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[bioontology-support] Feedback

Natasha Noy noy at
Mon Mar 30 15:35:48 PDT 2009

Hi Barry,

Yes, GO was a bit of a mess in BioPortal, being sort of broken up in  
three pieces, but not quite. For the moment, as Trish says, we are  
going to have just one entry for GO -- you can look at We will be removing the other three. This  
should fix the search and other issues.

It is not yet clear to me that we really ought to break it up at all,  
even when LexGrid will be able to process it that way. Something to  
discuss with the users as we move on. Barry, would you rather see a  
single entry for GO or three separate entries (assuming the separation  
works as one would expect, with searches landing in correct modules,  


On Mar 29, 2009, at 6:23 PM, Trish Whetzel wrote:

> Hi Barry,
> For the listing of the Gene Ontology in the Search and Browse pages,  
> that will be undergoing changes in future releases. The latest  
> information that I have is that BP, CC, and MF will be listed as 1  
> ontology under the label Gene Ontology in a near term release.  
> However, I believe there is also some discussion on splitting out  
> the components, BP, CC, and MF, and listing each one on BioPortal.
> Natasha, is this still the current thought on how GO will be  
> represented in BioPortal? A question I now have after looking at  
> various ways in which GO is represented on various sites (Amigo,  
> Gene Ontology web site, OLS, OBO Foundry) is whether the splitting  
> of the components is necessary and perhaps more importantly desired  
> by the GO developers?
> For the query on 'pain', I was able to see the term GO:0050967 in  
> the results from both the production and stage releases of  
> BioPortal. Barry, can you send more information on how the search  
> was performed in order to re-create the error? In the searches  
> below, the resulting term was displayed in quotes only in the  
> production release, so it looks like that issue has been fixed for  
> the upcoming release.
> Trish
> <image003.jpg>  <image006.jpg>
> >Comment:
> >When I attempt to filter a search to the Gene Ontology I need to do  
> this
> >three times (for Biological Process, Molecular Function and Cellular
> >Component); can you fix? Also no clue is given to the unitiated  
> reader
> >that these three alternative filters are somehow related to the GO.  
> Can
> >you fix (e.g. by listing them twice, once under 'Biological Process'
> >(etc.), once under 'Gene Ontology: Biological Process'
> >
> >Is there some reason why, when I query on 'pain' in Biological  
> Process,
> >I do not get terms such as
> >
> >GO:0050967: detection of electrical stimulus during sensory  
> perception
> >of pain
> >
> >among the results?
> >Why are synonyms given in double quotation marks? This seems an odd
> >convention, to me?
> >BS
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