Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Extended GO file

Jane Lomax jane at ebi.ac.uk
Thu May 20 02:44:14 PDT 2010


Hi Trish and Pradip -

The term details panel looks fine.

For the visualization, I would only ever show the asserted links (in 
this example the isa and regulates links) rather than the intersection 
links, if that makes sense. So in the fact the visualization you have it 
here: 
http://stage.bioontology.org/visualize/42780/?conceptid=GO%3A0080050#visualization

thanks,

Jane

Trish Whetzel wrote:
> 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
>>


-- 
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




More information about the bioontology-support mailing list