[tdwg-tag] Lobbing grenades: a challenge [SEC=UNCLASSIFIED]

greg whitbread ghw at anbg.gov.au
Thu Sep 22 16:13:37 CEST 2011


I have to admit that here in Canberra we have spent quite a bit of
time on this "RDF" thing.  There is little visible yet ( other than
names, taxa and publications) but from the process we have learnt a

The first thing is that simply converting biodiversity data to RDF
does not add anything of value - though it may work to simplify data
delivery or presentation.

Secondly, we have learned that the ways we have been modelling
biodiversity data and developing "standards" in the for our domain are
most inappropriate for the kinds of semantic interoperability that I
think we should be striving to achieve.     It is very obvious that we
need to get serious about stepping back and agreeing to keep our
ontologies small.  Just large enough to satisfy use cases within a
domain - adhering to that golden section that guarantees our
vocabularies and their classes exhibit the very best semantic
behaviour.  RDFS and OWL may represent our best opportunity to revisit
the "model" without breaking those parts of our legacy systems that
have proved so useful for aggregation and interchange - and protecting
sensitive toes.

Thirdly, our existing vocabularies do not offer the richness required
by client systems wanting to deliver the value added product that
might lead to real  community benefits.  It is not possible to use
these vocabularies to  publish scientifically accurate renderings of
our biodiversity information holdings.  Our institutional offerings
are bespoke yet our clients need to do what we do.  We lose so much in
translation to canonical representations that complicate the process
of reusing scientific content in scientifically defensible ways.

Last, but not least ( in this abbreviated list), it is quite hard to
do.  The mercurial nature of linked data in the wild means that we
have to get our API right before we really let it go.  It is much
easier to add something that proves necessary than it is to take an
unnecessary thing away.  We could use a moratorium on the "cool data"
contract to allow for a period for experimentation while we get the
schema right and develop the confidence to really do linked data - not
just RDF.


On 20 September 2011 18:40, Roderic Page <r.page at bio.gla.ac.uk> wrote:
> It's morning and the coffee hasn't quite kicked in yet, but reading through
> recent TDWG TAG posts, and mindful of the upcoming meeting in New Orleans
>  (which sadly I won't be attending) I'm seeing a mismatch between the amount
> of effort being expended on discussions of vocabularies, ontologies, etc.
> and the concrete results we can point to.
> Hence, a challenge:
> "What new things have we learnt about biodiversity by converting
> biodiversity data into RDF?"
> I'm not saying we can't learn new things, I'm simply asking what have we
> learnt so far?
> Since around 2006 we have had literally millions of triples in the wild
> (uBio, ION, Index Fungorum, IPNI, Catalogue of Life, more recently
> Biodiversity Collections Index, Atlas of Living Australia, World Register of
> Marine Species, etc.), most of these using the same vocabulary. What new
> inferences have we made?
> Let's make the challenge more concrete. Load all these data sources into a
> triple store (subchallenge - is this actually possible?). Perhaps add other
> RDF sources (DBpedia, Bio2RDF, CrossRef). What novel inferences can we make?
> I may, of course, simply be in "grumpy old arse" mode, but we have millions
> of triples in the wild and nothing to show for it. I hope I'm not alone in
> wondering why...
> Regards
> Rod
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com
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Greg Whitbread
Australian National Botanic Gardens
Australian National Herbarium
+61 2 62509482
ghw at anbg.gov.au

"And therfore, at the kynges court, my brother,
Ech man for hymself, ther is noon oother."
The Knight's Tale, l. 1181-1182

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