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[bioontology-support] Software Ontology (SVN pull)

Michael Dorf mdorf at stanford.edu
Mon Dec 14 10:27:31 PST 2009


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 

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