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Re: I read a challenge. was, Re: [gofriends] GO ontology in OWL format

From: Chimezie Ogbuji <ogbujic@ccf.org>
Date: Fri, 14 Sep 2007 08:40:00 -0400
To: "Alan Ruttenberg" <alanruttenberg@gmail.com>
cc: public-semweb-lifesci@w3.org, markov@mpiz-koeln.mpg.de, groscurt@mpiz-koeln.mpg.de, schoof@mpiz-koeln.mpg.de, "chris mungall" <cjm@fruitfly.org>
Message-ID: <1189773600.7958.1.camel@otherland>

On Fri, 2007-09-14 at 05:04 -0400, Alan Ruttenberg wrote:
> > 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

FYI: you don't necessarily need entailment to compute some of those
transitive traversals (at least if your RDF query language supports
functional recursion: like Versa [1]).  I could sketch out examples, but
I'm not quite familiar with the corresponding RDF terminology for the
queries on that (interesting) list.

For instance, you can evaluate ancestor / descendent traversals with
functions such as transitive-closure:

transitive-closure($listOfURIs,'.. Versa expression ..')

Apply an expression transitively, starting with the given RDF nodes,
making sure to avoid circularity. The expression could return nested
lists/sets, in which
case, every object in the topmost list is searched for a resource
terminating the leftmost path
in the tree and the found objects are used for the next transitive

[1] http://www.xml.com/pub/a/2005/07/20/versa.html

Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
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Received on Friday, 14 September 2007 12:40:29 UTC

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