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[bioontology-support] Extended GO file

Trish Whetzel whetzel at stanford.edu
Wed May 19 15:42:47 PDT 2010


Hi Jane,

The ontology loader is now updated and the cross-product information  
is displayed in the term details panel: http://stage.bioontology.org/visualize/42780/?conceptid=GO%3A0080050 
.  I included Pradip, the developer working on this, in the email  
thread to help fast-track discussions.

One question that came up was what to display for the visualization  
panel (http://stage.bioontology.org/visualize/42780/?conceptid=GO%3A0080050#visualization 
) if a user clicks on "biological regulation AND regulates SOME seed  
development" and selects "Show Hierarchy to Root".

Trish


On May 4, 2010, at 5:15 AM, Jane Lomax wrote:

> Hi Trish - sorry, my mistake, I had it set to 'show hierarchy to  
> root' rather than 'neighbourhood network'. That display looks spot on.
>
> There are another set of tags  - intersection_of - in the GO ext  
> file that may be of interest for display. These comprise the formal  
> definition of the term (we call them cross-products - I think it  
> means the same as intersectionOf in OWL). Not all GO terms have  
> these tags yet - at the moment it's only the regulation terms - but  
> I think people would be pretty interested to see them if there's a  
> suitable way of displaying them. Here's an example stanza:
>
> [Term]
> id: GO:0010029
> name: regulation of seed germination
> namespace: biological_process
> def: "Any process that modulates the frequency, rate or extent of  
> seed germination." [GOC:sm]
> is_a: GO:0048580 ! regulation of post-embryonic development
> intersection_of: GO:0065007 ! biological regulation
> intersection_of: regulates GO:0009845 ! seed germination
> relationship: regulates GO:0009845 ! seed germination
>
> cheers,
>
> Jane
>
> Trish Whetzel wrote:
>> Hi Jane,
>>
>> For the term GO:0071013, I do see 'has_part' in both the term  
>> details and visualization tabs (screenshots attached).  Do you have  
>> an image of how you expected this to be displayed?
>>
>> I have reported the error in display of 'Equivalent Class' and that  
>> the regulates relationships are missing. However, they are  
>> displayed in the production version using the regular file: http://bioportal.bioontology.org/visualize/42733/?conceptid=GO%3A0031341 
>> .
>>
>> Trish
>>
>>
>>
>>
>>
>>
>>
>>
>> On Apr 30, 2010, at 4:57 AM, Jane Lomax wrote:
>>
>>> Hi Trish - it doesn't seem to be showing any of the has_part  
>>> relations, e.g GO:0071013 has_part GO:0000974 isn't appearing
>>>
>>> Actually, it doesn't seem to be showing the regulates  
>>> relationships either and they're just in the regular file e.g. GO: 
>>> 0031341 regulates GO:0001906
>>>
>>> As an aside, what does Equivalent Class mean?
>>>
>>> thanks,
>>>
>>> Jane
>>>
>>>
>>>
>>> Trish Whetzel wrote:
>>>> Hi Jane,
>>>>
>>>> We have loaded the extended GO file to the Staging server of  
>>>> BioPortal. Would you mind reviewing and providing comments? It  
>>>> can be viewed at: http://stage.bioontology.org/visualize/42684
>>>>
>>>> Trish
>>>>
>>>
>>>
>>> -- 
>>> Dr Jane Lomax
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492516
>>> f: +44 1223 494468
>>>
>>
>
>
> -- 
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468
>




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