University of Glasgow

Roderic Page

Following on from the discussion of [BHL and
DOIs](http://iphylo.blogspot.com/2007/10/bhl-and-dois.html), I stumbled
across some remarkable work by Robert Cameron at SFU. Cameron has
developed Universal Serial Item Names (USIN). The approach is spelled
out in detail in [Towards Universal Serial Item
Names](http://journals.tdl.org/jodi/article/view/jodi-12/10) (also on
[Scribd](http://www.scribd.com/doc/432360/Toward-Universal-Serial-Item-Names)).
This lengthy document deals with how to develop user-friendly
identifiers for journal articles, books, and other documents. The
solution looks less baroque than SICIs, which I\'ve [discussed
earlier](http://iphylo.blogspot.com/2007/06/making-taxonomic-literature-online.html).  
  
There is also a web site ([USIN.org](http://usin.org)), complete with
examples and source code. Identifiers for books are straightforward, for
instance
[bibp:ISBN/0-86542-889-1](http://usin.org/bibp1.0/resolve?usin=ISBN/0-86542-889-1)
identifies a certain book:  

  
For journals things are slightly more complicated. However, Cameron
simplified things a little in his subsequent paper [Scholar-Friendly DOI
Suffixes with JACC: Journal Article Citation
Convention](ftp://fas.sfu.ca/pub/cs/TR/1998/CMPT1998-08.html) (also on
[Scribd](http://www.scribd.com/doc/432354/ScholarFriendly-DOI-Suffixes-with-JACC-Journal-Article-Citation-Convention)).  

> JACC (Journal Article Citation Convention) is proposed as an
> alternative to SICI (Serial Item and Contribution Identifier) as a
> convention for specifying journal articles in DOI (Digital Object
> Identifier) suffixes. JACC is intended to provide a very simple tool
> for scholars to easily create Web links to DOIs and to also support
> interoperability between legacy article citation systems and DOI-based
> services. The simplicity of JACC in comparison to SICI should be a
> boon both to the scholar and to the implementor of DOI responders.

  
USIN and JACC use the minimal number of elements in order to identifier
an article, such as journal code (e.g., ISSN or an accepted acronym),
volume number, and starting page. Using ISSNs ensures globally unique
identifiers for journals, but the scheme can also use acronyms, hence
those journals that lack ISSNs could be catered for. The scheme is
simple, and in many cases will provide the bare minimum of information
necessary to locate an item via an OpenURL resolver. Indeed, one simple
way to implement USIN identifiers would be to have a service that takes
URIs of the form :@ and resolves them behind the scenes using OpenURL.
Hence we get simple identifiers that are resolvable, without the baroque
approach of SICIs.  
  
When I get the chance I may add support for something like this to
[bioGUID](http://bioguid.info).


Following on from the discussion of BHL and DOIs, I stumbled across some remarkable work by Robert Cameron at SFU. Cameron has developed Universal Serial Item Names (USIN). The approach is spelled out in detail in Towards Universal Serial Item Names (also on Scribd). This lengthy document deals with how to develop user-friendly identifiers for journal articles, books, and other documents.

Universal Serial Item Names

In a series of emails [Chris Freeland](http://botanicus.blogspot.com/),
[David Shorthouse](http://ispiders.blogspot.com/), and I have been
discussing DOIs in the context of the Biodiversity Heritage Library
(BHL). I thought it worthwhile to capture some thoughts here.  
In an email Chris wrote:  

> Sure, DOIs have been around for a while, but how many nomenclators or
> species databases record them? Few, from what I\'ve seen - instead
> they record citations in traditional text form. I\'m trying to find
> the middle ground between guys like the two of you, who want
> machine-readable lit (RDF), and most everyone else I talk with,
> including regular users of Botanicus & BHL, who want human-readable
> lit (PDF). I\'m not overstating - it really does break down into these
> 2 camps (for now), with much more weight over on the PDF side (again,
> for now).

  
I think the perception that there are two \"camps\" is unfortunate. I
guess for a working taxonomist, it would be great if for a given
taxonomic name there was a way to see the original publication of the
name, even if it is simply a bitmap image (such as a JPEG). Hence, a
database that links names to images of text would be a useful resource.
If this is what BHL is aiming for, then I agree, DOIs may seem to be of
little use, apart from being one way to address the issue of persistent
identifiers.  
  
