University of Glasgow

Roderic Page

![TandFOnline
twitter](http://lh4.ggpht.com/-i7qw9Qqb3UE/ToV8dBsS_LI/AAAAAAAABAI/Os8U9scCt8U/TandFOnline-twitter.gif?imgmax=800 "TandFOnline-twitter.gif"){border="0"
width="72" height="72" style="float:right;padding:10px;"}DOIs are meant
to be the gold standard in bibliographic identifier for article. They
are not supposed to break. Yet some publishers seem to struggle to get
them to work. In the past I\'ve grumbled about BioOne, Wiley, and others
as cuplrits with broken or
[duplicate](http://iphylo.blogspot.com/2007/05/duplicate-dois.html) or
[disappearing](http://iphylo.blogspot.com/2008/05/when-dois-collide-and-then-disappear.html)
DOIs. 
 
Today\'s source of frustration is Taylor and Francis Online. T&F Online
is powered by ([Atypon](http://www.atypon.com/)), which recently issued
this glowing [press
release](http://www.atypon.com/news-and-events/press-release.php?id=2020): 

> 
> SANTA CLARA, Calif.---20 September 2011---Atypon®, a leading provider
> of software to the professional and scholarly publishing industry,
> today announced that its Literatum™ software is powering the new
> Taylor & Francis Online platform (www.TandFOnline.com). Taylor &
> Francis Online hosts 1.7 million articles. 
> \... 
> \"The performance of Taylor & Francis Online has been excellent,\"
> said Matthew Jay, Chief Technology Officer for the Taylor & Francis
> Group. \"Atypon has proven that it can deliver on schedule and achieve
> tremendous scale. We\'re thrilled to expand the scope of our
> relationship to include new products and developments.\"

 
Great, except that lots of T&F DOIs are broken. I\'ve come across two
kinds of fail. 
 
**DOI resolves to server that doesn\'t exist** 
The first is where a DOI resolves to a phantom web address. For example,
the DOI
[doi:10.1080/00288300809509849](http://dx.doi.org/10.1080/00288300809509849)
resolves to
<http://tandfprod.literatumonline.com/doi/abs/10.1080/00288300809509849>.
But the domain **tandfprod.literatumonline.com** doesn\'t exist, so the
DOI is a dead end. 
 
**DOI doesn\'t resolve** 
Taylor and Francis have digitised the complete *Annals and Magazine of
Natural History*, a massive journal comprising nearly 20,000 articles
from 1841 to 1966, and which has published some seminal papers,
including A. R. Wallace\'s \"On the law which has regulated the
introduction of new species\"
[doi\"10.1080/037454809495509](http://dx.doi.org/10.1080/037454809495509)
which forced Darwin\'s hand (see the Wikipedia page for the successor
journal [*Journal of Natural
History*](http://en.wikipedia.org/wiki/Journal_of_Natural_History).
Taylor and Francis are to be congratulated for putting such a great
resource online. 
 
Problem is, I\'ve not found a single DOI for any article in *Annals and
Magazine of Natural History* that actually works. If you try and resolve
the DOI for Wallace\'s paper,
[doi\"10.1080/037454809495509](http://dx.doi.org/10.1080/037454809495509),
you get the dreaded \"Error - DOI not found\" web page. So something
like 20,000 DOIs simply don\'t work. The only way to make the DOI work
is append it to \"http://www.tandfonline.com/doi/abs/\", e.g.
<http://www.tandfonline.com/doi/abs/10.1080/037454809495509>. This gets
us to the article, but rather defeats the purpose of DOIs. 
 
**Why?** 
Something is seriously wrong with CrossRef\'s quality control. It can\'t
be too hard to screen all domains to see if they actually exist (this
would catch the first error). It can\'t be too hard to take a random
sample of DOIs and check that they work, or automatically check DOIs
that are reported as missing. In the case the *Annals and Magazine of
Natural History* the web page for the Wallace article states that it has
been available online since 16 December 2009. That\'s a long time for a
DOI to be dead. 
 
There is a wealth of great content that is being made hard to find by
some pretty basic screw ups. So CrossRef, Atypon and Taylor and Francis,
can we please sort this out?

DOIs are meant to be the gold standard in bibliographic identifier for article. They are not supposed to break. Yet some publishers seem to struggle to get them to work. In the past I've grumbled about BioOne, Wiley, and others as cuplrits with broken or duplicate or disappearing DOIs.Today's source of frustration is Taylor and Francis Online.

