[Ontology-editors] GO Ontology QA (fwd)

[Jane Lomax]

I'll comment on the multi-organism process ones...

Jane

Midori Harris wrote:
> fyi
>
> ---------- Forwarded message ----------
> Date: Tue, 16 Jun 2009 17:01:19 -0600
> From: Karin Verspoor <Karin.Verspoor at ucdenver.edu>
> To: jdeegan at ebi.ac.uk, cjm at fruitfly.org, dph at informatics.jax.org,
>     rhee at acoma.Stanford.EDU, midori at ebi.ac.uk, huala at acoma.Stanford.EDU,
>     jblake at informatics.jax.org, musen at stanford.edu
> Cc: Larry Hunter <Larry.Hunter at ucdenver.edu>
> Subject: GO Ontology QA
>
> This was just logged in the sourceforge tracker system.  It was
> suggested to me by Larry Hunter that since you were participants in
> the workshop that defined the Ontology QA Univocality problem, you
> would be interested to see the analysis.
>
> Thank you,
> Karin
>
>
>
> -------------
>
> As a result of the analysis described in the ISMB paper 
> http://bioinformatics.oxfordjournals.org/cgi/content/full/btp195?ijkey=qvYcpVnIJMjd19Y&keytype=ref 
>
>   "Ontology quality assurance through analysis of term
> transformations" we have identified groups of terms in the GO that are
> not "univocal", where some rephrasing is warranted.
>
> Some general observations:
>
> ** in general, all "the" "an" and "a" determiners can be removed
> ** in general look for terms with "or" or "and" and eliminate the
> coordination in favor of 2 specific terms (or eliminate completely --
> in some cases it appears to be irrelevant)
> ** look at use of punctuation, in particular "," which in some cases
> seems to be used in place of a specific relational preposition
> **consider use of "within" vs "in"
> ** generally it seems that "other" or "another" is not necessary
>
> The clusters that should be looked at are in the attached file.  I'd
> appreciate knowing which of these turn out to be "true" true positives
> that result in some change in phrasing of the GO terms.
>
> Thanks,
> Karin
>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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