[API-users] Is there a GBIF specific LSID that can be used?

Roderic Page Roderic.Page at glasgow.ac.uk
Mon Aug 18 15:53:22 CEST 2014

Hi Rob,

At the risk of opening the whole taxon/name/concept can of worms, I’d see this a little differently.

For me a taxon name is a name + the original publication, rather than simply a text string. A taxon is different again, being essentially a statement about a collection of things that belong to the same taxon, and a statement of what to call them.

Taxon databases (e.g., GBIF) tend use strings for names, when it would be more elegant to use identifiers for names + publications.  We could go some way towards cleaning the mess we’ve accumulated if we adopted (and reused) identifiers for these things. For a start, name strings that don’t map to identifiers in nomenclators would immediately be under suspicion as being potentially erroneous. it also links names to evidence, which is something we’re spectacularly bad at doing at the moment.

For example,  "Pristimantis vilcabambae” is a text string which isn’t terribly useful. But if we combine that with details on where and when it was published we get something a bit more useful:

 "Pristimantis vilcabambae Lehr 2007 published in DOI http://dx.doi.org/10.3099/0027-4100(2007)159[145:NEFLPP]2.0.CO;2 “  This is the information I’m accumulating in BioNames, by combining metadata from ION LSIDs with data from CrossRef and BioStor , see http://bionames.org/names/cluster/1949681

Should this "name string + publication” get a DOI? Sure. Then I’d want GBIF (and other taxon databases) to link to this name on their taxon pages. In other words, http://www.gbif.org/species/2425396 should have an identifier for the taxon name, instead of simply using a text string.

I’m beginning to sound like Rich Pyle, and he and I would a lost certainly model these things differently, but name strings  <> taxon names <> taxa



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:  Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>
Tel:  +44 141 330 4778
Skype:  rdmpage
Facebook:  http://www.facebook.com/rdmpage
LinkedIn:  http://uk.linkedin.com/in/rdmpage
Twitter:  http://twitter.com/rdmpage
Blog:  http://iphylo.blogspot.com
ORCID:  http://orcid.org/0000-0002-7101-9767
Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ

On 18 Aug 2014, at 14:29, Robert Guralnick <Robert.Guralnick at colorado.edu<mailto:Robert.Guralnick at colorado.edu>> wrote:

  Markus --- I think the answer to the question: "Would a taxon DOI be a valuable feature for you?" really depends on some of the details.  With a taxon name, you are putting a DOI on a string and one that has been dissociated from its source(s).  I would think more valuable would be a DOI linked to the checklist that contained the name, and maybe a passthrough (a la suffix passthroughs in the EZID system) to the individual name.  That way I can resolve that taxon name to the source from whence it came.

Best, Rob

On Mon, Aug 18, 2014 at 3:44 AM, Markus Döring <mdoering at gbif.org<mailto:mdoering at gbif.org>> wrote:
Hello Geoff,

GBIF uses simples integers as taxon identifiers, for example 2396049 for Ecsenius bicolor.
These ids are stable, but obviously not globally unique. If you need a URI right now I would recommend for now to use our restful portal URL:

For the future I could imagine us assigning DOIs to taxa reusing the current integer ids, but that has to be carefully evaluated first.
Would a taxon DOI be a valuable feature for you?


Markus Döring
Software Developer
Global Biodiversity Information Facility (GBIF)
mdoering at gbif.org<mailto:mdoering at gbif.org>

On 05 Aug 2014, at 05:17, Geoff Shuetrim <geoff at galexy.net<mailto:geoff at galexy.net>> wrote:

> Working with a range of web services, I have found myself making extensive use of the LSIDs that are specific to each data source.  For example, for ITIS, I use the Ecsenius bicolor LSID: urn:lsid:itis.gov:itis_tsn:636326
> For WoRMS, the LSID for Ecsenius bicolor is: urn:lsid:marinespecies.org:taxname:277652
> For Atlas of living Australia the LSID for Ecsenius bicolor is:
> urn:lsid:biodiversity.org.au:afd.taxon:99c29e7c-5b04-4e57-8e6b-82aa442a801a
> Is there a GBIF LSID that can similarly be used as a unique identifier for a taxon? I have come across the various GBIF unique keys but these are not unique outside of the GBIF environment and within the Gaia Guide systems I am deciding how best to work with these, ensuring their uniqueness, alongside identifiers from other data sources.
> Thanks again for your assistance.
> Geoff Shuetrim
> Gaia Guide Association
> http://www.gaiaguide.info/
> _______________________________________________
> API-users mailing list
> API-users at lists.gbif.org<mailto:API-users at lists.gbif.org>
> http://lists.gbif.org/mailman/listinfo/api-users

API-users mailing list
API-users at lists.gbif.org<mailto:API-users at lists.gbif.org>

API-users mailing list
API-users at lists.gbif.org<mailto:API-users at lists.gbif.org>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.gbif.org/pipermail/api-users/attachments/20140818/588b10d2/attachment-0001.html 

More information about the API-users mailing list