- From: Alan Ruttenberg <alanruttenberg@gmail.com>
- Date: Fri, 14 Sep 2007 05:04:36 -0400
- To: public-semweb-lifesci@w3.org
- Cc: markov@mpiz-koeln.mpg.de, groscurt@mpiz-koeln.mpg.de, schoof@mpiz-koeln.mpg.de, chris mungall <cjm@fruitfly.org>
Seen on the gofriends list: On Sep 12, 2007, at 1:20 PM, Chris Mungall wrote: > Let me also give you some information on the results of our > experiments using OWL and Sesame, as part of a different project > outside GO. Triplestores such as Sesame seem to work best when you > are storing instances rather than classes and class level > relations. Sesame has no knowledge of OWL entailment rules (there > is an addon called OWLIM that provides this). This means you are > out of luck if you want to make queries over the GO such as "what > is the nuclear chromosome part of?". > > You may be tempted to treat GO classes as instances and query these > using normal RDFS semantics (for example, by loading the semi- > deprecated GO RDF-XML file). This will give you better results in > the short term, as you will be able to ask queries such as the > part_of one above. However, this approach may turn out to be a dead > end in the long run. > > In my opinion SQL (with entailments pre-computed) still turns out > to be a far superior choice to existing semantic web technology - > I'd be interested to see the SPARQL equivalents of the following > queries: > http://wiki.geneontology.org/index.php/Example_Queries (this is a great list to work from! Thanks Chris) > I'd like to continue this discussion with you, but right now we are > outside the realm of anything that is specifically to do with GO > and into the realm of semantic web technology. > > I would encourage you to subscribe to this list and post details of > what you are doing there: > http://lists.w3.org/Archives/Public/public-semweb-lifesci/ > There are many people on this list engaged in this kind of discussion > > Cheers > Chris 1) what is the nuclear chromosome part of PREFIX go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> select * where { graph <http://purl.org/commons/hcls/20070416/classrelations> { go:GO_0000228 <http://purl.org/obo/owl/obo#part_of>?whole.} graph <http://purl.org/commons/hcls/20070416> { ?whole rdfs:label ?label } } => http://purl.org/obo/owl/GO#GO_0044424 intracellular part http://purl.org/obo/owl/GO#GO_0044464 cell part http://purl.org/obo/owl/GO#GO_0043226 organelle http://purl.org/obo/owl/GO#GO_0005575 cellular_component http://purl.org/obo/owl/GO#GO_0005622 intracellular http://purl.org/obo/owl/GO#GO_0005623 cell http://purl.org/obo/owl/GO#GO_0005634 nucleus http://purl.org/obo/owl/GO#GO_0043231 intracellular membrane-bound organelle http://purl.org/obo/owl/GO#GO_0043227 membrane-bound organelle http://purl.org/obo/owl/GO#GO_0043229 intracellular organelle Get it as RDF for more information, see: http://tinyurl.com/39o72h , http:// tinyurl.com/3bywd2 and http://esw.w3.org/topic/HCLS/PartOfInference but note: http://tinyurl.com/3xczk9
Received on Friday, 14 September 2007 09:04:56 UTC