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

Chris Mungall cjm at fruitfly.org
Thu Nov 9 23:57:04 UTC 2006

On Nov 9, 2006, at 3:32 PM, Andrew Dalke wrote:

> Gregg:
>> 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  
unviolated; eg


Unfortunately jena has fatal problems with numbers immediately  
following the ':'. And Jena is one of the most commonly used RDF  
tools. Sigh

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  
scheme throughout

> 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?
>    url:lsid:biodas.org:go:0000147

LSIDs uniquely identify sequences of bytes. The sequence of bytes in  
the record GO:00000147 may change although the universal it refers to  
does not

>> 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.
> Eg,
>    <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
> this.
> 					Andrew
> 					dalke at dalkescientific.com
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