[tdwg-content] Identifier limbo

Peter DeVries pete.devries at gmail.com
Mon Jun 6 19:53:04 CEST 2011

Hi Rod,

There is no reason that the EoL, GBIF or both could not adopt and take
ownership of what I am working on.

We have been testing different approaches and models as well as discussing
various ways that this could be done.

I am actually with some of the MBL Woods Hole  people today.

Since my taxonconcepts don't entail  a particular classification, you can
apply what ever classification you think is most appropriate.

*A species concept can have many classifications*

I have created a basic classification ontology that follows the Catalog of
Life to Orders


HTML Doc http://lod.taxonconcept.org/ontology/phylo/CoL/doc/index.html

and Bio2RDF/Uniprot have a system based on NCBI taxon_id's

Example http://purl.uniprot.org/taxonomy/27807

<http://purl.uniprot.org/taxonomy/27807>In regards to DOI's, it don't see
how they add more value than simple URI's.

In addition, they continue the problem of an identifier that is not the same
as its form of resolution. With URI's, the identifier is the address to the
informative documentation.

In addition, if we were to adopted DOI's, we would have the same problem
that we have with LSID's - an identifier system that works unlike anything
else in the semantic web.

It is difficult for the EoL or GBIF to anticipate all the issues and design
a system *a priori* that will work and be accepted.

For now, I believe their best approach is to facilitate the discussion and
test various ideas and approaches. Which I believe they are doing.

Despite your argument that this process should really only include the
"major players", they seem to be open to considering ideas from the entire

In the area of computers and information technology, how many of the major
innovations came from the "major players" vs two drop outs in a garage or as
the side project of some graduate students?


- Pete

On Mon, Jun 6, 2011 at 4:21 AM, Roderic Page <r.page at 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
> ---------------------------------------------------------
> 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

Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries at wisc.edu
TaxonConcept <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
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