[DAS2] Ontology URIs (was RE: types.rnc)
cjm at fruitfly.org
Thu Nov 9 23:57:04 UTC 2006
On Nov 9, 2006, at 3:32 PM, Andrew Dalke wrote:
>> 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?
is this something we should be doing? Karen, is this why you wanted
to serve up per-term xml off of sequenceontology.org?
It may make more sense to serve up RDF/OWL here
I would really like to have a scheme that leaves the OBO ID
Unfortunately jena has fatal problems with numbers immediately
following the ':'. And Jena is one of the most commonly used RDF
This would work:
but unfortunately involves string hacking on the ID
>> I agree with Steve that we could collapse "so_accession" and
>> "ontology" down to one attribute and use a prefix shorthand for SO/
>> 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.
This seems overly defensive. It would seem cleaner to use the same ID
> 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
LSIDs uniquely identify sequences of bytes. The sequence of bytes in
the record GO:00000147 may change although the universal it refers to
>> 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
> DAS2 mailing list
> DAS2 at lists.open-bio.org
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