[DAS2] Ontologies in DAS/2

Chris Mungall cjm at fruitfly.org
Tue Feb 7 17:29:09 UTC 2006

Hi all

I'm concerned that the XML in the URL below isn't quite Obo-XML, it's
Allen's modified version of it. In particular, the adding of an "id"
attribute which is redundant with the id element, and the modification of
the ID scheme to use slashes instead of :s.

I believe the latter may have been to make the ID scheme more DAS-y?

OBO IDs are composed of a prefix and a local ID. These are always joined
with a :. The prefix can be specified as shortform (eg GO) or a URI
prefix. When the long form is combined with the local ID you get your URI.

If DAS wants to use a modified version of Obo-XML, that's fine, but please
don't call it Obo-XML, it will cause huge confusion!

I would much prefer if you used Obo-XML as it is - if there are things
you'd like to see changed about the format we can perhaps work that out.
I'm concerned by the changing the ID to use / instead of :. This is wrong,
and if it's something that's required for DAS, how will you interoperate
with RDF etc?

In fact there are other parts where the xml is definitely not Obo-XML - it
looks like Allen has coded these by hand rather than taking existing XML.
That's fine, but it should be marked as such. For example, there is no
develops_from element in Obo-XML; all relations bar is_a are encoded as
relationship elements.

There is a DTD at the moment

The docs are minimal as the explanation of all the fields is in the docs
for the obo text file format

We'll be converting to RNG+XSD soon

You can get Obo-XML examples from

You can see the default rule for creating a URI in the OWL files; these
currently all get the geneontology.org URI prefix by default, but this
will change (we were going to use LSIDs but the majority of OWL tools
don't seem to handle URNs very well)

As far as DAS/2 supporting different file formats, Obo-XML and RDFS/OWL
would seem to be the natural contenders. We currently go from the former
to the latter via a simple XSLT, the reverse transformation is a little
more difficult.

Allen has inlined some comments from an email exchange with me in the
document. I agree about keeping the API minimal. On the other hand you
will need at least some inferencing machinery - I'd encourage you to reuse
existing reasoning services here.


On Tue, 7 Feb 2006, Helt,Gregg wrote:

> I talked to Suzi, she's planning to join our teleconference today to
> discuss ontologies, wearing her hat as co-PI of the National Center for
> Biomedical Ontology.  Hopefully Lincoln can join too.
> I took a closer look at the DAS/2 ontology work Allen has done (see
> http://biodas.org/documents/das2/das2_ontology.html).  I urge anyone who
> wants to contribute to the ontology discussion to read this doc.  It
> specifies a way to retrieve ontologies in OBOXML format.  In this format
> each ontology term gets an absolute URI through the same mechanism that
> the rest of DAS/2 uses (URIs for ids, which can be either absolute or
> relative but resolvable).  As Allen pointed out yesterday this would
> solve our problem of how to uniquely specify ontology terms in the DAS/2
> I couldn't find any documentation for the OBOXML format, other than the
> code that generates it from OBO files.  But I'm using OBOXML as an
> example here because it clearly has resolvable URIs for each ontology
> term.  In Allen's spec, ontologies can also be returned in other
> formats, but it's unclear to me whether terms in these other formats
> would resolve to similar URIs.
> 	gregg
> > -----Original Message-----
> > From: das2-bounces at portal.open-bio.org
> [mailto:das2-bounces at portal.open-
> > bio.org] On Behalf Of Andrew Dalke
> > Sent: Tuesday, February 07, 2006 1:32 AM
> > To: DAS/2
> > Subject: Re: [DAS2] Notes from the DAS/2 teleconference for the code
> > sprint,6 Feb 2006
> >
> > > gh: would like a re-cast as xml document, hosted at so/sofa
> > > website. that xml would be like a std ontology representation so you
> > > could extend it. so someone could point to an extension of it.
> >
> > I asked as an action item if Gregg would look into the solution
> > for this.  Do we refer to the ontology by a "GO:0123456" identifier
> > or by some URL scheme?  If so, what's the mapping from URL scheme
> > to something that clients and people can understand, eg, to
> > ask for everything which is an exon?
> >
> > Does this mapping need a version number - does it change over time?
> >
> > 					Andrew
> > 					dalke at dalkescientific.com
> >
> > _______________________________________________
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