[DAS2] Ontology URIs (was RE: types.rnc)

Ed enwired at gmail.com
Thu Nov 9 01:13:19 UTC 2006

so_accession sounds fine with me.

2006/11/8, Steve Chervitz <Steve_Chervitz at affymetrix.com>:
> Seems like we may need to freeze the spec in a state that is fairly
> non-committal w/r/t how ontology identifiers work. I propose to remove the
> parts that are still not nailed down, so that we don't engender the
> creation
> of mutually incompatible implementations (one of the problems with DAS/1
> which DAS/2 is aiming at).
> The ontology attribute in the type element is currently documented as:
>   # ontology identifier.  The naming scheme is still undecided.
>   # This will be a URI.
>   attribute ontology { text }?,
> I think this is too vague. It's subject to lots of interpretation as to
> what
> it could point at and what it might resolve to. It could justifiably be
> used
> to identify any of these:
>   - a specific term in an ontology
>   - the ontology as a whole (e.g., homepage of GO)
>   - evidence code (as in the example below)
> The so_accession attribute gets us most of what we want and should suffice
> for this freeze. In one fell swoop it identifies the ontology and a
> particular term within it, and it defers the issue of ontology URIs.
> Some SO things to consider:
> 1) Should so_accession be restricted to SOFA (only locatable feature
> types)?
> If so, call it sofa_accession. (maybe too limiting)
> 2) What about SO versioning? Maybe a 'so_version' attribute would make
> sense
> (so_version="SOFA 2.1"). SO term IDs are stable across releases, but
> sometimes terms become obsolete and are no longer listed.
> Steve

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