[tdwg-guid] BioGUID
Roderic Page
r.page at bio.gla.ac.uk
Wed Mar 21 16:21:26 CET 2007
Dear Chris,
Damn, I was hoping nobody would ask about specifics as that would
expose the fact that I've not thought much (any) of this through.
My instinct is that for those bits that will interact with existing
publishers (e.g., will be cited in lists of references in papers), then
DOIs are the logical choice. Hence, article and monograph-level would
get DOIs. This would satisfy the desire to make taxonomic literature as
visible to readers. It would also not require CrossRef to change any
metadata that they serve.
For within-monograph (e.g., pages), then I guess the issue boils down
to (a) cost, and (b) what metadata would be served? Here, I'd be happy
with Handles (there's nothing stopping us having Handles for the
articles and monographs as well as DOIs).
So, we could have
Article: DOI:xxxxxx HDL:yyyyyyyy
Monograph: DOI:xxxxxxx HDL:yyyyyyyyy
p. 1 HDL:yyyyyyyy.1
p. 2 HDL:yyyyyyyy.2
.
.
p. n HDL:yyyyyyyy.n
In some ways it would be ideal to have a single GUID, but if DOIs are
too costly then I still think we need DOIs for integration. I also
wonder whether we need DOIs for page elements. When are they going to
be used? I suspect, only in the context of (a) old literature being
marked up, or new online taxonomic publications (say if BMC published a
journal). In both cases, the underlying XML could be structured in such
a way to recognise Handles.
Hope this makes sense. My instinct is that authors of a paper in
Science, say, just want to cite a monograph or article, but somebody
doing a taxonomic revision may want a much finder degree of
citation, and in an ideal world they would be doing this electronically
online.
Regards
Rod
On 20 Mar 2007, at 17:37, Chris Freeland wrote:
> Rod,
>
> Fascinating stuff, as always. DOIs have come up time and again in
> discussing the Biodiversity Heritage Library and I wondered if you had
> any thoughts about DOIs for historic literature. You were fairly
> adamant at the EoL meeting in Woods Hole in February that DOIs were
> critical for BHL, which we can all agree, but the unresolved question
> is
> at what level(s) we need DOIs. For serials it makes sense to assign at
> the article level, but what about as detailed as page-level DOI or as
> broad as title-level DOI? What then of monographs - would you want a
> DOI at the page for protologue linking? Looking forward to your
> thoughts,
>
> Chris
> *******************************
> Chris Freeland
> Application Development Manager
> Missouri Botanical Garden
> (314) 577-9548
>
> -----Original Message-----
> From: tdwg-guid-bounces at lists.tdwg.org
> [mailto:tdwg-guid-bounces at lists.tdwg.org] On Behalf Of Roderic Page
> Sent: Tuesday, March 20, 2007 9:15 AM
> To: tdwg-tag at lists.tdwg.org; tdwg-guid at lists.tdwg.org
> Cc: Simon Rycroft; Vince Smith; David Remsen; Donat Agosti; William
> Piel
> Subject: [tdwg-guid] BioGUID
>
> Dear All,
>
> I've put together a web site called http://bioguid.info which, rather
> grandly, is an attempt to bootstrap the biodiversity Semantic Web by
> providing resolvable URIs for biological objects, such as publications,
>
> taxonomic names, nucleotide sequences, and specimens.
>
> These URIs (or "GUIDs") can be resolved by a web browser to display
> HTML, but under the hood are resolved to RDF (which you can see by
> viewing the source of the web page you get for a URI).
>
> The web interface is really window dressing, I just wanted a way to
> display RDF that wouldn't frighten people (me included). For some URIs
> all I do is grab XML and reformat it (e.g., DOIs). For GenBank records,
>
> all manner of agony is involved in trying to extract specimen and
> publication links.
>
> A good place to get a sense of what bioguid.info is about is to start
> with this Pubmed record: http://bioguid.info/pmid:17079492
>
> From this, you can get a list of sequences. If you click on one of
> those, you'll see a link to a specimen, which you can then look at
> (you'll need Firefox 1.5, Camino, Webkkit, or a browser with a SVG
> plugin for the full effect).
>
> What I'm hoping to do is start doing things like taking a TreeBASE
> record, getting the linked sequences, running these through
> bioguid.info to extract georeferenced specimen links, so with minimal
> effort we get a map (and eventually a Google Earth tree a la Bill
> Piel).
>
> The glue to make this happen comprises HTTP URIs that are
> dereferenceable to RDF. This is my mantra for the day.
>
> Regards
>
> Rod
>
>
>
>
> -----------------------------------------------------------------------
> -
>
> ----------------------------------------
> Professor Roderic D. M. Page
> Editor, Systematic Biology
> DEEB, IBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QP
> United Kingdom
>
> Phone: +44 141 330 4778
> Fax: +44 141 330 2792
> email: r.page at bio.gla.ac.uk
> web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> iChat: aim://rodpage1962
> reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
>
> Subscribe to Systematic Biology through the Society of Systematic
> Biologists Website: http://systematicbiology.org
> Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
> Find out what we know about a species: http://ispecies.org
> Rod's rants on phyloinformatics: http://iphylo.blogspot.com
> Rod's rants on ants: http://semant.blogspot.com
>
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>
------------------------------------------------------------------------
----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom
Phone: +44 141 330 4778
Fax: +44 141 330 2792
email: r.page at bio.gla.ac.uk
web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
iChat: aim://rodpage1962
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
Subscribe to Systematic Biology through the Society of Systematic
Biologists Website: http://systematicbiology.org
Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org
Rod's rants on phyloinformatics: http://iphylo.blogspot.com
Rod's rants on ants: http://semant.blogspot.com
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