[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
today.
Dave.
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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