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[bioontology-support] Software Ontology (SVN pull)

James Malone malone at
Fri Dec 11 03:15:39 PST 2009

Hi Trish,

Sure I will do this today - I also need to send you the project 
description as well. We've had a fairly serious systems intrusion over 
the last few days so we're only just back on our feet again and I'm 
slowly catching up! On a related note - we released a new EFO on 
Wednesday but I see the update has not propagated to BioPortal. Can we 
add that to the ontologies that will also be auto-pulled from SVN 
please? I had previously sent the info I think so hopefully it should work.



Trish Whetzel wrote:
> Hi James, 
> The code to do the automatic pull from SVN repositories is now ready 
> for testing. Can you generate the ontology metadata file as described 
> below and send the following:
>     * Access information for the SVN repository for the Software ontology
>     * Full path to the ontology metadata file. I believe that one file
>       with information for both ontologies should be fine.
> Thanks,
> Trish
> On Dec 3, 2009, at 12:46 PM, Michael Dorf wrote:
>> 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
>> repositories.
>> 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
>> download
>> ro.obo
>> source
>> home CARO Wiki|
>> documentation
>> 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.
>> Thanks,
>> Misha
>> -----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.
>> Trish
>> 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
>> <ontologies.txt>

European Bioinformatics Institute, 
Wellcome Trust Genome Campus, 
Cambridge, CB10 1SD, 
United Kingdom
Tel: + 44 (0) 1223 494 676
Fax: + 44 (0) 1223 492 468 

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