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

From: Chris Mungall <cjm@fruitfly.org>
Date: Fri, 14 Sep 2007 16:11:23 +0100
Message-Id: <C7524879-F406-451B-97AF-BAEAD18481CB@fruitfly.org>
Cc: public-semweb-lifesci@w3.org, markov@mpiz-koeln.mpg.de, groscurt@mpiz-koeln.mpg.de, schoof@mpiz-koeln.mpg.de
To: Alan Ruttenberg <alanruttenberg@gmail.com>


On Sep 14, 2007, at 10:04 AM, Alan Ruttenberg wrote:

> 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 }
>  }

Ah yes, but let me just join the dots for everyone here - you are  
treating the classes as instances here, and relations at the class  
level become simple triples rather than restrictions. This means we  
can ignore OWL altogether and use RDFS semantics, which suits  
existing triplestores nicely. Mathias recommended as much on a  
separate thread.

Is this a trick or a long term strategy? I don't know. I can  
certainly see some problems with the approach.

> =>
>
> 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 15:11:42 UTC

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