[SEEK-Taxon] some notes on digital object identifiers
Kennedy, Jessie
J.Kennedy at napier.ac.uk
Thu Nov 20 02:49:53 PST 2003
Hi Jim
I guess I'm not really thinking about strategic questions at the moment, I
think that firstly we have to find a mechanism to handle concepts that is
acceptable and that allows us to reason about the similarity of concepts
first of all. Of course concepts will have unique ids in our system but
whether or not we use GSH or DOIs is not initially so important. When we get
a good meachanism for doing what we want, then I think we can decide on
which kind of id we opt for. I think we suggested that in SEEK we would not
see us as being the long term provider of a taxonomic concept service
(agreed?), but that we are developing a prototype to show the potential, so
maybe it's not the most important issue for us but will be for whomever will
be the group/organisation that does provide such a service long term.
I still think it is interesting to think about and dicsuss the pros and cons
of the different approaches as you have started it's only that I think it's
secondary to getting the cocnept resolution server issues sorted. Once we
can demonstrate it in the SEEK environement we can then dicsuss the issues
more widely and come to a better conclusion. If we need to use GSH to get
things working in SEEK then also I think we have to go that route. I guess
Matt has the best idea here of how much scope there is for different
approaches and should guide us there.
So I'm interested but not active on this.......
Jessie
> -----Original Message-----
> From: Beach, James H [mailto:beach at ku.edu]
> Sent: 18 November 2003 18:37
> To: seek-taxon at ecoinformatics.org
> Subject: RE: [SEEK-Taxon] some notes on digital object identifiers
>
>
> SEEK--Taxon Members:
>
> Here are some *strategic* thoughts on the choice of taxon name and
> concept identifiers for consideration. (I am not actually
> advocating for
> DOIs, but asking questions here about how we evaluate them as a
> strategic option.)
>
>
> I think we do want to consider and deliberate on the issue of
> DOIs very
> carefully. There are some immediate constraints like the
> economic model
> the DOI foundation uses to sell DOIs and their fees. I think the
> strategic value of the identifier for SEEK and for ECOINFORMATICS.ORG
> and for NSF.GOV and for the research community needs to be carefully
> considered in the evaluation of an ID architecture. Tactical
> implementation problems can be made to go away through clever
> design and
> negotiation with third parties--if the strategic value is great enough
> to justify any particular approach.
>
> The white paper that Jessie provides a URL for below is a
> thought piece
> that fairly points out the advantage of using DOIs for names and
> concepts because of their value as links into other active, related
> communities, especially scientific publishers that use them. Although
> none of them are to my knowledge using DOIs yet at the level of
> scientific names in their publications, the use of them for finer and
> finer levels of DO resolution is a long-term trend and the
> likely future
> direction of the technology - at least for publishers who are
> relatively
> rich compared to us and relatively longer-lived. It makes
> economic sense
> for them to use them for cross-referencing, it brings more
> eyes to their
> scientific content.
>
> The white paper points out several advantages in this context
> that would
> not be present in the foreseeable future with GRID resource IDs.
>
> So say, one of our *strategic* objectives for SEEK was to have a
> cross-sector demonstration of linking and navigation between the
> published scientific literature (mostly copyrighted and owned by the
> publishers) and the taxon name and concept services in SEEK. Which
> identifiers would you choose for that?
>
> Say you wanted to get BioOne or Allen Press which handle most of the
> worlds taxonomic literature involved with us perhaps on the advisory
> board or in some consultative collaboration--which kind of identifier
> would we have in common with them?
>
> In the early days of the Species Analyst, I promoted Z39.50 to Dave
> Vieglais for his consideration because it had a development
> community of
> 300+ souls and dozens of commercial library system vendors which could
> be counted on to move the standard forward with all of their
> funding and
> resource base. Using Z would also have made us very popular with the
> library integration crowd who would like to integrate other academic
> holdings besides serials and books into their campus collections
> management systems. But the story changed when HTTP and XML came on
> strong and DIGiR provided a more open accessible approach for more
> developers in more of the mainstream. But no library will ever speak
> DIGiR, we gave up that possibility, integration between research
> publication databases and research collections will happen but at
> another level, not with Z.
>
> But, here I think SEEK has another strategy-level
> consideration. Do we
> choose technologies (in this case identifiers) to make SEEK as
> internally homogeneous as possible as a deliberate strategic choice to
> increase our development efficiency and software supportability?
>
> Or do we look for technologies that would potentially (if the
> implementation and economic issues can be cleared) make SEEK more
> relevant and integrative with other segments of the research
> community,
> in this case research publishers-both for profit and not-for-profit
> (like all the society based publishers), but also potentially with
> places like NLM, libraries, OCLC, Zoo Record, ITIS, etc.
>
> Who's worrying about the strategic aspects of these technology choices
> besides me?
>
>
> --------------------------------
> James H. Beach
> Biodiversity Research Center
> University of Kansas
> 1345 Jayhawk Boulevard
> Lawrence, KS 66045, USA
> Tel: 785 864-4645, Fax: 785 864-5335
> Televideocon: (H.323): 129.237.201.102
>
>
>
> > -----Original Message-----
> > From: Kennedy, Jessie [mailto:J.Kennedy at napier.ac.uk]
> > Sent: 18 November, 2003 10:21 AM
> > To: 'thau at learningsite.com'; seek-taxon at ecoinformatics.org
> > Subject: RE: [SEEK-Taxon] some notes on digital object identifiers
> >
> >
> > 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
> > >
> > >
> > > _______________________________________________
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> > > seek-taxon at ecoinformatics.org
> > > http://www.ecoinformatics.org/mailman/listinfo/seek-taxon
> > >
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