[tdwg-content] Identifier limbo

Robert Huber rhuber at wdc-mare.org
Wed Jun 8 11:13:50 CEST 2011

This is a bit OT, but it's related to dois ...I'm sure you noticed L
Penevs (pensoft) post at taxacom:

>Instructions to authors wishing to submit Data Papers based on metadata
>entered via GBIF’s IPT can be found in the  Data Publishing Policies and G
>by Pensoft.

>From this document:

"The well-established norm for citing genetic data is that one simply cited the
Genbank identifier (accession number) in the text. Similar usage is
also commonplace
for items in other bioinformatics databases. Pensoft is not recommending a
change in that practice.
The following guidelines apply to more heterogeneous research
data published in other institutional or subject-specific data
repositories, frequently
described in related journal articles or Data Papers (see below). They are
intended to permit data citations to be treated as ‚first class‘
citation objects, on a par
with bibliographic citations, and to enable them to be more easily
harvested from
reference lists, so that those who have made the effort to publish
their research data
might more easily be ascribed academic credit for their work through the normal
mechanisms of citation recognition.
For such data in data repositories, each published data package and
each published
data file should always be associated with a persistent unique
identifier. A Digital
Object Identifier (DOI) issued by DataCite should be used wherever possible."

best regards,

On Mon, Jun 6, 2011 at 11:35 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
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Dr. Robert Huber,

WDC-MARE / PANGAEA - www.pangaea.de
Stratigraphy.net - www.stratigraphy.net
MARUM - Center for Marine Environmental Sciences
University Bremen
Leobener Strasse
POP 330 440
28359 Bremen
Phone ++49 421 218-65593, Fax ++49 421 218-65505
e-mail rhuber at wdc-mare.org

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