How would you answer your question about 1. XML 2. XML validated by XML-Schema 3. CSV 4. ASCII dumps of relational data If there is an answer, X, for one of those, an answer to your challenge will, often, be that RDF accomplishes things like X but without difficult D, for various values of D. It's also arguable, that the formal semantics available to the RDF stack and other ontology-based data representation schemes, allows the building hypothesis testing software, sometimes more easily than, for example, data mining. The biomedical community has been doing that for 30 years or more. Most other sciences are just now getting with the program. On Tue, Sep 20, 2011 at 4:40 AM, Roderic Page <r.page@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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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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-- Robert A. Morris Emeritus Professor  of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob@gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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. -hilmar 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: 10.1007/978-3-540-69828-9_15. 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: 10.1093/bib/bbp029. 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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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 : ===========================================================

Rod, 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 lot. 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. greg On 20 September 2011 18:40, Roderic Page <r.page@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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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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-- Greg Whitbread Australian National Botanic Gardens Australian National Herbarium +61 2 62509482 ghw@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

Rod, On Tue, 20 Sep 2011, 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?

How I would love for this to happen. I've created a page on the wiki to inventory the data that we'll probably want to load: http://code.google.com/p/tdwg-rdf/wiki/DataInventory I'll start populating this in the coming days, but invite you (and anyone else who knows of biodiversity triples ready for loading) to beat me to it. Thanks for the challenge - Joel.

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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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