[Ontology-editors] GO Ontology QA (fwd)

[David Hill]

They would fit in with what we do. We'll add it to out list.

David

Midori Harris wrote:
> 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
>>>
>>
>>
>>

-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430