[Ontology-editors] cellular components in the nervous system

[David Hill]

I've always been interested in teasing out the regions of the cell from 
the physical parts of the cell. I think we can think of a way to do this 
without invoking the 'material'immaterial entity' terminology.

David

Jane Lomax wrote:
> 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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>>>
>>
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>
>

-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430