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

Andrew Dalke dalke at dalkescientific.com
Thu Nov 9 23:32:59 UTC 2006

> The reason there is both an "ontology" and "so_accession" attribute is
> that we didn't have an official SO URI syntax to refer to,

Didn't -- and still don't, right?

> I agree with Steve that we could collapse "so_accession" and
> "ontology" down to one attribute and use a prefix shorthand for SO/SOFA
> terms, for example "SO:0000147".

We could.  When making the RNC I left the "SO:" prefix out
deliberately in the number, leaving "0000147".  The reason was to
be very insistent that it was SO and only SO that could to there.
Else people would start adding other terms, because after all the
format is obviously "namespace" + "version number".

> This has the nice property that the
> shorthand is in fact a legal absolute URI, and therefore unaffected by
> any "xml:base" attributes in the document.  I'd instead prefer this URI
> to be a URL that points to a description at the biomedical ontology
> center.  But specifying that the attribute is a URI allows both the
> shorthand and later a more official link.

But if we go for systems with no default resolver, why not use


> Andrew's comment below made me realize we may have another problem --
> not annotation with multiple ontologies, but rather annotation with
> multiple terms from the SO.

The type record (like most other records) have a slot at the end
for arbitrary non-das2-namespaced XML elements.  When this gets to
be a problem let people experiment with various ways to do it.

   <ONTOLOGY xmlns="http://example.com/" so="012323" />
   <ONTOLOGY xmlns="http://example.com/" so="003409" />

No reason to solve it now, as we've no data which needs

					dalke at dalkescientific.com

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