/0000-0002-6601-2165"^^xsd:string

Types:
    <http://purl.obolibrary.org/obo/HP_0001337>

Facts:

 Annotations: <http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-6601-2165"^^xsd:string,
             <http://purl.org/dc/elements/1.1/date> "2016-07-26"^^xsd:string

             <http://purl.obolibrary.org/obo/RO_0002488>  <http://model.geneontology.org/5797c67200000003/5797c67200000008>

Note that 5797c67200000007 is the ECO instance.

Two issues:

  1. it's using the old vocabulary for evidence (not a big deal, we haven't switched in GO yet)
  2. structurally it's not correct. It's placing the evidence instance as an annotation on the phenotype instance. It should be putting it as an axiom annotation on the doid->hp OPA

https://github.com/geneontology/minerva/blob/master/specs/owl-model.md#axiom-annotations-and-evidence

cc @kltmhttps://github.com/kltm @balhoffhttps://github.com/balhoff

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Melissa Haendel, PhD Associate Professor Library & Dept. of Medical Informatics and Clinical Epidemiology haendel@ohsu.edumailto:haendel@ohsu.edu 503-407-5970 www.monarchinitiative.orghttp://www.monarchinitiative.org