[Ontology-editors] GO Ontology QA (fwd)

[Alexander Diehl]

David,

I have added a comment to the SF item regarding a couple of the items on 
the list (not surprisingly involving immunology terms).

Thanks,

Alex


David Hill wrote:
> 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
>>>>
>>>
>>>
>>>
>


-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
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