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Re: [BioRDF] Meeting Notes Feb 27, 2006

From: Matthias Samwald <samwald@gmx.at>
Date: Wed, 1 Mar 2006 12:22:54 +0100
To: <public-semweb-lifesci@w3.org>
Message-ID: <200631131337.268614@cqueberel>

> I'm not too optimistic about technologies such as XSLT, except
> perhaps for trivial cases; my feeling is that most (bioinformatics)
> databases have data models that are such that nothing but a full
> blown programming language will do.

XSLT definitly is not sufficient for such conversions, I agree. XQuery, however, is much more powerful than XSLT and has most features of a 'full blown programming language'. Using XQuery abolishes the need to commit to a certain programming language - queries can be run from an XML editor like XMLSpy or from any program that has an API for XQuery.

> (And a lot of manual clean up
> work may be required in addition.)

I agree with that, too. This might be a major problem for the transition from non-RDF- to RDF - based bioinformatics. People will not switch to RDF from one day to the other, so you need a transitional period where you offer your data both in non-RDF and in RDF format (like Reactome does, for example). The problem is that most databases are growing steadily, and you have to keep both versions updated. This is severly complicated because of the inevitable need for manual clean-up work that has to be done prior to the conversion to RDF.

kind regards,
Matthias Samwald
Received on Wednesday, 1 March 2006 12:13:50 UTC

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