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GO XML/RDF format and anatomy ontologies

Bradley Marshall bradmars at yahoo.com
Tue Aug 26 13:28:16 PDT 2003


Hi,

Thanks for adding this to the discussion.  It's really
useful to have someone well-versed in RDF/OWL comment
on this type of thing.  Before I comment specifically
on the RDFS/OWL schemas, I want to make sure that I
have correctly interpreted the points you've made
about the current format.

First of all, there is a typo and using GO:XXXXXXX as
an ID is not a valid Qname.  Those are straightforward
and will be changed.

Secondly, n_associations needs to become a new element
rather than an attribute?  I was under the impression
that RDF treated attributes and data elements in the
same way.  DO I have this wrong?

Next is the difference between rdf:about and rdf:ID. 
When we made this format there was great debate about
whether or not fully qualified URI ids had to be
supported by an HTML page.  I also felt that the fully
qualified URI might be more useful universally. 
However, the method you suggest is much more
concise/readable.  Is the current general feeling in
the RDF community that notional URIs are not valid? 
Also, is it accepted that rdf:about should be used for
URI refs and rdf:ID used for local IDs?

Finally, if I made the changes you suggested to the
current format, I'd be fully compliant with current
RDF standards, but more needs to be done for RDFS or
OWl compliance.  Yes?  I'm going to peruse the RDFS
and OWL schemas a little more and comment specifically
on them in another email.

Brad Marshall  

--- stuart at inf.ed.ac.uk wrote:
> 
> Continuing the XML vs flat file discussion, the GO
> XML/RDF format as
> used in the termdb.xml (latest version
> go_200307-termdb.xml) is a
> good option for anatomy ontologies as it is common
> to want to
> specialise relations e.g. to have  'descends' and
> 'descends-in-male' and defining this is
> straightforward in RDF. RDF has tool
> support e.g. the HP Jena toolkit, and is actually
> intended to be an
> ontology language. Also, RDF could be used to store
> all the information
> associated with a GO term (although, technically,
> RDF is rather
> unconstrained hence DAML-OIL and OWL are layered on
> RDFS - constraining what
> you can say).   
> But in trying to extend the RDF element I found the
> XML go.dtd no longer
> defines correct RDF (perhaps standards have
> changed). Also the go.dtd seems to
> be incorrect so it is not possible to validate the
> XML either. Some
> problems are: 
> 1. the dtd uses go:isa and go:is_a, plus go:part-of
> and go:part_of 
>    which seem like typos. 
> 2. go:term has the attribute n_associations which
> produces incorrect RDF.
> 3. the URI references:
>    go:term
>
rdf:about="http://www.geneontology.org/go#GO:0003674"
> 
>    are notional, that is, there is no file at this
> URI.
> These problems are easily fixed, allowing the
> validation of
> the XML and use of checking in RDF. Tools like VRP
> from ICS-FORTH 
> http://athena.ics.forth.gr:9090/RDF/VRP/
> are able to check syntax and semantic errors such as
> loops in the class
> hierarchy, loops in the property hierarchy, domain
> and range checks
> plus make inferences using external RDF sources.
> 
> The differences are not great:
> Proposed:
>  <go:term rdf:ID="&GOQ;0003673">
>      <go:n_associations>0</go:n_associations>
>      <go:accession>&GOQ;0003673</go:accession>
>      <go:name>Gene_Ontology</go:name>
>  </go:term>
> 
> Current:
>   <go:term
>
rdf:about="http://www.geneontology.org/go#GO:0003673"
> n_associations="0">
>    <go:accession>GO:0003673</go:accession>
>    <go:name>Gene_Ontology</go:name>
>  </go:term>
> 
> A small GO file in the slightly modified format is
> here:
> http://www.aiai.ed.ac.uk/resources/go/go
> the modified dtd plus a RDFS file that defines what
> the GO vocabulary
> means can be seen here:
> http://www.aiai.ed.ac.uk/resources/go/go.dtd
> http://www.aiai.ed.ac.uk/resources/go/go.rdfs
> (but it is notable that is_a and part_of are no
> longer in the go file,
> they are defined in the go.rdfs file.)
> 
> RDF, and the RFD Schema that comes with it, can be
> used to define a
> richer ontology for GO, for example, go:isa should
> really be replaced with
> rdfs:subClassOf, lineage and part-of relations
> should be related by 
> rdfs:subPropertyOf and so on. see
> http://www.aiai.ed.ac.uk/resources/go/
> However, the syntactic problems mean that the
> current GO
> XML/RDF format files need editing before a valid RDF
> file can be obtained.  
> 
> Two issues arise - to encourage the use of RDF, and
> semantic analysis,
> is it easier to generate a new RDFS termdb file than
> correct the current
> XML ? this depends on the way current tools make use
> of the XML.  
> Finally, GO IDs such as GO:0003673 are not valid
> 'Qnames' (qualified
> names) in XML as they contain a colon, and colons
> are reserved for
> namespace delimiters
>
http://www.w3.org/TR/1999/REC-xml-names-19990114/#NT-NCName
> so completely migrating GO to the current
> recommended standards for
> the 'Semantic Web' is in some conflict with the
> existing GO naming
> convention. A simple solution would be to make the
> ID part of the term
>  <go:term rdf:ID="Gene_Ontology.0003673">      :the
> URI ref (a unique Qname)
>      <go:id>GO:0003673</go:id>		       :the ID
>      <go:name>Gene_Ontology</go:name>	       :the
> name
> 
> Neither the XML or RDF is easily read, so tools must
> be used. However,
> I really wonder whether flat anatomy files of
> 6000-7000 lines are easily and
> correctly read and modified either?
> Thoughts, comments?
> Stuart
> 
> 
> 
> Dr Stuart Aitken
> Artificial Intelligence Applications Institute
> The University of Edinburgh
> Appleton Tower, Room 3.08
> Crichton St
> Edinburgh EH8 9LE
> United Kingdom
> 
> http://www.aiai.ed.ac.uk/~stuart
> 
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