[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
community.
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?
Regards
Rod
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
>
>
> _______________________________________________
> Tdwg-tag mailing list
> Tdwg-tag at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-tag_lists.tdwg.org
>
>
------------------------------------------------------------------------
----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom
Phone: +44 141 330 4778
Fax: +44 141 330 2792
email: r.page at bio.gla.ac.uk
web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
Subscribe to Systematic Biology through the Society of Systematic
Biologists Website: http://systematicbiology.org
Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org
Rod's rants on phyloinformatics: http://iphylo.blogspot.com
___________________________________________________________
Yahoo! Messenger - NEW crystal clear PC to PC calling worldwide with voicemail http://uk.messenger.yahoo.com
More information about the tdwg-tag
mailing list