But it seems to me that there are lots of tasks for which DOIs (or more
precisely, the infrastructure underlying them) can help. For example,
given a bibliographic citation such as  
  
Fiers, F. and T. M. Iliffe (2000) *Nitocrellopsis texana* n. sp. from
central TX (U.S.A.) and *N. ahaggarensis* n. sp. from the central
Algerian Sahara (Copepoda, Harpacticoida). Hydrobiologia, 418:81-97.  
  
how do I find a digital version of this article? Given this citation  
  
Fiers, F. & T. M. Iliffe (2000). Hydrobiologia, 418:81.  
  
how do I decide that this is the same article? If I want to see whether
somebody has cited this paper (and perhaps changed the name of the
copepod) how do I do that? If I want follow up the references in this
paper, how do I do that?  
  
These are the kinds of thing that DOIs address. This article has the DOI
[doi:10.1023/A:1003892200897](http://dx.doi.org/10.1023/A:1003892200897).
This gives me a globally unique identifier for the article. The DOI
foundation provides a resolver whereby I can go to a site that will
provide me with access (albeit possibly for a fee) to the article.
CrossRef provides an OpenURL service whereby I can  

- Retrieve metadata about the article given the DOI
- Given metadata I can search for a DOI

  
To an end user much of this is irrelevant, but to people building the
links between taxonomic names and taxonomic literature, these are
pressing issues. Previously I\'ve given some examples before where
taxonomic databases such as [Cataloggue of
Life](http://iphylo.blogspot.com/2007/05/catalogue-of-life-openurl-and-taxonomic.html)
and [ITIS](http://iphylo.blogspot.com/2007/05/itis-and-dois.html) store
only text citations, not identifiers (such as DOIs or Handles). As a
result, the user has to search for each paper \"by hand\". Surely in an
ideal world there would be a link to the publication? If so, how do we
get there? How do IPNI, Index Fungorum, ITIS, Sp2000, ZooBank, and so on
link their names and references to digitised content? This is where a
CrossRef-style infrastructure comes in.  
  
Publishers \"get this\". Given the nature of the web where users expect
to be able follow links, CrossRef deals with the issue of converting the
literature cited section of a paper into a set of clickable links.
Don\'t we want the same thing for our databases of taxonomic names? And,
don\'t we want this for our taxonomic literature?  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi547oJFhbfPgpTtiAVwFPvBuPgjMpIeIMeADKmflkpgh6P67VgOtU64f-GPyRS4CWyG7_31bGedJiEE5b0Ho0E3hQG5oBUS37BcyEIGHulpNOSyVEWi5RVi1G-AwQOZaB7aVn7/s320/mn012340_lg.jpg){#BLOGGER_PHOTO_ID_5125301262996709154
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi547oJFhbfPgpTtiAVwFPvBuPgjMpIeIMeADKmflkpgh6P67VgOtU64f-GPyRS4CWyG7_31bGedJiEE5b0Ho0E3hQG5oBUS37BcyEIGHulpNOSyVEWi5RVi1G-AwQOZaB7aVn7/s1600-h/mn012340_lg.jpg)  
It is worth noting that the perception that DOIs only cover modern
literature is erroneous. For example, here\'s the description of
*Megalania prisca* Owen
([doi:10.1098/rstl.1859.0002](http://dx.doi.org/10.1098/rstl.1859.0002)),
which was published in 1859. The Royal Society of London has DOIs for
articles published in the 18th century.  
  
If the Royal Society can do this, why can\'t BHL?


In a series of emails Chris Freeland, David Shorthouse, and I have been discussing DOIs in the context of the Biodiversity Heritage Library (BHL). I thought it worthwhile to capture some thoughts here. In an email Chris wrote:  I think the perception that there are two "camps" is unfortunate.

BHL and DOis

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis7a8R5-gblbzh3Gy7cm3RvezPh9ZclAfAmW4HwTdhChaQ-Jifu9USYH_1WQTQu9YlUfp3vZ-vjWwynZQ2O8NEWomhyhVNId1ppRIeSl5warQdYlMnKCpGEZmnrkvj3IE-9IS6/s320/header_logo.gif){#BLOGGER_PHOTO_ID_5111565866040816466
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis7a8R5-gblbzh3Gy7cm3RvezPh9ZclAfAmW4HwTdhChaQ-Jifu9USYH_1WQTQu9YlUfp3vZ-vjWwynZQ2O8NEWomhyhVNId1ppRIeSl5warQdYlMnKCpGEZmnrkvj3IE-9IS6/s1600-h/header_logo.gif){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
[Nature precedings](http://precedings.nature.com/) is pre-publication
server launched by Nature a few months ago. To quote from the website:  

> Nature Precedings is a place for researchers to share pre-publication
> research, unpublished manuscripts, presentations, posters, white
> papers, technical papers, supplementary findings, and other scientific
> documents. Submissions are screened by our professional curation team
> for relevance and quality, but are not subjected to peer review. We
> welcome high-quality contributions from biology, medicine (except
> clinical trials), chemistry and the earth sciences.

