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[bioontology-support] Software Ontology (SVN pull)

James Malone malone at ebi.ac.uk
Tue Dec 15 02:43:47 PST 2009


Misha,

Ok, done. Cheers. Trish, re: EFO details, once this is working for SWO 
I'll do the same for EFO as well - should be much easier second time 
round :)

Thanks to you both,

James



Michael Dorf wrote:
> James,
>
> Sorry I missed it the first time, but the namespace attribute is used in
> BioPortal to define the abbreviation for the ontology (don't ask why ;)).
> Can you change the value in the descriptor file from
> http://www.ebi.ac.uk/efo/swo/ to just SWO.
>
> Thanks,
>
> Misha
>
> -----Original Message-----
> From: James Malone [mailto:malone at ebi.ac.uk] 
> Sent: Monday, December 14, 2009 11:16 AM
> To: Michael Dorf
> Cc: 'James Malone'; support at bioontology.org; 'Trish Whetzel'
> Subject: RE: [bioontology-support] Software Ontology (SVN pull)
>
> 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
>>
>>     
>
>
>   


-- 
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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