On Mon, Jun 6, 2011 at 4:21 AM, Roderic Page <r.page@bio.gla.ac.uk> wrote:

Reading this thread makes me despair. It's as if we are determined not to make progress, forever debating identifiers and what they identify, with seemingly little hope of resolution, and no clear vision of what the goals are. We wallow in acronym soup, and enjoy the technical challenges, but don't actually get anywhere (http://iphylo.blogspot.com/2010/04/biodiversity-informatic-fail-and-what.html )

Here's one vision of a way forward.

1. Someone or some entity shows a little vision and courage, and provides a taxonomic classification where every node in the tree gets a DOI.

2. The nodes in the taxonomic classification are citable objects (hence the DOIs).

3. Nodes in the classification can be accessed either by DOI or by name-based HTTP URI (multiple nodes for a name bounce to ambiguity resolution pages).

4. A taxon-name extraction service locates names in text.

5. We build a taxon name/literature index (which we pretty much have already, albeit distributed and partly proprietary).

Now, when an author (in any field) writes a paper or publishes some data on a taxon they cite the node in the classification as they would any scientific paper. Through CrossRef's citation tracking mechanism, the taxon database automatically accumulates the scientific literature relevant to that taxon.

When a journal publishes an article it calls the name extraction service to make the names clickable, avoiding the need for the journal to create its own taxon pages (a la Pensoft), and automatically building a taxonomic index to the literature. Publishers get enriched content, we get an always up to date taxonomic index.

So, we have services that authors and publishers can use, and use an identifier scheme that publishers understand (and so do some, if not most authors).

But you say "what about RDF and the linked web?". Relax, DOIs are now linked data compliant.

But you say "what about versions?" OK, to a first approximation nobody cares about versions. They really don't. Obviously previous versions will be accessible, but the identifier always points to the most recent version.

But you say "ah but it costs money". Yep, anything worthwhile does. Last time I checked journals costs money, yet we seem to have lots of those.

But you say, "which classification to use?" Does anybody (outside taxonomy) actually care? Classification is a navigational convenience. If you care deeply, you'll make a phylogeny.

But you say, "why DOIs?" Several reasons, 1) publishers and authors understand them, 2) they avoid branding 3) there's an infrastructure underpinning them 4) they show that we are serious

But "what about different taxon concepts?" To a first approximation nobody cares, and for the bulk of life we know too little for there to be much ambiguity. If we do care we can read the literature, which we have conveniently indexed.

Now, there are lots of things we could argue about, but if, say, EOL had done something like this at the start, namely embedded itself in the publication process, and major journals were citing EOL pages and linking to EOL pages, we would have a wonderful tool that was actually useful, way outside our own narrow concerns. Note that I'm using EOL has an example of an organisation with sufficient scope, GBIF would be another candidate.

I suspect a major reason for our continued failure is a the lack of clearly identified users (and I don't mean people who read this list, or TAXACOM), and a failure of ambition.

Anyway, my coffee has arrived. I don't hold out much hope of any of this happening, and I fully expect us to be debating these issues in a year from now. Pity.

Regards

Rod

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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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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries@wisc.edu
TaxonConcept & GeoSpecies Knowledge Bases
A Semantic Web, Linked Open Data Project
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