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[bioontology-support] Extended GO file

Jane Lomax jane at ebi.ac.uk
Tue May 4 05:15:10 PDT 2010


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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