  
Unable to resist, I\'ve uploaded three manuscripts previously
languishing as \"[Technical
Reports\"](http://taxonomy.zoology.gla.ac.uk/publications/tech-reports/index.html)
on my old server. The three I uploaded now have bright shiny DOIs, which
may take a little while to register with CrossRef. The manuscripts
are:  
  
**Treemap Versus BPA (Again): A Response to Dowling**
[doi:10.1038/npre.2007.1030.1](http://dx.doi.org/10.1038/npre.2007.1030.1)
(a response to a critique of my ancient TreeMap program).  
  
**On The Dangers Of Aligning RNA Sequences Using \"Conserved\" Motifs**
[doi:10.1038/npre.2007.1029.1](http://dx.doi.org/10.1038/npre.2007.1029.1)
(a short note on [Hickson *et al.*\'s
(2000)](http://mbe.oxfordjournals.org/cgi/content/abstract/17/4/530) use
of conserved motifs to evaulate RNA alignment).  
  
**Towards a Taxonomically Intelligent Phylogenetic Database**
[doi:10.1038/npre.2007.1028.1](http://dx.doi.org/10.1038/npre.2007.1028.1)
(a paper written for [DBiBD 2005](http://dbibd-05.inf.ed.ac.uk/),
basically a rewrite of a grant proposal).  
  
All three are under the [evolution and
ecology](http://precedings.nature.com/subjects/evolution-and-ecology)
subject heading. Visitors to [Nature
precedings](http://precedings.nature.com/) can comment on papers, and
vote for which ones they like. The fact that I\'ve uploaded some
manuscripts probably says nothing good about me, but I\'ll be checking
every so often to see if anybody has anything to say\...


Nature precedings is pre-publication server launched by Nature a few months ago. To quote from the website:  Unable to resist, I've uploaded three manuscripts previously languishing as "Technical Reports" on my old server. The three I uploaded now have bright shiny DOIs, which may take a little while to register with CrossRef.

Nature Precedings

[![](http://www.catalogueoflife.org/images/ITIS.gif){style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 160px;"
border="0"}](http://www.catalogueoflife.org/images/ITIS.gif){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Following on from my [earlier
grumble](http://iphylo.blogspot.com/2007/05/catalogue-of-life-openurl-and-taxonomic.html)
about how the catalogue of Life handles literature, I\'ve spent an
afternoon mapping publications in the **\"itis\".publications** table in
a copy of [ITIS](http://www.itis.gov) to external GUIDs, such as DOIs,
Handles, and SICIs in JSTOR. The mapping is not complete by any means,
but gives an idea of how many publications have GUIDs.You can view the
mapping [here](http://linnaeus.zoology.gla.ac.uk/~rpage/itis/). Many of
the publications in ITIS are books, which don\'t have DOIs. A lot of the
literature is also old (although this doesn\'t always mean it won\'t
have a DOI).  
  
Of 4296 records, 324 have DOIs (around 7.5%). Not a lot, but a still a
reasonable chunk. At least 700 of the ITIS publications are books (based
on having an ISBN), so the percentage is a little higher.  
  
The point of this exercise (following on from my comments on the [design
flaw](http://iphylo.blogspot.com/2007/05/catalogue-of-life-design-flaw.html)
in the catalogue of life), is that I think taxonomic databases need to
use GUIDs internally to maximise their stability and utility.  
  
Indeed, this is another reason to be disappointed with
[ZooBank](http://www.zoobank.org). In addition to a poor way to navigate
trees (which prompted me to explore tools such
[PygmyBrowse](http://iphylo.blogspot.com/2006/09/pygmybrowse.html)),
ZooBank does exactly what ITIS and the Catalogue of Life do when it
comes to displaying literature \-- it displays a text citation (albeit
with an invitation to view that record in Zoological Record, a
subscription-based service).  
  
