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

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"?