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
