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[bioontology-support] Software Ontology (SVN pull)

James Malone malone at ebi.ac.uk
Mon Dec 14 11:15:33 PST 2009


Hi Michael,

Sorry about that, not sure what went happened. It's in SVN now, cheers.

James




> Hi James,
>
> Can you please override your metadata descriptor file in SVN with the
> attached file?  I've fixed some formatting problems in it.  The rest
> should be OK.  I'll test it in our Staging environment and let you in case
> I run into any issues.
>
> Please let me know when the file is in place.
>
> Thanks,
>
> Misha
>
> -----Original Message-----
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of James
> Malone
> Sent: Monday, December 14, 2009 9:52 AM
> To: Trish Whetzel
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] Software Ontology (SVN pull)
>
> Hi Trish,
>
> Further info that you needed. So the metadata file is now available here
> if you are accessing from sourceforge svn, anonymous check out is
> enabled and the file is at URL:
> https://efo.svn.sourceforge.net/svnroot/efo/trunk/src/softwareontologyinow
> l/InferredSWOOWLview/SWO_Bioportal/SWO_Bioportal_details.txt
> The Software Ontology OWL file is at URL:
> https://efo.svn.sourceforge.net/svnroot/efo/trunk/src/softwareontologyinow
> l/InferredSWOOWLview/SWO_inferred.owl
>
> I hope this enough, but if it's not let me know if there are problems
> and we'll fix them asap. Once we have this working I will do same for EFO.
>
> Cheers,
>
> James
>
>
> Trish Whetzel wrote:
>> 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 <mailto: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
>>>>>> <mailto: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 <mailto:whetzel at stanford.edu>
>> http://www.bioontology.org
>>
>>
>>
>
>
> --
> 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
>


-- 
EMBL Outstation - Hinxton,
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD,
United Kingdom
Fax: + 44 (0) 1223 492 468




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