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

[Jim Hu]

Hi Alex

You are correct on the absence of keratin in bacterial spore coats.   
One thing to keep in mind is that there are many different kinds of  
bacterial spores.  I'm not even sure that they all involve cross- 
linking.  I also don't know if the definitions suggested cover the  
wide diversity of fungal spores.

A review of bacillus-type endospore structure is here:

http://arjournals.annualreviews.org/doi/full/10.1146/annurev.micro.61.080706.093224

Jim

On Feb 18, 2009, at 12:13 PM, Alexander Diehl wrote:

> 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
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Ontology-editors mailing list
>> Ontology-editors at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>
>
> -- 
> 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
> fax:  +1 (207) 288-6131

=====================================
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/20090218/7ef12463/attachment-0001.html>