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Re: reasoning on gene ontology

From: Samuel Croset <croset@ebi.ac.uk>
Date: Fri, 6 Apr 2012 10:14:57 +0100
Message-ID: <CA+SUvprjF=ER5uYEG7n-HG2nh=4E8uMTxfUPt99+rvjMeLd3sg@mail.gmail.com>
To: bin chen <binchen@indiana.edu>
Cc: public-semweb-lifesci <public-semweb-lifesci@w3.org>
Hi Bin,

I have been playing around the GO and looking for interesting cases too. I
believe the reasoner could help for the following tasks:

1- Terms retrieval/search, as you pointed out, SW queries are more powerful
and intuitive than relational databases one.

2- Ontology re-factoring: When new terms are added by the curators, a
reasoner can check for inconsistencies.

3- GO annotations: Can help to check whether a series of annotations are
consistent and legitimate, or could re-map some annotations with a more
accurate term or remove the redundant annotations. However, you would need
to introduce some extra relations not present at the moment in GO (such as
'has_function' or something similar) and define how these relations
interact with the existing ones.

I found it difficult to generate useful biological deductions using the GO
as such, as the relations are existential restrictions, with limited
inferring potential in OWL. This is most-likely due to the fact that the GO
has been first designed to be species/system independent.

However, the relations used by the GO are coming from the Relation Ontology
(http://code.google.com/p/obo-relations/) and they could be re-used and
extended for different purposes. I am currently working on biological
pathways representations in OWL, and in this context it seems that you
could deduce much more, as you are dealing with a concrete system, problem

Hope it helps,


On Thu, Apr 5, 2012 at 9:10 PM, bin chen <binchen@indiana.edu> 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

Samuel Croset
PhD student @ EMBL-EBI | Rebholz Group <http://www.ebi.ac.uk/Rebholz/>
www.samuelcroset.com <http://www.SamuelCroset.com>
Received on Saturday, 7 April 2012 11:47:33 UTC

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