For example, the copepod *Nitocrellopsis texana* was described in ITIS
publication **3072**, which I\'ve discovered has the the DOI
[doi:10.1023/A:1003892200897](http://dx.doi.org/10.1023/A:1003892200897){target="_new"}.
Given a DOI we have a GUID for the publication, and a direct link to it.
In contrast, ZooBank merely gives us:  

> Nitocrellopsis texana n. sp. from central TX (U.S.A.) and N.
> ahaggarensis n. sp. from the central Algerian Sahara (Copepoda,
> Harpacticoida). Hydrobiologia 418 (1-3) 15 January: 82

  
and a link to Zoological Record. Interesting, even with the resources of
ISI behind it, the Zoological Record result doesn\'t have the DOI.  
  
This for me is one reason ZooBank was so disappointing, it actually
provided little of value.  
  
What next? Well, with the 300 or so references mapped to DOIs, one could
link those to the ITIS records for the corresponding taxonomic names,
and serve these up through somehting like
[iSpecies](http://ispecies.org), for example. These would be links to
the literature, in many cases original descriptions, to supplement the
other literature found by iSpecies.


Following on from my earlier grumble about how the catalogue of Life handles literature, I've spent an afternoon mapping publications in the
<strong>
 "itis".publications
</strong>
table in a copy of ITIS to external GUIDs, such as DOIs, Handles, and SICIs in JSTOR. The mapping is not complete by any means, but gives an idea of how many publications have GUIDs.You can view the mapping here.

ITIS and DOIs

I think this isn\'t supposed to happen, but here\'s a paper with **two**
DOIs.  
  
The first DOI is
[doi:10.1651/0278-0372(1997)17\[253:MPAOTC\]2.0.CO;2](http://dx.doi.org/10.1651/0278-0372(1997)17%5B253:MPAOTC%5D2.0.CO;2),
which links to a record served by BIOONE. The second is
[doi:10.2307/1549275](http://dx.doi.org/10.2307/1549275), which links to
a JSTOR record
([sici:0278-0372(199705)17:2\<253:MPAOTC\>2.0.CO;2-O](http://links.jstor.org/sici?sici=0278-0372%28199705%2917%3A2%3C253%3AMPAOTC%3E2.0.CO%3B2-O&origin=crossref)).  
  
The paper is:  

> **Morphology-Based Phylogenetic Analysis of the Clawed Lobsters
> (Family Nephropidae and the New Family Chilenophoberidae)**  
> Dale Tshudy, Loren E. Babcock  
> *Journal of Crustacean Biology*, Vol. 17, No. 2 (May, 1997), pp.
> 253-263  

  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGUfm6xtCqbfnNUiTGZLC8TpHIf7Do3Armifezmmh11FtLOrOzCVYm6pqo0HT69ZFYhFQ7I94aokGfbUioiJZ4hOqKbJ0Bxf-hLNFDgvTGYYIMDbHiksC2bn2OUDKPZadbeL4M/s320/jstor.jpg){#BLOGGER_PHOTO_ID_5062151852948349250
style="float:middle; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGUfm6xtCqbfnNUiTGZLC8TpHIf7Do3Armifezmmh11FtLOrOzCVYm6pqo0HT69ZFYhFQ7I94aokGfbUioiJZ4hOqKbJ0Bxf-hLNFDgvTGYYIMDbHiksC2bn2OUDKPZadbeL4M/s1600-h/jstor.jpg)  
Now, the digital versions served by BIOONE and JSTOR is different, in
that BIOONE serves full text HTML and a PDF, whereas JSTOR serves
scanned images, but this is the **same** article.  
  
As an added \"feature\", the BIOONE DOI **doesn\'t work**, which in my
experience is often the case with BIOONE DOIs.


I think this isn't supposed to happen, but here's a paper with
<strong>
 two
</strong>
DOIs. The first DOI is doi:10.1651/0278-0372(1997)17[253:MPAOTC]2.0.CO;2, which links to a record served by BIOONE.

