[tdwg-tag] Lobbing grenades: a challenge

Hilmar Lapp hlapp at nescent.org
Wed Sep 21 00:32:20 CEST 2011

Hi Rod -

that's a great question, and a good challenge. To be fair, I think  
this question, and the challenge, applies as much to the life sciences  
as a whole, and I'll admit that my view on what's been accomplished so  
far is rather skeptical, if we ask of the things that have been done,  
what couldn't also have been accomplished with "traditional" data  
integration approaches, in possibly less time. So with biodiversity  
science lagging behind the biomedical and other fields in this regard,  
it isn't a surprise that there aren't glaring success stories here yet.

That notwithstanding, there has been quite a bit of work in other  
fields (especially biomedicine) on using linked data and semantic web  
technologies towards data integration for the purposes of (enabling)  
scientific discovery (see refs below, and also http://www.w3.org/wiki/HCLSIG/LODD) 
, and these may help in imagining what could be achievable in our own  
domain. I'll also say, although I haven't been getting much traction  
on that among biodiversity informatics folks, that the most impactful  
of these relied critically on abilities to reason over the data.  
That's a step beyond RDF.

Belleau, François, Marc-Alexandre Nolin, Nicole Tourigny, Philippe  
Rigault, and Jean Morissette. 2008. “Bio2RDF: towards a mashup to  
build bioinformatics knowledge systems.” Journal of Biomedical  
Semantics 41 (5) (October): 706-16. doi:10.1016/j.jbi.2008.03.004.

Belleau, François, Nicole Tourigny, Benjamin Good, and Jean  
Morissette. 2008. Bio2RDF: A Semantic Web Atlas of Post Genomic  
Knowledge about Human and Mouse. In Data Integration in the Life  
Sciences (DILS), ed. Amos Bairoch, Sarah Cohen-Boulakia, and Christine  
Froidevaux, 153-160. Springer Berlin / Heidelberg. doi: 

Cheung, Kei-Hoi, Ernest Lim, Matthias Samwald, Huajun Chen, Luis  
Marenco, Matthew E Holford, Thomas M Morse, Pradeep Mutalik, Gordon M  
Shepherd, and Perry L Miller. 2009. “Approaches to neuroscience data  
integration.” Briefings in Bioinformatics 10 (4) (July): 345-53. doi: 

On Sep 20, 2011, at 4:40 AM, Roderic Page 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
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> _______________________________________________
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :

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