University of Glasgow

Roderic Page

![](http://www.jstor.org/templates/jsp/_jstor/images/jstor_logo.gif){align="right"}  
As much as I like the idea of a globally unique, resolvable identifier,
my recent experience with JSTOR is making me wonder.  
  
JSTOR has three identifiers for articles it archives, DOIs, SICIs, and
stable URLs (the later being introduced with the new platform released
April 4, 2008). Previously JSTOR would publish DOIs for many of its
articles. However, not all of these work, and many are now embedded in
the HTML (say, in [Dublin Core meta
elements](http://dublincore.org/documents/dcq-html/)) but not publicly
displayed.  
  
I suspect the issue is the [moving
wall](http://www.jstor.org/page/info/about/archives/journals/movingWall.jsp):  

> Journals in JSTOR have \"moving walls\" that define the time lag
> between the most current issue published and the content available in
> JSTOR. The majority of journals in the archive have moving walls of
> between 3 and 5 years, but publishers may elect walls anywhere from
> zero to 10 years.

Now, imagine that a publisher has an article on its web site, complete
with a DOI, and that article is then add to JSTOR, but is still
displayed on the publisher\'s site.  
  
![](http://www.jstor.org/covergifs/systbiol/cover.gif){align="left"
hspace="7"}  
To make this concrete, consider the article by Baum *et al.* . On the
InformaWorld site this is displayed with
[doi:10.1080/106351598260879](http://dx.doi.org/10.1080/106351598260879).
The same article is also in JSTOR, with the URL
<http://www.jstor.org/pss/2585367>. No DOI is displayed on the page, but
if you look at the HTML source, we find:  

. The DOI prefix **10.2307** is used for all JSTOR DOIs, and some for
Systematic Biology still work, e.g.
[10.2307/2413524](http://dx.doi.org/10.2307/2413524).  
  
Now, what happens when the JSTOR moving wall overlaps with publisher\'s
material? What happens if a publisher digitises back issues, then
assigns them DOIs? Do the JSOR DOIs then die (as some of them seem to
have already done)? And what happens to the poor sap like me, who has
been linking to JSTOR DOIs in the naive belief that DOIs don\'t die?  
  
Suddenly separating identity from resolution is starting to look very
attractive\...  
  


As much as I like the idea of a globally unique, resolvable identifier, my recent experience with JSTOR is making me wonder.JSTOR has three identifiers for articles it archives, DOIs, SICIs, and stable URLs (the later being introduced with the new platform released April 4, 2008). Previously JSTOR would publish DOIs for many of its articles.

When DOIs collide and then disappear: when is a unique, resolvable identifier a bad idea?

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhfQfJ_qKaHDWCGypQzExFiLbOVthnC52tNrhgFKsVo-JODIOLgTcX_FAKqzIvRhMF1ogifeWRzHsGCDst0gurnqWfWShyphenhypheneXrz9hsanY6IPWEi35CcIrIuEjOhTpwB0gTdoCLr7/s320/cover.gif){#BLOGGER_PHOTO_ID_5194920985396578738
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhfQfJ_qKaHDWCGypQzExFiLbOVthnC52tNrhgFKsVo-JODIOLgTcX_FAKqzIvRhMF1ogifeWRzHsGCDst0gurnqWfWShyphenhypheneXrz9hsanY6IPWEi35CcIrIuEjOhTpwB0gTdoCLr7/s1600-h/cover.gif){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Bit of a rarity these days. My paper on identifiers in biodiversity
informatics, which I mentioned
[earlier](http://iphylo.blogspot.com/2008/04/biodiversity-informatics-challenge-of.html)
when I deposited the preprint at [Nature
Precedings](http://precedings.nature.com/), has been published in
*Briefings in Bioinformatics*
([doi:10.1093/bib/bbn022](http://dx.doi.org/10.1093/bib/bbn022)).  
  
Here\'s the abstract:  

> A major challenge facing biodiversity informatics is integrating data
> stored in widely distributed databases. Initial efforts have relied on
> taxonomic names as the shared identifier linking records in different
> databases. However, taxonomic names have limitations as identifiers,
> being neither stable nor globally unique, and the pace of molecular
> taxonomic and phylogenetic research means that a lot of information in
> public sequence databases is not linked to formal taxonomic names.
> This review explores the use of other identifiers, such as specimen
> codes and GenBank accession numbers, to link otherwise disconnected
> facts in different databases. The structure of these links can also be
> exploited using the PageRank algorithm to rank the results of searches
> on biodiversity databases. The key to rich integration is a commitment
> to deploy and reuse globally unique, shared identifiers \[such as
> Digital Object Identifiers (DOIs) and Life Science Identifiers
> (LSIDs)\], and the implementation of services that link those
> identifiers.


Paper published

Leigh Dodds has a nice post [How Shall I Integrate Thee? Let Me Count
the Ways\...](http://www.ldodds.com/blog/archives/000314.html) about
different ways to integrate data.  

- The one where we share identifiers
- The one where we\'re describing the same thing
- The one where we\'re speaking different languages
- The one where we\'re using different units
- The one where we\'re speaking at different levels of abstraction

  
Apart from the suggestion that Leigh has been watching way too much
[Friends](http://en.wikipedia.org/wiki/List_of_Friends_episodes),
there\'s much food for thought here. I suspect that \"The one where
we\'re describing the same thing\" is the one I\'ll be making most use
of.  
  