Duplicate DOIs

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEippjrDnOFur6xx-k8l7N4N6VU0A0WgipzXsCwjSKranaLruDYwpD1C9bN7LAgpbwHDfo7KndicK8RLnPnKX1ZE545mM96FC7qR594-WexKSeo7FFsbL8DGWFvVxfQ5OnugmbOZ/s320/2007_checklist_cd_front_cover.jpg){#BLOGGER_PHOTO_ID_5061841674705199410
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEippjrDnOFur6xx-k8l7N4N6VU0A0WgipzXsCwjSKranaLruDYwpD1C9bN7LAgpbwHDfo7KndicK8RLnPnKX1ZE545mM96FC7qR594-WexKSeo7FFsbL8DGWFvVxfQ5OnugmbOZ/s1600-h/2007_checklist_cd_front_cover.jpg)  
Playing with the recently released \"Catalogue of Life\" CD, and
pondering Charles Hussey\'s recent post to TAXACOM about the \"European
Virtual Library of Taxonomic Literature (E-ViTL)\" (part of
[EDIT](http://www.e-taxonomy.eu)) has got me thinking more and more
about how primitive our handling of taxonomic literature is, and how it
cripples the utility of taxonomic databases such as the Catalogue of
Life. For example, none of the literature listed in the Catalogue of
Life is associated with any digital identifier (such as a DOI, Handle,
SICI, or even a URL). In the digital age, this renders the literature
section nearly useless \-- a user has to search for the reference in
Google. Surely we want identifiers, not (often poorly formed)
bibliographic citations? For example, I think
[hdl:2246/4613](http://hdl.handle.net/2246/4613) is more useful than  

> Schmidt, K. P. 1921. New species of North American lizards of the
> genera Holbrookia and Uta. American Museum Novitates (22)

  
Given the Handle [hdl:2246/4613](http://hdl.handle.net/2246/4613), we
get straight to the bibliographic resource, **and** in this case, a PDF
of the paper. In the digital age this is what we need.  
  
So, how to get there? Well, I think we need to focus on developing
services to associate references with identifiers. Imagine a service
that takes a bibliographic record and returns a globally unique
identifier for that reference. This, of course, is part of what CrossRef
provides through its [OpenURL
resolver](http:///www.crossref.org/openurl).  
  
OpenURL has been around a while, and despite the fact that it is
probably over complicated (see [I hate library
standards](http://cavlec.yarinareth.net/archives/2006/10/13/i-hate-library-standards/)
for more on the seeming desire of librarians to make things harder than
they need to be), I think it is a useful way to think about the task of
linking taxonomic names to literature, especially if we keep things
simple (see [Rethinking
OpenURL](http://onebiglibrary.net/story/rethinking-openurl)). In
particular, drop the obsession with local context \-- I don\'t care what
my local library has, my library is the cloud.  
  
So, what if we had an OpenURL service that took a bibliographic citation
and queried local and remote sources for a digital identifier, such as a
DOI or a Handle, for that citation? If there is no such identifier, then
the next step is to create one. For example, the service could create a
SICI (see [my del.icio.us bookmarks for
sici](http://del.icio.us/rdmpage/sici)) for that item. Ideally, for
those items that were digitised, we could have a database that
associated SICIs with the resource location. For example, most of the
journal *[Psyche](http://psyche.entclub.org/)* is available free online
as PDFs, and has XML files for each volume providing full bibliographic
details (including URLs). It would be trivial to harvest these and add
this information to an OpenURL service.  
  
These ideas need a little more fleshing out, but I think it\'s time the
taxonomic community started thinking seriously about digital identifiers
for literature, and how they would be used.
[CrossRef](http://www.crossref.org) is a great example of what can be
done with some simple services (Handles + OpenURL), and it\'s a tragedy
that every time DOIs come up people get blinded by cost, and don\'t
spend time trying to understand how CrossRef works. If nyou want a good
demonstration of what can be done with CrossRef, just look at
[Connotea](http://www.connotea.org), which builds much of its
functionality on top of CrossRef web services.  
  
It is also interesting that CrossRef is much simpler to use than
repositories such as DSpace (used by the AMNH\'s digital library) \--
each DSpace installation has it\'s own hooks to retrieve metadata (in
some cases, such as the AMNH, appallingly badly formed), and as a result
there is no easy way to discover what metadata is associated with a
given handle, nor given a citation whether a handle exists for that
citation.  
  
So, when projects such as EDIT start talking about taxonomic libraries,
I think they need to think in terms of simple web services that will
serve as the building blocks for other tools. An OpenURL service would
be a major boon, and would speed us towards the day when databases such
as the Catalogue of Life would not contain (often inconsistently formed)
text records of bibliographic works, but actionable identifiers. Any
thing less and we remain in the dark ages.


Playing with the recently released "Catalogue of Life" CD, and pondering Charles Hussey's recent post to TAXACOM about the "European Virtual Library of Taxonomic Literature (E-ViTL)" (part of EDIT) has got me thinking more and more about how primitive our handling of taxonomic literature is, and how it cripples the utility of taxonomic databases such as the Catalogue of Life.

Messaggi di Rogue Scholar

Universal Serial Item Names

BHL and DOis

Nature Precedings

ITIS and DOIs

Duplicate DOIs

Catalogue of Life, OpenURL, and taxonomic literature