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

[Alexander Diehl]

Chris,

Is there anything wrong with prefixing the bacterial specific term names 
with the word "bacterial":  "bacterial spore cortex" and "bacterial 
spore outer membrane".  This might avoid confusion.

Also, the definition of "spore coat" states that the spore coat is "made 
up of highly cross-linked keratin and layer of specific proteins."  As 
far as I know, keratins are found only in multicellular animals, so this 
definition cannot apply to bacterial spore coats.  Perhaps Jim could 
correct me here.

Thanks,

Alex


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 
>>>> <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
>
>
>
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-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
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