Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Software Ontology (SVN pull)

Trish Whetzel whetzel at stanford.edu
Fri Dec 11 09:18:51 PST 2009


Sorry to hear about the system intrusion. WRT to the pull of EFO, the  
metadata file referred to in the earlier email is needed for testing  
and then this feature is expected to be rolled out to production on  
Monday.

Trish


On Dec 11, 2009, at 3:15 AM, James Malone wrote:

> Hi Trish,
>
> Sure I will do this today - I also need to send you the project  
> description as well. We've had a fairly serious systems intrusion  
> over the last few days so we're only just back on our feet again and  
> I'm slowly catching up! On a related note - we released a new EFO on  
> Wednesday but I see the update has not propagated to BioPortal. Can  
> we add that to the ontologies that will also be auto-pulled from SVN  
> please? I had previously sent the info I think so hopefully it  
> should work.
>
> 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




More information about the bioontology-support mailing list