Re: [SO-devel] new polypeptide terms

[Chris M. <cj...@fr...>]

On Aug 21, 2007, at 2:10 AM, Colin Batchelor wrote:

> Hello Karen,
>
> Good.  I see Gabby's (hello Gabby) in the Thornton group, so will be
> able to set me right if I've got the details wrong.
>
> I wonder if it would be useful to include terms like tetrapeptide,
> pentapeptide, and so forth, in SO.  I can see the case for  
> verifying the
> assertions in a paper (such as "we synthesized the hexadecapeptide"
> followed by a string of letters which may or may not have 16 members).
>
> Chris was talking about a has_part{n} relation elsewhere---would it be
> better to have beta_turn, asx_turn and st_turn with has_part{4}  
> residue
> and gamma_turn with has_part{3} residue, or have them as children of
> tetrapeptide_turn and tripeptide_turn respectively?

This is indeed possible in obo-format 1.2
http://www.geneontology.org/GO.format.obo-1_2.shtml

The cardinality would be encoded in a trailing qualifier on the  
relationship tag and could be harmlessly ignored by parsers.

SO doesn't explicitly represent single residues, but this could be  
added - or imported from chebi

> Best wishes,
> Colin.
>
>
>> -----Original Message-----
>> From: Karen Eilbeck [mailto:kei...@ge...]
>> Sent: 20 August 2007 18:07
>> To: SO developers
>> Cc: Gabrielle Reeves
>> Subject: Re: [SO-devel] new polypeptide terms
>>
>> Hi Colin,
>> I think Gabby should take a look at this when she gets back from
>> vacation.
>>
>> Thank you for being on top of our synonyms. Its great that we have a
>> group that uses them so extensively. I checked in the changes you
>> requested on the tracker.
>>
>> Cheers,
>> Karen
>>
>>
>> On Aug 20, 2007, at 3:57 AM, Colin Batchelor wrote:
>>
>>> Hello,
>>>
>>> I'm delighted to see the collection of new polypeptide terms in SO.
>>>
>>> A thought with regard to the asx_* terms (SO:0000912, SO:0001106
>>> etc.):
>>> "asparagine turn" exists in the literature, as might "aspartate
> turn".
>>> How ought SO to represent those phrases?  The same applies to the
> st_*
>>> terms (SO:0001141, SO:00011126, SO:0001127), where "serine turn",
> for
>>> example, could turn up.
>>>
>>> I'll put specific requests for extra synonyms or changing synonym
>>> scopes
>>> on the tracker.
>>>
>>> Best wishes,
>>> Colin.
>>>
>>> --
>>> Dr Colin Batchelor MChem MRSC, Production Systems Analyst
>>> RSC Publishing,
>>> Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4
> 0WF
>>> bat...@rs... t: +44 1223 432280
>>>
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