Re: protein entities (was Re: Rules (was Re: Ambiguous names. was: Re: URL +1, LSID -1)

Indeed, yes.  I did not mean to imply that the elucidation of the 
different biochemical entities are dependent upon a difference in 
biological function.  It will be just as you state--if it exists, it 
will be described.  The function statement I made is just a relatively 
obvious "justification" for the project.

I should make a statement here pertaining to scope.  To begin with, we 
will concentrate on human and mouse proteins.  Also, while we recognize 
that there are different qualities that can be ascribed to a basically 
identical biochemical entity in different structural conformations or 
states of ligand binding, we are not attempting (at least in the 
beginning) to describe these structural conformations or bound vs 
unbound forms.

Michel_Dumontier wrote:
>> Sequence form is again a placeholder term ...
> 
>> ... distinguish between a phosphorylated version of a
>> protein and the non-phosphorylated version (as an example).  The need
>> for the latter derives from the fact that the two versions might have
>> different functions.
> 
> Independent of whether there is a (known) difference in function,
> chemistry (and circumstance) defines function. Any chemical modification
> results in a different biochemical entity with potentially different
> function. Proteins and their "version" derivatives are no exception. The
> relationship between them is that they participate in a chemical
> process, but they are fundamentally different entities.
> 
> Cheers,
> 
> -=Michel=-
>  
> 
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org
> [mailto:public-semweb-lifesci-
>> request@w3.org] On Behalf Of Darren Natale
>> Sent: Thursday, July 19, 2007 11:24 AM
>> To: Eric Jain
>> Cc: Alan Ruttenberg; Chris Mungall; Bijan Parsia;
> public-semweb-lifesci
>> hcls
>> Subject: Re: protein entities (was Re: Rules (was Re: Ambiguous names.
>> was: Re: URL +1, LSID -1)
>>
>>
>> We don't yet have formal definitions for many of the classes and
>> relations (the effort only began in earnest a few months ago).  But,
>> basically, there is a distinction made between the full-length (in
> terms
>> of amino acid sequence) protein and the sub-length parts of proteins
>> (commonly called domains by protein scientists, unfortunately).  The
>> term "whole protein" is somewhat of a placeholder; it is used to
> signify
>> the evolutionary classes (families) of full-length proteins as opposed
>> to the evolutionary classes of domains.  Sequence form is again a
>> placeholder term used to denote the initial translation product from
> an
>> mRNA, which itself might be based on a "normal" gene or a mutant
>> thereof, or which might be one of several possible alternatively
> spliced
>> transcripts from the normal or mutant gene.  The cleaved or modified
>> product is a further breakdown of those initial translation products,
>> and allows one to distinguish between a phosphorylated version of a
>> protein and the non-phosphorylated version (as an example).  The need
>> for the latter derives from the fact that the two versions might have
>> different functions.
>>
>> Eric Jain wrote:
>>> Darren Natale wrote:
>>>> We recently began a new Protein Ontology (PRO) effort geared
> precisely
>>>> toward the formal definition of the "smaller entities" referred to
> by
>>>> Alan.  By "we" I mean the PRO Consortium, comprising the PIs Cathy
> Wu
>>>> of PIR (which is also a member organization of the UniProt
>>>> Consortium), Barry Smith of SUNY Buffalo, and Judy Blake of Jackson
>>>> Labs.  PRO is being developed within the framework of the OBO
> Foundry,
>>>> and aims to specify protein entities at the level mentioned by
> Chris
>>>> (accounting for splice variation and post-translational
> modification
>>>> and cleavage). Where appropriate, PRO will indeed make reference to
>>>> both other ontologies and to UniProt Knowledgebase (UniProtKB)
>>>> records. Furthermore, we are also undertaking the "wildly
> ambitious"
>>>> job of representing broader, more-inclusive classes of similar
>>>> proteins based on evolutionary relatedness.
>>>>
>>>> A further description of PRO (with examples and link to a paper)
> can
>>>> be found at http://pir.georgetown.edu/pro
>>> This will no doubt be interesting to quite a few people here! For
> the
>>> sake of this discussion, could you elaborate a bit more on how the
>>> different concepts in PRO are defined, i.e. what is a "protein",
> "whole
>>> protein", "sequence form" and "cleaved and/or modified product"?

Received on Thursday, 19 July 2007 20:15:42 UTC