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monarch-initiative / monarch-legacy

Monarch web application and API
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Genotype MGI:5759474 appears not to be a valid identifier #1338

Open jmcmurry opened 8 years ago

jmcmurry commented 8 years ago

MGI:5759474 found here. I thought it was odd that there were no phenotypes so I tried looking at the source but it failed; even a google search failed. It appears to come from IMPC; @ are they given placeholder a block of private MGI IDs or something? Any idea what is going on? @TomConlin?

screen shot 2016-08-17 at 5 35 44 pm
kshefchek commented 8 years ago

It's coming from MGI, but unclear why it doesn't exist.

jmcmurry commented 8 years ago

Apparently the ID didn't come from IMPC but from MGI? This was an ID sourced from MGI but which was marked as being from IMPC? @kshefchek ? The reason I thought it was from IMPC was because it was in the source column of the tsv and here.

screen shot 2016-08-18 at 9 47 22 am
kshefchek commented 8 years ago

The source column represents additive or corroborative evidence for an association, in this case between a genotype and gene.

For this association:

    Spata6<tm1b(KOMP)Wtsi>/Spata6<+> [C57BL/6N-Spata6<tm1b(KOMP)Wtsi>/Ucd](MGI:5759474) - has_variant_part -> Spata6<tm1b(KOMP)Wtsi>/Spata6<+>(_:genid1182014) -
    has_variant_part -> Spata6<tm1b(KOMP)Wtsi>(MGI:5548554) - has_allele -> Spata6(MGI:1915196)

It's not particularly helpful in disambiguating provenance, but that is in another ticket.

jmcmurry commented 8 years ago

So let me see if I understand correctly:

kshefchek commented 8 years ago 
    Spata6<tm1b(KOMP)Wtsi>/Spata6<+> [C57BL/6N-Spata6<tm1b(KOMP)Wtsi>/Ucd](MGI:5759474)

was fetched from MGI, gxd_genotype_summary_view, on June 29th.

I'm unclear on the provenance of the rest since the json evidence graph doesn't differentiate at the moment, but I can look into it.