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Re: Answers to questions about BioPortal

From: Trish Whetzel <whetzel@pcbi.upenn.edu>
Date: Wed, 10 Jan 2007 22:52:00 -0500 (EST)
To: kc28 <kei.cheung@yale.edu>
cc: Alan Ruttenberg <alanruttenberg@gmail.com>, w3c semweb hcls <public-semweb-lifesci@w3.org>
Message-ID: <Pine.LNX.4.61.0701102204300.4603@hera.pcbi.upenn.edu>

> Are we talking about versioning at a very high granularity level (e.g., a URI 
> that points to an entire ontology)? Should we also consider versioning at 
> finer granularity levels such as the levels of concepts or terms and their 
> relationships within an ontology? Some of these concepts, terms and their 
> relationships may evolve over time. We many need a versioning scheme for 
> these. I think some of these finer granularity versioning examples can be 
> found in the UMLS (Unified Medical Language System). At the instance level, 
> we may need versioning as well. Also, the semantics of versioning may be 
> unclear sometimes. For example, two different SNPs (Single Necleotide 
> Polymorphisms) that were submitted to dbSNP may refer to the same location in 
> the genome. Do we say they are two different versions of the same SNP? There 
> may not be a standard notion/definition of versioning for biomedical 
> entities.

I think that both types, high-level e.g. this is a new release of the 
ontology, and low-level, e.g. a term (class or property) is deprecated, 
are needed. Not sure about versioning at the instance level.

Mechanisms that I have seen or am aware of are either 1) add annotation 
properties in the ontology for this purpose or 2) use a database backend 
that provides a mechanism to store information about deprecated terms. 
The database backend solution may be too heavy weight for a general 
solution?. As for the annotation property mechanism. the developers of the 
MGED Ontology have put together a policy of how to indicate deprecated 
terms for this resource: 
https://www.cbil.upenn.edu/magewiki/index.php/TermDeprecationPolicy
Although there may be some items that are particular to the MGED Ontology 
and it's peculiarities, I believe that there are also items that can be 
generalized for use with other ontologies.

Cheers,
Trish
Received on Thursday, 11 January 2007 03:52:15 UTC

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