[Ontology-editors] GO Ontology QA (fwd)

[Midori Harris]

Jane - thanks!

David - would the non-MOP ones fit in with the QC work you and Tanya do? 
I'm happy to help too; I had a quick look at the list, and it seems like 
about 2/3 to 3/4 would be good to fix, and the rest are meaningful 
differences.

m

On Wed, 17 Jun 2009, Jane Lomax wrote:

> 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
>> 
>
>
>