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

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Fri, 14 Sep 2007 05:04:36 -0400
Message-Id: <9C26D6B7-FFA6-44A5-B150-6213B9CD7CAF@gmail.com>
Cc: markov@mpiz-koeln.mpg.de, groscurt@mpiz-koeln.mpg.de, schoof@mpiz-koeln.mpg.de, chris mungall <cjm@fruitfly.org>
To: public-semweb-lifesci@w3.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

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