[DAS2] Ontologies in DAS/2

Allen Day allenday at ucla.edu
Wed Feb 8 03:14:49 UTC 2006 

Chris,

Why have you chosen to make <id/> a subelement of <term/>?  Is it expected
that there will be multiple IDs for a given term, and if so is there not a
primary ID?  having an id attribute is a defacto standard for DOM libs, so
you can call getElementById().

-Allen

On Tue, 7 Feb 2006, chris mungall wrote:

> 
> On Feb 7, 2006, at 1:20 PM, Allen Day wrote:
> 
> > 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
> 
> it's actually equivalent to:
> /das/ontology/obo/1/ontologySO/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.
> 
> Why not just define a qname for every idspace? This is the standard way 
> of doing this in XML
> 
> Using xml:base is not a big gain for brevity, since fairly soon some 
> obo ontologies will reference other obo ontologies.
> 
> In fact is this even as issue if you get rid of the id attribute to 
> conform to obo-xml? ids in obo-xml are encoded as elements, so xml:base 
> rules are not applied. Obo has it's own rules for ID generation. This 
> has the arguable disadvantage that we can't directly use xml:base and 
> the whole xml namespace system for OBO IDs, we layer our own system on 
> top. This is actually preferable for us.
> 
> >   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.
> 
> I'm still not sure what the problem is, and I think you may be stuck 
> anyway when it comes to RDF/OWL ontologies
> 
> >
> >> 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.
> 
> hmmm, I don't think so, but the point is moot anyway, just so long as 
> the final version uses xml that validates, either against obo-xml or 
> your own documented variant
> 
> >
> >>
> >> 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.
> 
> it did, it's just not well signposted! sorry about that
> 
> look forward to seeing a demo. I do this you have to work out the 
> semantics of retrieval by ontology term though.
> 
> cheers
> chris
> 
> >
> > -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
> >>>>
> >>>> _______________________________________________
> >>>> DAS2 mailing list
> >>>> DAS2 at portal.open-bio.org
> >>>
> >>>
> >>> _______________________________________________
> >>> DAS2 mailing list
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> >>> http://portal.open-bio.org/mailman/listinfo/das2
> >>>
> >>
> >>
> >> _______________________________________________
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> >>
>

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