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

Steve Chervitz Steve_Chervitz at affymetrix.com
Thu Nov 9 01:07:42 UTC 2006

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.


> From: Chris Mungall <cjm at fruitfly.org>
> Date: Wed, 8 Nov 2006 17:11:09 -0500
> To: "Helt,Gregg" <Gregg_Helt at affymetrix.com>
> Cc: DAS/2 <das2 at lists.open-bio.org>
> Subject: Re: [DAS2] Ontology URIs (was RE: types.rnc)
> There absolutely needs to be a stable URI scheme for referencing
> types defined in ontologies. The details of the scheme aren't clear
> yet. It will probably be http based (ie not LSID).
> Do you have specific requirements? Should the URI be a URL
> dereferenceable in any browser? Should it dereference to html or RDF
> or use content negotion to decide which? etc
> On Nov 8, 2006, at 2:54 PM, Helt,Gregg wrote:
>> I'll talk to Suzi in her role as co-PI at NCBO (National Center for
>> Biomedical Ontolgoy).  We may be able to quickly work out a URI
>> syntax (even if implementation of what the URIs resolve to comes
>> later).
>> gregg
>>> -----Original Message-----
>>> From: Andrew Dalke [mailto:dalke at dalkescientific.com]
>>> Sent: Tuesday, November 07, 2006 6:23 PM
>>> To: Ed
>>> Cc: Helt,Gregg
>>> Subject: Re: types.rnc
>>> Ed:
>>>> What bothers me is "still undecided".  That doesn't belong in a
>>>> "frozen" spec.  Though I have no idea what the correct text to put
>>>> here is.
>>> Take for example
>>> http://genome.cbs.dtu.dk:9000/das/secretomep/types
>>>      <TYPE id="NC-SECRETORY" method="SecretomeP-1.0"
>>>        category="protein sorting" description="Ab initio
>>> predictions of
>>> non-classical i.e. not signal peptide triggered protein secretion"
>>>        evidence="IEA"
>>> ontology="http://www.geneontology.org/GO.evidence.shtml">35138</TYPE>
>>> It uses an ontology URI to describe which ontology scheme is
>>> used to describe the "evidence" value.  In this case it means
>>> "Inferred from Electronic Annotation"
>>> There is no long-term/stable URL scheme for GO.  Do we
>>> make something up?  Do we say "use a URL" and leave it
>>> at that?  I'll go for the latter as every reasonable
>>> scheme should end up as a URL.
>>> Except for those which are annotated from multiple ontologies.
>>> Andrew
>>> dalke at dalkescientific.com
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