In [Rethinking LSIDs versus HTTP
URI](http://iphylo.blogspot.com/2007/06/rethinking-lsids-versus-http-uri.html)
I argued that most applications will use HTTP URIs, which makes them
accessible, but not terribly useful as identifiers, the reason being
that I think it is unlikely that people will reuse HTTP URIs (\"The one
where we share identifiers\"). A good example is Connotea, which has its
own URIs for each paper its users bookmark. I won\'t use these URIs as
identifiers in my database (if only because if a user resolves them,
they get taken to Connotea\'s web site, not mine). However, I will store
any PubMed and DOI identifiers, so that somebody aggregating information
from Connotea (say to retrieve user tags) and my database (say, to get
links to sequences and specimens) can work out that the Connotea URI and
my URI are talking about the same thing.


Leigh Dodds has a nice post How Shall I Integrate Thee?

How Shall I Integrate Thee? Let Me Count the Ways...

Well, the LSID discussion has just exploded in the last few weeks. I
touched on this in my earlier post [Rethinking LSIDs versus HTTP
URI](http://iphylo.blogspot.com/2007/06/rethinking-lsids-versus-http-uri.html),
but since then the [TDWG
discussion](http://lists.tdwg.org/pipermail/tdwg-guid/2007-July/thread.html)
has become more vigourous (albeit mainly focussed on technical issues,
although I suspect that these are symptoms of a larger problem), while
**public-semweb-lifesci@w3.org** list [for
July](http://lists.w3.org/Archives/Public/public-semweb-lifesci/2007Jul/)
has mushroomed into a near slugfest of discussion about URIs, LSIDs,
OWL, the goals of the Semantic Web, etc. There are also blog posts, such
as Benjamin Good\'s [The main problem with
LSIDs](http://i9606.blogspot.com/2007/06/main-problem-with-lsids.html),
Mark Wilkinson\'s numerous posts on [his
blog](http://semanticmusings.blogspot.com/), and Pierre Lindebaum\'s
[commentary](http://plindenbaum.blogspot.com/2007/07/url-1-lsid-1.html).  
  
I have no comment to make on this, I\'m merely bookmarking them for when
I find the time to wade through all this\...


Well, the LSID discussion has just exploded in the last few weeks.

LSID wars

[![](http://upload.wikimedia.org/wikipedia/commons/thumb/5/52/Pinnotheres_pisum.jpg/799px-Pinnotheres_pisum.jpg){style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 200px;"
border="0"}](http://upload.wikimedia.org/wikipedia/commons/thumb/5/52/Pinnotheres_pisum.jpg/799px-Pinnotheres_pisum.jpg)  
A bit more browsing of the [Catalogue of
Life](http://www.catalogueoflife.org) annual checklist for 2007 reveals
a rather annoying feature that, I think, cripples the Catalogue\'s
utility. With each release the checklist grows in size. From their [web
site](http://www.catalogueoflife.org/info_about_col.php):  

> The Species 2000 & ITIS Catalogue of Life is planned to become a
> comprehensive catalogue of all known species of organisms on Earth by
> the year 2011. Rapid progress has been made recently and this, the
> seventh edition of the Annual Checklist, contains 1,008,965 species.

  
However, with each release the identifiers for each taxon change. For
example, if I were to link to the record for the peacrab *Pinnotheres
pisum* this year (2007), I would link to record
[3803555](http://www.catalogueoflife.org/show_species_details.php?record_id=3803555),
but last year I would have linked to
[872170](http://www.catalogueoflife.org/annual-checklist/2006/show_species_details.php?record_id=872170).
Record **872170** no longer exists in the 2007 edition.  
  
So, what would a user who based their taxonomic database on the
Catalogue of Life do? All their links would break (not just because the
URL interface has changed, but the underlying identifiers have changed
as well). It\'s as if the authors of the catalogue have been oblivious
to the discussion on globally unique identifiers (GUIDs) and the need
for stable, persistent identifiers.  
  
Anybody building a database that gets updated, and possible rebuilt
needs to thik about how their identifiers will change. If identifiers
are simply the primary keys in a table, then they will likely be
unstable, unless great care is taken. Althernatively, databases that are
essentially aggregations of data available elsewhere could use GUIDs as
the primary keys. This means that even if the database is restructured,
the keys (and hence the identifiers) don\'t change. For the user,
everything still works.  
  
Despite the favourable press about its progress (e.g.,
[doi:10.1038/news050314-6](http://dx.doi.org/10.1038/news050314-6),
[Environmental Research
Web](http://environmentalresearchweb.org/cws/article/futures/27461), and
[CNN](http://www.cnn.com/2007/TECH/science/04/09/catalog.oflife.ap/index.html)),
I think the catalogue needs some serious rethinking if it is to be
genuinely useful. For more on this, see [my earlier
posting](http://iphylo.blogspot.com/2007/05/catalogue-of-life-openurl-and-taxonomic.html)
on how the catalogue handles literature.  
  
Image of *Pinnotheres pisum* by [Hans
Hillewaert](http://commons.wikimedia.org/wiki/User:Lycaon) obtained from
[Wikimedia
Commons](http://commons.wikimedia.org/wiki/Image:Pinnotheres_pisum.jpg).


A bit more browsing of the Catalogue of Life annual checklist for 2007 reveals a rather annoying feature that, I think, cripples the Catalogue's utility. With each release the checklist grows in size. From their web site:However, with each release the identifiers for each taxon change.

Postagens de Rogue Scholar

When DOIs collide and then disappear: when is a unique, resolvable identifier a bad idea?

Paper published

How Shall I Integrate Thee? Let Me Count the Ways...

LSID wars

Catalogue of Life design flaw