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Re: Answers to questions about BioPortal

From: Trish Whetzel <whetzel@pcbi.upenn.edu>
Date: Wed, 10 Jan 2007 22:57:31 -0500 (EST)
To: William Bug <William.Bug@DrexelMed.edu>
cc: Tim Clark <twclark@nmr.mgh.harvard.edu>, Mark Wilkinson <markw@illuminae.com>, dirk.colaert@agfa.com, Daniel Rubin <rubin@med.stanford.edu>, w3c semweb hcls <public-semweb-lifesci@w3.org>, public-semweb-lifesci-request@w3.org
Message-ID: <Pine.LNX.4.61.0701102253110.4603@hera.pcbi.upenn.edu>

Hi Bill,

Is the work that you mention below part of that for BIRN and is there a 
pointer to a policy?

Also, have you found it necessary to be able to re-create the graph within 
the same version of the ontology on a day-to-day basis or is a 
version-to-version basis acceptable?


> As to Dirk's original point below, this is a requirement for OBO Foundry 
> ontologies - "the original URI should still point to the old term or concept, 
> even if it is deprecated" - though I take it not all BioPortal ontologies 
> will follow the OBO Foundry guidelines.
> There's also been a lot of work on ontology class metadata standards recently 
> - much focused within the OBI ontology development group - with a specific 
> eye toward helping to support the link between deprecated classes and those 
> classes to which the original semantic content covered by the defunct class 
> has been transferred.  To fully represent this evolutionary graph, there will 
> likely be a need for some ruled-based formalism to deal with scenarios where 
> the deprecated class has not simply been decomposed into 2 or more newer 
> classes - or scenarios where multiple deprecated classes map to multiple 
> current classes. Even under the simple case where 1 entity --> 2 entities, 
> rules may be required to more fully and formally express the semantic 
> transference asserted by the ontological evolutionary graph.
> For the time being, we at least are working to include metadata properties to 
> make it possible to - in theory - reconstruct the ontology graph as it 
> existed on a particular date.
Received on Thursday, 11 January 2007 03:57:47 UTC

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