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Re: reasoning on gene ontology

From: robert Stevens <robert.stevens@manchester.ac.uk>
Date: Sat, 7 Apr 2012 11:32:25 +0100
Message-ID: <3A981E79C21449998AF3153A50AE90E9@manchestcc7bbd>
To: "Chris Mungall" <cjmungall@lbl.gov>, "bin chen" <binchen@indiana.edu>
Cc: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
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.

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

  ----- Original Message ----- 
  From: Chris Mungall 
  To: bin chen 
  Cc: public-semweb-lifesci 
  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
Received on Saturday, 7 April 2012 10:32:22 GMT

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