- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Thu, 26 Mar 2009 10:07:05 -0400
- To: Michel_Dumontier <Michel_Dumontier@carleton.ca>
- Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, Matthias Samwald <samwald@gmx.at>
In addition to Uniprot, in light of Matthias' earlier email, what about http://en.wikipedia.org/wiki/Protein, http://dbpedia.org/page/Protein, and the protein related ontologies listed in OBO (http://www.obofoundry.org/)? -Kei Michel_Dumontier wrote: > Pursuant to my email, and in light of several other comments, if our > goal is to now rectify what Uniprot:Protein _actually_ means in our > domain, and how it can be semantically mapped to other bio-ontologies, > then I might also suggest that instances of Uniprot:Protein are > aggregates of proteins (err... :ProteinAggregate anyone?), possibly > separated by both space and time, having a similar (base sequence + > mutations / ptms) composition, sharing certain characteristics (e.g. > functionality, domains) and observed to participate in biological > processes. Clearly not a type of protein of the single molecule form, > but again, certainly not a Record. > > -=Michel=- > > > > >> If however, what we've been talking about is that identifiers like >> http://purl.uniprot.org/uniprot/Q16665 >> >> are actually database records, and not molecular entities, then we can >> settle this quickly: >> >> Uniprot RDF file: http://www.uniprot.org/uniprot/Q16665.rdf >> (is this what people were referring to as a Record???) >> >> Contains: >> >> <rdf:Description rdf:about="http://purl.uniprot.org/uniprot/Q16665"> >> <rdf:type rdf:resource="http://purl.uniprot.org/core/Protein" /> >> >> >> It's clear that the entity denoted by :Q16665 is rdf:type :Protein and >> is the subject of statements that are biological in nature such as >> being >> located in sub-cellular compartments or being involved in biochemical >> reactions. It is clearly not a Record. This is generally the case for >> nearly all entries in biomolecular databases. >> >> Cheers, >> >> -=Michel=- >> >> Anxiously waiting see if this clears up things or generates >> > controversy > >> .. it's hard to predict! >> >> >> >> >>> If nobody ever wants to use the same property to talk about the >>> database >>> record as was used to talk about the molecule, and nobody ever makes >>> >> an >> >>> assertion that implies that the class of database records is >>> > disjoint > >>> from the class of molecules, then I don't see any harm in using the >>> same >>> URI to ambiguously denote both. But if one is trying to design >>> > data > >>> to >>> be reusable by others in unforeseen ways, there clearly *is* a risk >>> that >>> someone will want to make such assertions in conjunction with the >>> >> data, >> >>> and if that happens there is a clear harm. This risk is easy to >>> >> avoid >> >>> by using separate URIs. >>> >>> There *are* trade-offs. Minting two URIs instead of one *does* add >>> some >>> complexity, though as I pointed out that additional complexity can >>> > be > >>> mitigated to the point that it is a *very* low cost. Still, >>> >> different >> >>> people will weigh these trade-offs differently, and what's best for >>> >> one >> >>> situation may not be best for another, as I indicated in my original >>> post. >>> >>> Furthermore, even if one does use the same URI to ambiguously denote >>> both a database record and a molecule, that is not the end of the >>> >> world >> >>> either. It is possible (though more difficult) to later separate >>> > out > >>> and relate the different senses of an ambiguous URI, as I have >>> described: >>> http://dbooth.org/2007/splitting/ >>> Ambiguity is inescapable, and ambiguity between a thing and a page >>> >> that >> >>> describes that thing is not fundamentally different from other kinds >>> >> of >> >>> ambiguity (except perhaps that we are aware of it in advance and it >>> >> can >> >>> be easily avoided), as explained here: >>> http://dbooth.org/2007/splitting/#httpRange-14 >>> >>> Finally, although it is flattering that you have named this >>> >> suggestion >> >>> after me, I cannot take credit. As I pointed out in my original >>> >> post, >> >>> the suggestion to differentiate between a molecule and the database >>> record that describes that molecule originates with the Architecture >>> >> of >> >>> the World Wide Web: >>> http://www.w3.org/TR/webarch/#URI-collision >>> and best practices for implementing this distinction are described >>> > in > >>> Cool URIs for the Semantic Web: >>> http://www.w3.org/TR/cooluris >>> >>> David Booth >>> >>> >>> > > >
Received on Thursday, 26 March 2009 14:07:53 UTC