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

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Tue, 18 Sep 2007 04:48:34 -0400
Message-Id: <483A99D8-4082-4E92-A707-3F6C853EFA07@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>
To: ogbujic@ccf.org

Agreed, although it can get complicated quickly. For example, the  
part of relations go through is_a, (a part_of some b, b subclassOf c  
=> a part_of some c) and there can be negations in the GO  
annotations. If you get into subproperties, some of which are  
transitive and some not it gets even more complicated.
However, the reason that I did the part_of computation in Pellet,  
aside from wanting to make sure it was correct, was to demonstrate  
one way to go about getting the correct inferences and then deploying  
them in a system that could respond quickly to queries.


On Sep 14, 2007, at 8:40 AM, Chimezie Ogbuji wrote:

> 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
> lookup.
> ]]]
> [1] http://www.xml.com/pub/a/2005/07/20/versa.html
> -- 
> Chimezie Ogbuji
> Lead Systems Analyst
> Thoracic and Cardiovascular Surgery
> Cleveland Clinic Foundation
> 9500 Euclid Avenue/ W26
> Cleveland, Ohio 44195
> Office: (216)444-8593
> ogbujic@ccf.org
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Received on Tuesday, 18 September 2007 08:48:45 UTC

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