[Ontology-editors] cellular components in the nervous system

[Midori Harris]

agreed ... I'll let you know if inspiration strikes.

m

On Mon, 26 Jan 2009, 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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>