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:cjmung...@lbl.gov>
*To:* bin chen <mailto:binc...@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/
