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Re: Gene Ontology

From: Chris Mungall <cjm@fruitfly.org>
Date: Tue, 21 Nov 2006 12:05:03 -0800
Message-Id: <60510F0D-29E3-4E84-A59A-841D5A728797@fruitfly.org>
Cc: Asad Bajwa <asad.bajwa@gmx.de>, public-semweb-lifesci@w3.org
To: Phillip Lord <phillip.lord@newcastle.ac.uk>


On Nov 21, 2006, at 9:10 AM, Phillip Lord wrote:

>
>>>>>> "AB" == Asad Bajwa <asad.bajwa@gmx.de> writes:
>
>   AB> Dear Group,
>
>   AB> Today i have a question regarding the Gene Ontology. It was
>   AB> originally build on the OBO format. Well i want to find out the
>   AB> most i can about the gene ontology. but my interests are in
>   AB> using the OWL Format. I don't know how "good" this owl file is,
>   AB> because it is generated automatically form the OBO format. So is
>   AB> there anyone having experience with the Gene Ontology and maybe
>   AB> advising me on that. The second point is, that the OWL File is
>   AB> about 10 MB. I did not test, trying to load it into my
>   AB> memory. As i know there are about 45.000 label declared in this
>   AB> ontology.
>
>
> OWL is just a syntax. The semantics of OBO is nowadays officially
> stated to be the same as that of OWL (or a subset of it) so the OWL
> file should be fine for use.

A subset. Note that the current obo2owl mapping used in the exports  
you can get from the GO website are lossy. We'll soon be using the  
official new mapping (a result of the combined effort of the GO  
Consortium, NCBO and University of Edinburgh):

http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page

(note the new mapping will result in an even larger OWL file)

> As for size, it's possible to reason over GO. It's quite big but
> structurally relatively simple.

The current public exports of the GO are indeed simple w.r.t of how  
much of the text definitions are captured in the syntax. The curators  
are right now working with a separate branch of the ontology that  
have necessary + sufficient conditions that are captured  
computationally - which means you can do more with reasoning.

> Cheers
>
> Phil
>
>
Received on Tuesday, 21 November 2006 20:05:28 GMT

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