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

thau@learningsite.com thau at learningsite.com
Tue Nov 18 08:55:51 PST 2003

This is very helpful!  I'll start sinking my teeth into the GSH mechanism


On Tue, 18 Nov 2003, Matt Jones wrote:

> 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 
> non-proprietary.
> 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: 
> ecogrid://some.registered.institution/identifier/subid/subid/...
> 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.
> Matt
> 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 
> >>Identifiers
> >>(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
> >>metadata.  
> >>
> >>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 
> >>information
> >>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?
> >>
> >>Dave
> >>
> >>
> >>_______________________________________________
> >>seek-taxon mailing list
> >>seek-taxon at ecoinformatics.org
> >>http://www.ecoinformatics.org/mailman/listinfo/seek-taxon
> >>
> > 
> > _______________________________________________
> > seek-taxon mailing list
> > seek-taxon at ecoinformatics.org
> > http://www.ecoinformatics.org/mailman/listinfo/seek-taxon
> -- 
> -------------------------------------------------------------------
> 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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