RE: Versioning vs Temporal modeling of Patient State

>> If a class has a particular 'definition' (i.e., the criteria
>> for membership of its instances) at a particular time and
>> that definition 'changes' then we are talking about a
>> different class altogether not a 'version' of the same class
>
> Yes. That is why I consider the OBO Foundry's wording "the original URI
> should still point to the old term or concept, even if it is deprecated"
> (From William Bug) is a bit self-contradicted.
>
> In software engineering, if a class or a function is labeled as
> "deprecated", it intends to warn the programmers that the code/functionality
> might not be available some point in the future.
>
> But when crafting an ontology, we present our view on certain reality.  If
> the view is wrong or inadequate, there will certainly less cited (i.e.,
> linked) by others and eventually die.  Hence, the notion of deprecation
> seems not apply if the URI is to be persisted. (I strongly support this OBO
> policy).
>
> But on the other hand, there is situiations that the crafted ontology is due
> to errors but not due to different theories or views.  Hence, we need to
> "deprecate" certain URIs. I think it is necessary to make distinctions
> between the two and give different URI policies.
My understanding of the OBO Foundry's wording is that if a term is 
deprecated, it is not recommended for use (because it was split, 
merged, replaced or no longer necessary). However, the deprecated term 
continues to exist in the ontology  and therefore the URI for the 
term persists. Not all data producers, repositories etc. update the 
annotations of their data when an ontology is updated.

With the ontologies from OBO that I am familiar with, when the resource 
is in production use any terms that are deprecated still exist in the 
ontology, but are marked in some way as being deprecated. Perhaps it is 
the notion of what deprecation of a term means WRT to it's URI that is at 
question?

Trish

Received on Thursday, 11 January 2007 22:55:50 UTC