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dustine32 avatar dustine32 commented on June 12, 2024

Had another instance of this occur during the 2022-02-20 snapshot with this line in fb.gaf:

FB      FBgn0003334     Scm     located_in      GO:0005634      FB:FBrf0179383|PMID:15280237    IC      GO:0016458      C       Sex comb on midleg      CG9495|SCM|Sex Comb on Midleg|Sex Comb on the Midleg|Sex combs on midleg|Sex combs on midlegs|Su(z)302|l(3)85Ef|scm|sex comb on midleg  protein taxon:7227      20050203        UniProt

With/from value GO:0016458 is obsolete w/o a replaced_by term (though it has two "consider" terms, I don't think ontobio treats these like replaced_by).

Testing with the #603 code change gets around this error, just printing blank for the line's with/from value along with a warning:

* WARNING - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0016458)

@kltm @sierra-moxon I'm thinking we just go ahead and merge #603, then release and update go-site reqs.txt?

from ontobio.

kltm avatar kltm commented on June 12, 2024

I believe this is now fixed.

from ontobio.

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