[DAS2] Ontologies in DAS/2

Tue Feb 7 21:20:53 UTC 2006

Hi Chris,

On Tue, 7 Feb 2006, Chris Mungall wrote:

> 
> 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?

The slash was introduced to take advantage of xml:base and the
hierarchical relationship between namespaces and terms, e.g.

  xml:base="/das/ontology/obo/1/ontology" + id="SO/0000001"

is equivalent to:

  /das/ontology/obo/1/ontology/SO/0000001

If we want the identifier to be SO:0000001, it means that we have to make
xml:base="/das/ontology/obo/1/ontology/SO.  This is problematic for two 
reasons:

  1) multiple xml:base cannot be defined for the entire document, meaning
     that URIs for other records referenced become very long.

  2) different ontologies cannot use the same xml:base

The only way I see out of this ATM is to treat : as a / internal to the
Ontology-DAS service.

> 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.

The XML provided by the Ontology-DAS server is using templates to mark up
ontology records that have been loaded to a chado database using
perl-go-perl.  The develops_from node, IIRC, was created because there is
a section in a perl-go-perl .xslt that creates elements for all
relationship types.

> 
> There is a DTD at the moment
> http://www.godatabase.org/dev/xml/dtd

This didn't exist at the time I wrote my templates ( 4-6 months ago), or I
would have validated.

-Allen

> 
> The docs are minimal as the explanation of all the fields is in the docs
> for the obo text file format
> http://www.godatabase.org/dev/doc/obo_format_spec.{html,txt,pdf}
> 
> We'll be converting to RNG+XSD soon
> 
> You can get Obo-XML examples from
> http://www.fruitfly.org/~cjm/obo-download
> 
> 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.
> 
> Cheers
> Chris
> 
> 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
> > TYPES XML.
> >
> > 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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> > > DAS2 at portal.open-bio.org
> >
> >
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> >
> 
> 
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