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legumeinfo / legumemine

An InterMine which contains multiple legumes
GNU Lesser General Public License v3.0
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trait ontology terms unlinked with QTLs, I think #13

Closed adf-ncgr closed 6 years ago

adf-ncgr commented 6 years ago

this is likely something I told you not to worry about and it is still not a huge deal; was just looking at defining a template that would find genes annotated with "defense response" that were spanned by QTLs for "biotic stress" (or whatever the TO class is); I got the former, but as far as I can tell the QTLs I get returned can't be restricted by an ontology term. Could be that I got confused about something and it isn't an issue at all. just noting it for future exploration

sammyjava commented 6 years ago

Yeah the trait ontology annotation loader bombed unbeknownst to me. Fixed and will appear in the next DB update. (A lot of minor updates to deal with multiple organisms and required merging on taxonId,variety.)

sammyjava commented 6 years ago

Yeah, fixed in new dev db. Don't know why those didn't load the previous time. Don't think I really changed anything. INTERMINE.

adf-ncgr commented 6 years ago

reopening this rather than creating a new one, but this is just a reminder for myself; I put in a hack of a template on production as a proof of concept: "QTLs spanned by GO-annotated Genes". Currently this just relies on trait naming conventions in soybase but should use the ontology when it is available again.

sammyjava commented 6 years ago

We seem to be good on dev. Close this when you've done your template update on production, I'll be promoting LM this aft.

sammyjava commented 6 years ago

Closing this, you'll have to remember to do your template updates with a separate issue. My work is done. :)

adf-ncgr commented 6 years ago

just the threat of having to open my own issue gave me the needed kick to get this done; and it works now, using "biotic stress trait" TOs...