[Ontology-editors] spore parts (was Re: [Obo-...) (fwd)

[Midori Harris]

Hi all,

I hope you've seen this thread on the ontology-developers list ... in the 
comments on the SF item, Rachael and I have determined that we need input 
from someone who knows about plant spores, and can tell whether we need 
more terms or can adapt some existing terms. Do any of  you either (a) 
know your spores or (b) know who does?

(This is in addition to asking Debby for help with bacterial spores.)

Thanks,
m

---------- Forwarded message ----------
Date: Thu, 19 Feb 2009 11:00:05 +0000 (GMT)
From: Midori Harris <midori at ebi.ac.uk>
To: Jim Hu <jimhu at tamu.edu>
Cc: Chris Mungall <cjm at berkeleybop.org>, Rachael Huntley <huntley at ebi.ac.uk>,
     Debby Siegele <siegele at mail.bio.tamu.edu>,
     Ontology Editors <ontology-editors at genome.stanford.edu>
Subject: Re: [Ontology-editors] spore parts (was Re: [Obo-cell-type] [Fwd:
     removing "sensu" from the CTO])

Hi all,

Thanks for the comments so far. I'm replying mainly to add Rachael to the 
recipient list, since she opened the item in question.

midori

On Wed, 18 Feb 2009, Jim Hu wrote:

> 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
> 
> 
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