[tdwg-content] Identifier limbo
parrc at si.edu
Tue Jun 7 03:44:31 CEST 2011
Just wanted to chime in that I'm associated with one of those "major
players" (though not in a particularly technical way) and we very much
appreciate having researchers exploring the options and proposing fruitful
approaches. I'm glad you are in Woods Hole, Pete. And we're working to
convince publishers that linking is of value. We'll get there.
On Mon, Jun 6, 2011 at 2:36 PM, Roderic Page <r.page at bio.gla.ac.uk> wrote:
> Dear Pete,
> A few quick comments:
> 1. The point about DOIs is that (if we are talking about CrossRef DOIs) we
> get citation and cross linking. Identifiers by themselves aren't much use,
> it's the links that matter, both forward and back. If we had a "CrossRef for
> biology" we'd be well on the way to being able to do useful things.
> 2. DOIs can be linked data compliant (this happened a few weeks ago when
> CrossRef flicked a switch and started pumping out RDF.
> 3. Enough with the "major players" already -- I'm all for two guys in a
> garage (or one guy in my case), that's where innovation comes from. But
> we're not talking about innovation, we're talking about getting a large
> bunch of disparate organisations to effect a change in the way we do things.
> If, say, GBIF started issuing resolvable identifiers for every specimen, and
> go publishers, authors, and GenBank to use those, we could do some cool
> things. But there seems to me to be a lack of ambition, hence we muck around
> with toy projects.
> On 6 Jun 2011, at 18:53, Peter DeVries wrote:
> > 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
> > http://lod.taxonconcept.org/ontology/phylo/CoL/CoL_2010_base.owl
> > 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
> > In regards to DOI's, it don't see how they add more value than simple
> > 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?
> > Respectfully,
> > - Pete
> > On Mon, Jun 6, 2011 at 4:21 AM, Roderic Page <r.page at bio.gla.ac.uk>
> > 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 (
> > 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
> > 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 & GeoSpecies Knowledge Bases
> > A Semantic Web, Linked Open Data Project
> 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
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
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