[Ontology-editors] spore parts (was Re: [Obo-cell-type] [Fwd: removing "sensu" from the CTO])

[Jim Hu]

Hi Chris,

I believe there was a group discussing spore terms.  I'm cc'ing Debby,  
who participated in it (I think).

Jim

On Feb 18, 2009, at 11:19 AM, Chris Mungall wrote:

>
> On Feb 18, 2009, at 7:42 AM, Midori Harris wrote:
>
>> Hi Chris,
>>
>> A GO-centric tangent ...
>>
>>>>>>> Furthermore, for the Cell Ontology, sensu actually makes a lot
>>>>>>> more sense than even the GO, since we can see that a common term
>>>>>>> like 'spore' does mean different thing to bacterialogists and
>>>>>>> mycologists, even though there is an abstract relationship in  
>>>>>>> the
>>>>>>> function and structure of bacterial spores and fungal spores.
>>>
>>> Actually, today we had a request for more spore parts in GO:
>>> http://sourceforge.net/tracker/index.php?func=detail&aid=2609548&group_id=36855&atid=440764
>>
>> In light of this exchange, any comments on the terms requested in  
>> this item, or objections to adding them? The Swiss-Prot curators  
>> are apparently trying to make the terms and definitions species- 
>> neutral, so I'd appreciate hearing what you think.
>
> I don't know much about spores. From the proposed definitions it  
> certainly sounds as if there is a lot structurally in common between  
> these parts across widely divergent species. Be good to quickly check.
>
>>
>>
>> thanks,
>> m
>>
>>> [Alex]
>>>>>>> I don't care if we eliminate the sensu formulation in favor of
>>>>>>> species specific term names and definitions, but I do care very
>>>>>>> much about conflating terms that really ought to be kept
>>>>>>> separate.  And in this particular example (spore), there ought
>>>>>>> not to be a common cell type at all, and favor the retention of
>>>>>>> (the poorly defined) 'spore (sensu Mycetozoa) ; CL000029'.  We
>>>>>>> ought split out other types of spores without a common parent.
>>
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://fafner.stanford.edu/pipermail/ontology-editors/attachments/20090218/25413098/attachment-0001.html>