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 19:14:01 GMT
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