[seek-dev] Re: [SEEK-Taxon] some notes on digital object identifiers

Matt Jones jones at nceas.ucsb.edu
Tue Nov 18 08:38:14 PST 2003

Hey Dave,

I've looked at DOIs in particular for SEEK and earlier for Metacat 
development.  They hit all of the right points in terms of indirection, 
but miss a few other important features: 1) they are far too expensive, 
  2) they aren't human readable and have a restrictive syntax, and 3) 
they require a semi-proprietary lookup mechanism.

An alternative that provides the same functionality is the Open Grid 
Services Architecture Grid (OGSA) Grid Service Handle (GSH).  A GSH is 
an abstract identifier for an object without location semantics, and 
takes the form of a URI.  The GSH is resolved by a Grid HandleResolver 
into one or more actualy physical locations called Grid Service 
References (GSR), which are also URIs.  These services are "free" with 
the installation of grid software like the Globus Toolkit, and are 

The EcoGrid group is using the GSH/GSR mechanism to identify and locate 
data objects in the grid as well as identify and locate Grid Service 
instances (such as the EcoGrid Query servers, and computational services 
such as Garp).  We've been discussing the exact format of the URIs we'll 
be using for our handles, and so far are thinking of something along 
these lines, although its not final: 

If the taxon name services are going to be integrated as grid services, 
you'll need to support the GSH mechanism at least in terms of 
registering the name service nodes.  It might make sense to extend it 
further for your uses.

Hope this helps.

Kennedy, Jessie wrote:
> Hi Dave
> Remember I mentioned somebody using DOIs in taxonomy while in Lisbon - well
> it was George Garrity, Michigan - it was for prokaryotes - which might be
> different in terms of nomenclatural/concept taxonomy - but anyway - here's a
> link to the white paper he presented at the meeting I was at:
> http://www.eecs.umich.edu/~jag/wdmbio/garrity.htm
> you could maybe follow up to see if anything's happenned.
> Jessie
>>-----Original Message-----
>>From: thau at learningsite.com [mailto:thau at learningsite.com]
>>Sent: 17 November 2003 18:13
>>To: seek-taxon at ecoinformatics.org
>>Subject: [SEEK-Taxon] some notes on digital object identifiers
>>Hello everyone,
>>I've spent a little time looking into the role Digital Object 
>>(www.doi.org) might play in SEEK specifically, and taxon concept
>>registries in general.  Has anyone else looked at this stuff, or taken
>>interest in it?
>>DOI is a system for identifying, registering and sharing intellectual
>>property.  Many scientific journals are now giving their articles DOI
>>numbers and registering them with the DOI system.  In the 
>>simplest form,
>>the DOI number basically maps onto a URL.  The owner of the 
>>DOI number can
>>change the URL that the number maps to.  So, anyone 
>>referencing the number
>>using standard DOI resolution techniques will get sent to the 
>>correct URL.
>>That's the simplest incarnation of DOI.  You can also attach lots of
>>metadata to the number and search on the metadata.  The DOI 
>>doesn't have
>>to map to a URL, it can map to lots of different services too.
>>DOI is mainly targeted at publishers who use it to provide 
>>better access
>>to their content.  To get your DOIs, you have to make a deal with a
>>registering agent, kind of like with IP addresses.  
>>Alternatively you can
>>become a registering agent yourself, in which case you have 
>>to make a deal
>>with doi.org (officially, the International DOI Foundation (IDF)).  
>>Different registering agents allow for different metadata.  To get the
>>most out of using DOI for taxonomic information, someone 
>>would have to set
>>up what they call an application, which is an XML schema for 
>>the metadata
>>you want to attach to DOIs and potentially a set of services 
>>to query the
>>I think it's a pretty interesting type of registry.  If publishers of
>>species descriptions tagged the species names with DOIs, we'd have a
>>pretty good way of specifying which taxonomic concept someone 
>>meant when
>>they used a name, and a good way to link directly to the species
>>description.  Right now, publishers aren't doing this, but if 
>>there was a
>>project which supported DOIs, they might.
>>In terms of SEEK, it wouldn't be tough to include a way to 
>>include a spot
>>for storing a DOI (or any other registry identifier) in our 
>>about taxonomic concepts.  They just look like this: 10.1000/1234
>>All DOIs start with 10. something.  The something is a prefix 
>>assigned by
>>an registering agent. For example Nature has prefix: 1038. 
>>Following the
>>prefix, the publisher can use more or less any set of characters to
>>represent whatever piece of intellectual property they want 
>>to represent.  
>>An example article in Nature has doi:10.1038/35057062.  To get to the
>>article you can do this: http://dx.doi.org/10.1038/35057062
>>Has anyone else looked at DOIs?
>>seek-taxon mailing list
>>seek-taxon at ecoinformatics.org
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Matt Jones                                     jones at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
National Center for Ecological Analysis and Synthesis (NCEAS)
University of California Santa Barbara
Interested in ecological informatics? http://www.ecoinformatics.org

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