Gene Ontology

Dear Group,

Today i have a question regarding the Gene Ontology. It was
originally
build on the OBO format. Well i want to find out the most i
can about
the gene ontology. but my interests are in using the OWL
Format. I
don't know how "good" this owl file is, because it
is generated
automatically form the OBO format. So is there anyone having
experience with the Gene Ontology and maybe advising me on
that. The
second point is, that the OWL File is about 10 MB. I did not
test,
trying to load it into my memory. As i know there are about
45.000
label declared in this ontology.

Well i am thinking about building a search agent by using
this
ontology. Before i need to start, i would like to know if
someone is
working with it.

Thanks in advance

Kind Regards

Asad Bajwa

>>>>> "AB" == Asad Bajwa
<asad.bajwagmx.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. 

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

Cheers

Phil

Hi Asad,

The National Center for Biomedical Ontology has created an
OBO to OWL
mapping, which can be found at:

http://www.bioontology.org/wiki/index.php/OboInOwl:M
ain_Page

We will soon (soon = less than 10 days) release protégé
plugins to
read in any OBO format file (including the GO) and convert
them to
OWL. The bleeding edge code for the plugins can be found at:

http://smi-protege.stanford.edu/svn/obo-converter/trunk/


The GO in OWL loads fine into protégé (make sure you have
the max heap
size set to about 1GB).

Regards,
Nigam.

public-semweb-lifesci-requestw3.org wrote on Tuesday,
November 21,
2006 2:26 AM:

> Dear Group,
> 
> Today i have a question regarding the Gene Ontology. It
was
> originally build on the OBO format. Well i want to find
out
> the most i can about the gene ontology. but my
interests are
> in using the OWL Format. I don't know how
"good" this owl file
> is, because it is generated automatically form the OBO
format.
> So is there anyone having experience with the Gene
Ontology
> and maybe advising me on that. The second point is,
that the
> OWL File is about 10 MB. I did not test, trying to load
it
> into my memory. As i know there are about 45.000 label
declared in
> this ontology. 
> 
> Well i am thinking about building a search agent by
using this
> ontology. Before i need to start, i would like to know
if someone is
> working with it. 
> 
> Thanks in advance
> 
> Kind Regards
> 
> Asad Bajwa

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

>
>>>>>> "AB" == Asad Bajwa
<asad.bajwagmx.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:M
ain_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
>
>