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

[Midori Harris]

Jim - thanks! Debby - very interested to hear what you think

m

On Wed, 18 Feb 2009, Jim Hu wrote:

> 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
>
>