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[bioontology-support] Software Ontology (SVN pull)

Michael Dorf mdorf at
Thu Dec 3 12:46:13 PST 2009

Hi Trish/James,

First, I'd like to clarify that the current production version of
BioPortal only supports CVS based ontology auto-pull.  Our next release,
due in production in about ten days, does introduce support for SVN

Below are the artifacts we will need for including the repository into our
automatic pull:

1. SVN Access URL with the full path to the ontology file location
2. Username/password (if any)
3. Full path (in the repository) to a text file that stores ontology
metadata in the following format (also, see the attached sample):

id	caro
title	Common Anatomy Reference Ontology
namespace	CARO
foundry	Yes
status	Discussion and review
home	CARO Wiki|
contact	Melissa Haendel	obo-anatomy
format	obo
description	The Common Anatomy Reference Ontology (CARO) is being
developed to facilitate interoperability between existing anatomy
ontologies for different species, and will provide a template for building
new anatomy ontologies. CARO will be described in Anatomy Ontologies for
Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and
Richard Baldock (Editors)
relevant_organism	all
subtypes_of	bfo:IndependentContinuant
domain	anatomy
patho_type	canonical
granularity	organismal

I recommend pasting this snippet into an editor that lets you view the
tabs, spaces and line breaks so you can distinguish between the various
delimiters used in the file.  These are important for proper parsing of
the values on our end.

Let me know if you have questions.



-----Original Message-----
From: Trish Whetzel [mailto:whetzel at] 
Sent: Thursday, December 03, 2009 9:34 AM
To: James Malone; Michael Dorf
Cc: support at
Subject: Re: [bioontology-support] Software Ontology

Hi James,

Very much interested to see the Software Ontology. Has the location of  
this ontology been included in your SVN repository file for the  
automatic pull?
***Misha, can you confirm if anything additional to the repository  
file is needed to include this ontology in the automatic pull?

James, do you have mappings generated for the Software Ontology? Also,  
would it make sense to load this as a 'view' of EFO - is this a subset  
of EFO or does this extend from the software class in EFO? I can talk  
to via Skype about views further if you like.


On Dec 3, 2009, at 9:17 AM, James Malone wrote:

> Hi,
> We have had a project working on creating a software ontology that  
> we needed for a branch of EFO. We've kept it separate though so it  
> can be reused as separate ontology. I'd like to get this Software  
> Ontology uploaded to BioPortal if possible please!  I've uploaded to  
> our public SVN, but can you let me know what details you require for  
> me to get it uploaded to BioPortal. I guess you might need some  
> extra bits like a description etc.
> Many thanks in advance!
> James
> -- 
> European Bioinformatics Institute, Wellcome Trust Genome Campus,  
> Hinxton, Cambridge, CB10 1SD, United Kingdom
> Tel: + 44 (0) 1223 494 676
> Fax: + 44 (0) 1223 492 468
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

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