[MOBY-l] [moby] Question about Object Ontology

[Sean Zhou]

Dear Mark,

Thanks a lot for answering my question. At this stage I don't want to write a
script to retrieve the ontologies through API. So, the "Fast" way you
suggested is more suitable for my current interest. But unfortunately, the
url (http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/) you
provided didn't give me the object ontology file that I wished to download. 

I've also tried the CVS-> moby-live
(http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomo
by). But not sure which one I should dig into. The object ontology is
definitely I want. Also, I wonder whether there is a service-ontology too.

I found on the BioMOBY homepage that Mr. Yan Wong has developed an Object
Ontology browser for Windows
(http://biomoby.open-bio.org/index.php/moby-clients/ontology_clients ). But
the username and password didn't work. This problem actually has been
mentioned in the previous discussion (
http://biomoby.org/pipermail/moby-l/2005-July/002612.html). But it is not
solved.

Anyway, I would really appreciate if you or some other experts of BioMOBY can
help me with these questions.

Thanks a lot.

Sean

-----Original Message-----
From: Mark Wilkinson [mailto:markw at illuminae.com] 
Sent: Tuesday, March 07, 2006 12:26 PM
To: Sean Zhou
Cc: moby-l at biomoby.org
Subject: Re: [moby] [MOBY-l] Question about Object Ontology

=================
The Official way:

The "retrieveResourceURLs" API call of MOBY Central (implemented in both
the Perl and the Java clients, I believe) will give you the URL's from
which you can download the various MOBY ontologies.
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-
S_API/XMLPayloads.html#retrieveResourceURLs
===================

===================
"Fast" (but not supported) way:

At the moment, the Object ontology is at:
http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
====================


The ontologies are returned in RDF, and can be viewed in any RDF-capable
viewer.  There are some tools in the MOBY CVS that are specifically
designed to browse/edit the ontologies - e.g. Martin Senger's MOBY
Dashboard.  Which tool you chose depends on what you need to use the
ontologies for, I guess...

Hope that helps!

M



On Tue, 2006-03-07 at 12:06 -0500, Sean Zhou wrote:
> Hi there,
> 
>  
> 
> I am a new comer for BioMOBY. I have two questions related to Object
Ontology
> in BioMOBY. 
> 
> 1) Where can I download Object Ontology?
> 
> 2) What tool shall I use to view it?
> 
>  
> 
> Thank you very much for the help.
> 
>  
> 
> Best,
> 
>  
> 
> Sean
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 

--
Mark Wilkinson
Asst. Professor, Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics, iCAPTURE Centre
St. Paul's Hospital, Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future