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Proposed change to GO RDF-XML export

chris mungall cjm at fruitfly.org
Tue Jun 6 15:12:21 PDT 2006


Hi all

We would like to make a change to the current GO RDF-XML. If you're  
not a user of the GO rdf exports, you can safely ignore this email

Currently the RDF is embedded in a root "go:go" element. If we  
removed this and made the rdf:RDF element the root element (currently  
nested under go:go) then the document would be RDF compliant without  
the need for modification of the file.

I realise some of you may be dependent on this file, and even minor  
changes may cause problems for your in-house tools or dataflow. If  
this is the case, let me know and I won't make changes until you're  
ready, and instead look into providing two separate files.

A little history may be in order: RDF is a W3C standard language for  
representing resources on the semantic web. It's graph or triple  
based. It has different serialisations, but the most common one is  
XML - the standard XML serialisation is often regarded as being  
awkward, and has certain disadvantages from an XML point of view,  
such as difficulty of processing and validation using standard XML  
tools. The Web ontology language OWL can be serialised in RDF,  
although other representations are possible.

The current GO OWL export is expressed as an RDF-XML document, but it  
should not be confused with the GO RDF-XML document. The GO RDF  
representation predates OWL. People are encouraged to use the OWL  
representation for the ontology - there is no OWL representation of  
the gene product associations, though this is coming soon. The first  
GO RDF export predated the Obo-XML exports, and at the time (and now)  
there was more demand for an XML format. As a result, the GO RDF  
drifted into a bona-fide XML format with its own DTD (which is  
unusual for an RDF representation). However, due to the nature of RDF  
this DTD will not remain stable in the face of certain changes to GO,  
such as the addition of new relations. With the proposed change, the  
RDF export will still be validatable by DTD, but it will also a valid  
RDF document. This change is being proposed as a recent increase in  
interest in RDF. Nevertheless, we'd still like to encourage use of  
the OWL version for the semantic webophiles.

Cheers
Chris

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