- From: Xiaoshu Wang <wangxiao@musc.edu>
- Date: Mon, 10 Sep 2007 11:07:57 +0100
- To: Andrea Splendiani <andrea.splendiani@univ-rennes1.fr>
- CC: Nigam Shah <nigam@stanford.edu>, satya30@uga.edu, public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org
Andrea Splendiani wrote: >> Using RDF as an "exchange format" is just outright wrong. How do you >> decide if an RDF document is in BioPAX format or not? I don't know >> how active BioPAX is now (their website shows the last conference >> call was more than two years ago). But such line of thought will doom >> (and have perhaps already doomed) their fate > > Hi, let me add my two cents o this thread. > > *) BioPAX is active, but its current "real" website is the wiki, not > the main site (link under "community"). Unfortunately, nobody had time > untill now to make this more explicit. > > That RDF is "outright wrong" as an exchange format is questionable. At > least we had the experience of RDF 1.0 in this direction. But I agree > that the distiinction between data and meta-data is not so clear. The problem is not about what is data and what is metadata. The problem is that how you think will dictate how you design your artifact. In the case of data standard, it subsequently determines how much inter-operable your ontology is with others. Let's use a concrete term as example, the biopax:AUTHORS. (By the way, it is very strange that bioPAX, use Capticalized term for property and small-cased term for class, where the most conventions is the other way around). Is its semantics any different from the "creator" defined by the dublin core? If there isn't any, (at least from what I can tell), then bioPAX SHOULD NOT reinvent the wheel to mint this term because, if every "ontology" developed its own author term, then, there will be hundreds of "authors/creators" etc., that we have to align when the so-called BioPAX data is mixed with other kind of data. And if you think it doesn't matter, why bother developing ontologies, what is wrong with using XML schema then? The reason, I guess, that "biopax:AUTHORS", is developed is because the bioPAX people wants it to be a "format" rather making it a knowledge. To make it a format, you then think it in a closed world because you want to "control" your own terminology. Ontology is different, its development is based on an open world semantics (at least RDF/OWL are). When you developed your term, you should only care about the consistency of your terms and not the completeness. And don't worry those terms that are not in your domain, for instance, I don't think AUTHORS are pathway knowledge. If you have to use it for your application, then reuse other people's ontology. If there isn't any, develop your own but at least put them under a different namespace so you can later switch to others..... If an ontology is developed to be a "format", it will fail and fail miserably. Cheers, Xiaoshu
Received on Monday, 10 September 2007 10:11:11 UTC