[Tdwg-tag] RDF instead of xml schema

Roderic Page r.page at bio.gla.ac.uk
Mon Mar 27 15:11:26 CEST 2006

Dear Gregor.

My initial reaction would be that RDF is great for data sharing, in  
fact it makes it easy because it comes with built in semantics so that  
applications can "know" which tags refer to what entities. One doesn't  
need to struggle with XML schema to figure out what is going on, and  
the use of standard vocabularies and URIs makes it easy to share widely  
(i.e., way beyond this community).

In the case of marking up taxonomic literature, I would use RDF for  
summary metadata (such as bibliographic details, lists of taxonomic  
names, etc.), but use XML to markup the document itself. The main  
reason for this is that in a document order matters, there is clear  
structure, and one could borrow existing efforts, such as the US NLM's  
DTD (http://dtd.nlm.nih.gov/publishing/1.1/journalpublishing.dtd),  
which is being adopted by Open Access journals such as PLoS and BMC.  
Indeed, I think the simplest strategy would be to add to this DTD,  
given that it defines a lot of the basic structure of a publication,  
and comes with additional tools (for examples, there are XSLT style  
sheets around to render this XML into something nice). Again, I fear  
there are a lot of wheels being reinvented.

Furthermore, if the goal of marking up taxonomic literature is to get  
to the point where taxonomic publications are produced with this markup  
in the first instance (i.e., not done after the fact), then you really  
want to use something that publishers use. For instance, why not add a  
taxonomic name module to the NLM DTD, and start an Open Access journal?  
OK, so there ar eother issues involved, but this would be a quick way  
to get there, rather than with a DTD/Schema that is unique to this  

For SDD, well I'd be inclined to go for RDF, and keep it as lightweight  
as possible by referring to things like taxa, publications, images  
using URIs. My sense from looking at SDD is that it is enormously  
complex, partly because it tries to include far more information than  
it needs to (why does it need to know about people, telephone  
numbers(!), publications, etc. -- these can all be dealt with by other  
vocabularies and referred to by URIs). Why not have a core that covers  
what SDD is actually about?



On 27 Mar 2006, at 09:59, Gregor Hagedorn wrote:

> (Moving this from SDD list to Tdwg-tag list...)
> Dear Roderic
> many thanks for your answers.
>> triples in one table with three columns (subject, predicate, object).  
>> I
>> guess for most people the issue is getting data out of RDBMS into RDF,
>> not the other way around.
> SDD and TaxMLit are about building tools for biology to create and  
> share
> descriptive data, identification keys, online digital taxonomic  
> monographs.
> These are knowledge documents - intended to replace their printed  
> equivalents.
> Many people hopefully will produce them and share (or even sell them)  
> under
> various schemes - hopefully often under open licenses like cc.
> Building these tools is a huge amount of work. The vision of SDD is  
> not only to
> share data in a one-way street, but to share the work of applications  
> by having
> specialized application that read data, do the thing they can best,  
> write them
> back for the next app that does something else better. Ideally nothing  
> should
> be lost in this process.
> I realize that RDF is a good solution for the DiGIR kind of data  
> advertisement,
> but is it good for data sharing?
>> Tools
>> -------
>> As one who positively hates the diagrams XMLSpy produces I'm biased,
>> but when  I played with Altova SemanticWorks I was distinctly
>> underwhelmed.
> What can we use then? Is there any UML-tool (static class class  
> diagram would
> be fine for a start) that automatically produces RDFS?
> (I still do not understand whether RDFS attempts to cover the  
> syntactical
> knowledge required for static class diagram - but other posts seem to  
> imply
> this)
> Gregor----------------------------------------------------------
> Gregor Hagedorn (G.Hagedorn at bba.de)
> Institute for Plant Virology, Microbiology, and Biosafety
> Federal Research Center for Agriculture and Forestry (BBA)
> Königin-Luise-Str. 19           Tel: +49-30-8304-2220
> 14195 Berlin, Germany           Fax: +49-30-8304-2203
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Professor Roderic D. M. Page
Editor, Systematic Biology
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University of Glasgow
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