[Ontology-editors] cellular components in the nervous system

[Jane Lomax]

I suspect we'll struggle with these new high-level terms, especially as 
I think we can rule out any possibility of changing the name of the root 
node. Be interested to see how it looks though. Great that they're using 
GO-CC.

Jane


Chris Mungall wrote:
>
> One tricky thing is the naming - any upper level term in GO must be 
> meaningful to biologists and not cause distress such as the 
> once-proposed material/immaterial distinction.
>
> BIRN/NIF call the separable things "cellular components", which seems 
> quite reasonable, but I think any attempt to change the root term in 
> CC will be met with resistance.
>
> On Jan 26, 2009, at 4:52 AM, Midori Harris wrote:
>
>> Thanks; sounds good. My only objection to adding those upper level 
>> terms would have been that we don't have time to work on it, but if 
>> they're doing the work, yay!
>>
>> m
>>
>> On Fri, 23 Jan 2009, Chris Mungall wrote:
>>
>>> I'm with the BIRN neuroinformatics group at the moment.
>>>
>>> They have their own cell and cellular component ontology (used to be 
>>> called SAO, now NIF subcellular). They are keen to swap out their 
>>> own ontology and swap in GO-CC instead. However, there are a few 
>>> things they have in their own ontology which they'd miss. Some are 
>>> things we're planning on adding eventually anyway, such as 
>>> disjointness relations 
>>> (http://wiki.geneontology.org/index.php/Cellular_component_disjoint_classes) 
>>> and relations to cells 
>>> (http://wiki.geneontology.org/index.php/XP:cellular_component_xp_cell). 
>>> They're also keen on having upper level terms that discriminate 
>>> between seperable objects (what they call cellular components) from 
>>> cell component regions (what they call regional parts). They're 
>>> going to do the work of mapping GO-CC terms into these categories, I 
>>> said we'd take a look and consider it (if we don't like it it can 
>>> always live outside GO as a bridge ontology resource).
>>>
>>> I think it would be a major coup to have the BIRN group use GO-CC, 
>>> they're integrating massive amounts of neuroscience data.
>>>
>>> More details as they emerge, just keeping you informed
>>>
>>> Chris
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>>> Ontology-editors at geneontology.org
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>>
>
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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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