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Re: BioPortal

From: Daniel Rubin <rubin@med.stanford.edu>
Date: Tue, 09 Jan 2007 12:10:02 -0800
Message-Id: <>
To: Trish Whetzel <whetzel@pcbi.upenn.edu>,Mark Musen <musen@stanford.edu>
Cc: helen.chen@agfa.com,Alan Ruttenberg <alanruttenberg@gmail.com>, "Eric Prud'hommeaux" <eric@w3.org>, w3c semweb hcls <public-semweb-lifesci@w3.org>

Hi Trish,

You can contact me regarding questions about this.
BioPortal provides an ontology library containing the different 
release versions of ontologies, as submitted to us by the content 
owners, but is not a content management system such as cvs. Different 
ontology developers will use their preferred local systems to keep 
alpha versions of their ontologies, and submit the release versions 
to BioPortal. We are also working on a mechanism to pull current 
versions of ontologies from the source systems, and we'd be 
interested in exploring doing this for your ontologies as well.
We will be adding ontology diff, supported through PROMPT.

We can identify deprecated terms, and this service is provided by LexGrid.


At 09:07 AM 1/9/2007, Trish Whetzel wrote:

>Hi Mark,
>Are you the person to request updates of information currently 
>displayed on the site?
>Also, can you provide more details on how the BioPortal will provide 
>versioning? Last I understood, there were no SVN capabilities with 
>the BioPortal - has that changed or did I misunderstand the set-up?
>Will there be a general way to identify deprecated terms in the 
>ontologies posted in BioPortal, how does LexGrid handle this information?
>Trish Whetzel, Ph.D.
>Programmer Analyst
>University of Pennsylvania
>Ph: 215-573-4793
>On Tue, 9 Jan 2007, Mark Musen wrote:
>>Let me emphasize that this is a pre-release version on the Web 
>>site.  There will be lots of changes between now and February 1.
>>The system handles versioning very well, and you will be able to go 
>>back and review older versions in addition to the most current 
>>posting.  There is planned support for a variety of features that 
>>will be of particular interest, including alignment with other 
>>ontologies, support for additional metadata and annotations, and 
>>advanced visualization capabilities.
Received on Tuesday, 9 January 2007 21:07:48 UTC

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