> 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: [EMAIL PROTECTED] [mailto:public-semweb-lifesci- > [EMAIL PROTECTED] 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"? >