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[bioontology-support] Software Ontology (SVN pull)

James Malone malone at ebi.ac.uk
Fri Dec 11 08:06:59 PST 2009


Hi Trish,

I'm trying to complete the metadata for the software ontology. Some of 
it made no sense to me outside of the context of the example given and i 
didn't know what valid values for these fields were. Is there a 
definition for some of the fields and the values they can take (I've 
listed them below)? Thanks.

Access info is:

SVN directory:
/trunk/src/softwareontologyinowl/InferredSWOOWLview
OWL file is:
/trunk/src/softwareontologyinowl/InferredSWOOWLview/SWO_inferred.owl

Anonymous check out is enabled.
For metadata, I need help on these fields:

status
patho_type    
granularity 
relevant_organism    - *no idea for software
domain
subtypes_of
is_obsolete   
format 

Cheers,

James



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
>> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/ca
>> ro.obo
>> source
>> home CARO Wiki|http://www.bioontology.org/wiki/index.php/CARO:Main_Page
>> documentation
>> contact Melissa Haendel obo-anatomy lists.sourceforge.net
>> 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 stanford.edu]
>> Sent: Thursday, December 03, 2009 9:34 AM
>> To: James Malone; Michael Dorf
>> Cc: support at bioontology.org
>> 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 lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>> <ontologies.txt>
>


-- 
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 




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