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[bioontology-support] Software Ontology (SVN pull)

Trish Whetzel whetzel at stanford.edu
Fri Dec 11 09:14:48 PST 2009


Hi James,

Here are some suggestions for values:
-status - Discussion and review
-domain - Biomedical Resources
-format - OWL
-patho_type - can be left blank, but include tab for spacing
-subtypes_of - can be left blank, but include tab for spacing
-is_obsolete - can be left blank, but include tab for spacing
-granularity - can be left bank, but include tab for spacing

I think that should take care of things. A metadata file for EFO is  
also needed. It was not clear previously that 2 files are needed for  
the process, one with repository information that we keep on our side  
and another with the ontology metadata that needs to be within a  
subfolder where the ontology is located within SVN on your side.

Trish


On Dec 11, 2009, at 8:06 AM, James Malone wrote:

> 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

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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