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Re: reasoning on gene ontology

From: Mikel Egaña Aranguren <megana@fi.upm.es>
Date: Sun, 08 Apr 2012 13:35:03 +0200
Message-ID: <4F8177E7.4060301@fi.upm.es>
To: public-semweb-lifesci@w3.org
Just for completeness and shameless self-promotion, Robert, you have 
forgotten a paper of ours! :-)

Mikel Egaña Aranguren, Chris Wroe, Carole Goble, Robert Stevens. /In 
situ/ migration of handcrafted ontologies to Reason-able Forms. /Data & 
Knowledge Engineering/ 2008, 66, 147-162

http://dx.doi.org/10.1016/j.datak.2008.02.002

On lr., 2012.eko apiren 07a 12:32, robert Stevens wrote:
> wwe've put a little query tool on-line at
> http://owl.cs.manchester.ac.uk/goal/
> that uses the ELK reasoner to form queries over mouse proteins 
> annotated with GO, MPO and HDO. There's a paper coming out in a 
> special issue of JBMS real soon - a version can be found at 
> http://www.cs.man.ac.uk/~stevensr/papers/goal-2012.pdf 
> <http://www.cs.man.ac.uk/%7Estevensr/papers/goal-2012.pdf>.
> Also have a look at some of rob Hoendorf and co's work doing this sort 
> of thing and then some mining over all the integrated sufff.
> Also, the KB to be found at http://www.kupkb.org mainly uses sprql, 
> but has a little owl reasoning in the background over some OWL that 
> includes GO.
> as chris says, a lot of the OWL like reasoning  happens in the 
> ontology development  stage - we've done stuff in the past:
> C.J. Wroe, R.D. Stevens, C.A. Goble, and M. Ashburner. A Methodology 
> to Migrate the Gene Ontology to a Description Logic Environment Using 
> DAML+OIL. In 8th Pacific Symposium on biocomputing (PSB), pages 
> 624--636, 2003.
> which we did a bit more systmatically in
> Jesualdo Tomás Fernández-Breis, Luigi Iannone, Ignazio Palmisano, Alan 
> L. Rector, and Robert Stevens. Enriching the gene ontology via the 
> dissection of labels using the ontology pre-processor language. In 
> Philipp Cimiano and Helena Sofia Pinto, editors, Knowledge Engineering 
> and Management by the Masses - 17th International Conference, EKAW 
> 2010, Lisbon, Portugal, October 11-15, 2010. Proceedings, volume 6317 
> of Lecture Notes in Computer Science, pages 59--73. Springer, 2010.
> You can find versions of these papers on my Web site via 
> http://www.cs.man.ac.uk/~stevensr <http://www.cs.man.ac.uk/%7Estevensr>
>
>     ----- Original Message -----
>     *From:* Chris Mungall <mailto:cjmungall@lbl.gov>
>     *To:* bin chen <mailto:binchen@indiana.edu>
>     *Cc:* public-semweb-lifesci <mailto:public-semweb-lifesci@w3.org>
>     *Sent:* Friday, April 06, 2012 4:20 PM
>     *Subject:* Re: reasoning on gene ontology
>
>     Hi Bin,
>
>     We use OWL reasoning extensively within the GO consortium, primarily
>     for automated classification of new terms, and for validation of the
>     ontology and gene associations. For some more background, see
>     PMID:20152934 and PMID:20973947 (note that in those papers we used
>     some custom reasoning tools, but current implementations use OWL
>     reasoners).
>
>     There are not so many applications of non-trivial reasoning over GO
>     outside the usual ontology development lifecycle use cases (but this
>     is perhaps true of many ontologies). Most of the analysis and query
>     tools that are currently in use perform a simple transitive closure
>     over a subset of the relations, and barely count as
>     reasoning. However, I expect this situation will slowly change as some
>     of the more advanced axioms that allow for reasoning are
>     publicized. There is a lot of work happening now that involves
>     reasoning over collections of orthogonal OBO library ontologies to
>     mine gene phenotype associations for example.
>
>     I suppose it depends how you define reasoning - I assume here you mean
>     it in strictly in the sense of deductive reasoning as employed by OWL
>     and semantic web inference engines, rather than, say, probabilistic
>     inference.
>
>     Regards
>     Chris
>
>     On Apr 5, 2012, at 1:10 PM, bin chen wrote:
>
>>     Hi,
>>     Does anyone perform some reasoning using gene ontology? Any
>>     intereting story to share? I recently ran reasoning based
>>     on extended GO relations [1], and found that the triples doubled
>>     after reasoning. I was also aware of some queries are not able to
>>     be performed in relational database. but I havenot found very
>>     interesing cases to utlize the inferred results. Any reference?
>>     Thanks.
>>     Best, Bin
>>     [1] http://www.geneontology.org/GO.ontology-ext.relations.shtml
>>
>>     -- 
>>     Bin Chen
>>     PHD student, Informatics,
>>     Indiana University at Bloomington
>>     http://cheminfo.informatics.indiana.edu/~binchen
>>     <http://cheminfo.informatics.indiana.edu/%7Ebinchen>
>


-- 
Mikel Egaña Aranguren, PhD
http://mikeleganaaranguren.com

Marie Curie post-doc at Ontology Engineering Group, UPM
http://www.oeg-upm.net/
Received on Sunday, 8 April 2012 11:35:26 GMT

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