monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Add check for diseases that lack names #668

Open cmungall opened 6 years ago

cmungall commented 6 years ago

These have caused issues in importing via kgx into medikanren (cc @webyrd)

For example: https://monarchinitiative.org/disease/OMIA:000284-9825

this has one gene associated, but no name for the disease, which makes for a very sparse page

This is an odd one. OMIA:000284 is Blood group system L. 9825 is Sus scrofa domesticus.

Nothing here: http://omia.org/OMIA000132/9825/

However, there is something here, for 'Sus scrofa': http://omia.org/OMIA000132/9823/

TomConlin commented 6 years ago

The statements I see associated with OMIA_000284-9825 post refactor are below;
still do not include a disease label but might that not best come in best through a clique merge (if possible)

ns1:MONARCH_b0e7001727d58f8cd69f a OBAN:association ;
    OBAN:association_has_object OBO:OMIA_000284-9825 ;
    OBAN:association_has_predicate OBO:RO_0002200 ;
    OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/389358675VL> .

<https://monarchinitiative.org/.well-known/genid/389358675VL> a OBO:GENO_0000512 ;
    rdfs:label "some variant of GIPR" ;
    OBO:GENO_0000408 <https://www.ncbi.nlm.nih.gov/gene/389358675> ;
    OBO:GENO_0000418 <https://www.ncbi.nlm.nih.gov/gene/389358675> ;
    OBO:RO_0002200 OBO:OMIA_000284-9825 ;
    ns1:MONARCH_anonymous true .

OBO:OMIA_000284-9825 a owl:Class ;
    dc:description "Genetically-modifed organism; GMO",
        "Renner et al. (2010) used transgenesis of the glucose-dependent insulinotropic polypeptide receptor gene (GIPR) to create an animal model of this human disorder due to a dominant-negative GIP receptor in pancreatic cells. [mol_gen]" ;
    rdfs:subClassOf OBO:OMIA_000284,
        <https://monarchinitiative.org/.well-known/genid/RO0002162NCBITaxon9825> .
cmungall commented 6 years ago

Thanks!

Not sure how the label would come in through a clique merge, as omia.ttl is the only source that would refer to this.

Odd that presumably OMIA have it in their export but not visible on their site

TomConlin commented 6 years ago

in other cases the OMIA may be linked with OMIM