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
