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[bioontology-support] Feedback

Trish Whetzel whetzel at stanford.edu
Sun Mar 29 18:23:09 PDT 2009


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

 

 

  

 

 

 

 

 

>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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