#338 verification check for duplicated synonym

open
nobody
OBO-Edit (271)
4
2011-02-09
2011-02-09
Midori Harris
No

Hi,

This came from a GO helpdesk query, but would probably be generally useful:

Can a verification check be created that would detect when one term has two (or more) synonyms with the same text string? If the scope, category or dxref differ, the identical synonyms should still be reported, because a given synonym should only have one scope, and multiple categories or xrefs can be included in one line in the file.

relevant tags from two examples in GO (e.g. http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/~checkout~/go/ontology/editors/gene_ontology_write.obo?rev=1.1766;content-type=text%2Fplain - fixed in later revisions)

thanks,
midori

Discussion

  • Midori Harris
    Midori Harris
    2011-02-09

    ... and these are the examples that I meant to paste in but didn't:

    [Term]
    id: GO:0004152
    name: dihydroorotate dehydrogenase activity
    synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT systematic_synonym [EC:1.3.5.2]
    synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT [EC:1.3.5.2]

    [Term]
    id: GO:0021513
    name: spinal cord dorsal/ventral patterning
    synonym: "spinal cord dorsal-ventral patterning" EXACT [GOC:mah]
    synonym: "spinal cord dorsal-ventral patterning" EXACT []

    <sigh>

     
  • Ramona Walls
    Ramona Walls
    2011-09-20

    It is odd that OE doesn't find this, because it detects when two different terms have the same synonym:

    root stele (PO:0020124) generated 1 warning:
     The terms root vascular system (PO:0003011) and root stele (PO:0020124) share the name or synonym "sistema vascular de la raíz".
    root vascular system (PO:0003011) generated 1 warning:
     The terms root vascular system (PO:0003011) and root stele (PO:0020124) share the name or synonym "sistema vascular de la raíz".

     
  • Nomi Harris
    Nomi Harris
    2011-09-20

    Duplicate synonyms for the same term are not reported because the redundant synonym is apparently eliminated when the file is read in. If you look at the term in the text editor, you will see only one copy of the synonym, and if you save, the term will only have one copy of the synonym. If you try to add a duplicate synonym in the Synonym Editor, it won't show up--it will just ignore the redundant addition.

    Is that good enough?

     
  • Midori Harris
    Midori Harris
    2011-09-21

    Interesting ... I wonder how those duplicates got into GO if OE normally fuses them upon loading. But that's just fodder for speculation; the current behavior will do.

    thanks,
    m