Taylor and Francis Online breaks DOIs - lots of DOIs

![C2914D0E-13E9-4CA6-BE0A-7A8645BC6A72.jpg](http://lh5.ggpht.com/_Gct8lVAxKqQ/S-JwM7E3ykI/AAAAAAAAApU/0rTmoQ5bAlA/C2914D0E-13E9-4CA6-BE0A-7A8645BC6A72.jpg?imgmax=800){border="0"
width="200" align="right"}To much fanfare (e.g., *Nature News*,
\"Linnaeus meets the Internet\"
[doi:10.1038/news.2010.221](http://dx.doi.org/10.1038/news.2010.221)),
on May 5th *PLoS ONE* published Sandy Knapp\'s \"Four New Vining Species
of *Solanum* (Dulcamaroid Clade) from Montane Habitats in Tropical
America\"
[doi:10.1371/journal.pone.0010502](http://dx.doi.org/10.1371/journal.pone.0010502).
To quote the *Nature News* piece: 

> The paper represents the culmination of a campaign to institute the
> electronic publication of scientific names, a case Knapp and others
> have made in journals including
> *Nature*\[[doi:10.1038/446261a](http://dx.doi.org/10.1038/446261a)\].
> Allowing electronic publication should make accessing information
> easier for scientists worldwide --- especially those in developing
> countries who may not have access to fully stocked libraries. This, in
> turn, will aid conservation efforts, Knapp says.

 
Given the profile of this paper, \"\...the first time new plant names
have been published in a purely electronic journal and still complied
with ICBN rules\", you\'d think the participants would ensure the
electronic aspects of the publication worked. Sadly, this is not the
case. 
 
The four names in question have apparently been deposited in
[IPNI](http://www.ipni.org) with the following LSID\'s: 

- *Solanum aspersum*: urn:lsid:ipni.org:names:77103633-1
- *Solanum luculentum*: urn:lsid:ipni.org:names:77103634-1
- *Solanum sanchez-vegae*: urn:lsid:ipni.org:names:77103635-1
- *Solanum sousae*: urn:lsid:ipni.org:names:77103636-1

 
Today is May 6th. None of these names are returned by a search of IPNI,
for example
<http://www.ipni.org/ipni/simplePlantNameSearch.do?find_wholeName=>
returns this: 
 

::: {style="text-align:center;"}
![ipni1.png](http://lh3.ggpht.com/_Gct8lVAxKqQ/S-JrY0MRj7I/AAAAAAAAApQ/7ZoTuQMpF44/ipni1.png?imgmax=800){border="0"
width="400"}
:::

 
Resolving the LSID returns this: 

``` brush:xml

xmlns:dc="http://purl.org/dc/elements/1.1/" 
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:tn="http://rs.tdwg.org/ontology/voc/TaxonName#"
xmlns:tm="http://rs.tdwg.org/ontology/voc/Team#" 
xmlns:tcom="http://rs.tdwg.org/ontology/voc/Common#" 
xmlns:p="http://rs.tdwg.org/ontology/voc/Person#" 
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#">
 

Yes
 
```

 
Hmmm, so apparently this record has been \"deleted\"? 
 
The paper also states that: 

> The IPNI LSIDs (Life Science Identifiers) can be resolved and the
> associated information viewed through any standard web browser by
> appending the LSID contained in this publication to the prefix
> <http://ipni.org/>.

 
This sentence mirrors similar ones in other PLoS ONE papers saying we
can resolve ZooBank LSIDs by appending the LSID to <http://zoobank.org>
(e.g., see
[doi:10.1371/journal.pone.0001787](http://dx.doi.org/10.1371/journal.pone.0001787)). 
 
Thing is, URLs such as
<http://ipni.org/urn:lsid:ipni.org:names:77103633-1> return a 404 from
Kew (any IPNI LSID I\'ve tried does this). 
 

::: {style="border:1px dotted black;"}
 
**Update** As per Alan Paton\'s [comment
below](http://iphylo.blogspot.com/2010/05/linnaeus-meets-internet-plos-botany.html#comment-48654343),
the http://ipni.org prefix now works. 
:::

 
 
So, to recap: 

1. The names aren\'t in IPNI
2. The LSIDs state the record has been deleted
3. The LSID\'s can\'t be resolved by the means stated in the paper

Now, I don\'t know what happened (perhaps IPNI wanted to hold off until
the paper actually appeared before releasing the names), but the paper
is out, the buzz in [*Nature*](http://dx.doi.org/10.1038/news.2010.221)
is out, and IPNI doesn\'t have the resolver in place, yet alone the
names. 
 
Given the [milestone this paper
represents](http://everyone.plos.org/2010/05/05/newplantspecies/), and
the
[fuss](http://blogs.discovermagazine.com/loom/2009/05/20/does-darwinius-exist/)
over the publication of the name *Darwinius*, you\'d expect the
bioinformatics side of it to be, you know, actually working. In these
circumstances, how on Earth do we make the case that the LSID and name
databasing side of taxonomic publication is useful?

To much fanfare (e.g.,

 Nature News

, "Linnaeus meets the Internet" doi:10.1038/news.2010.221), on May 5th

 PLoS ONE

published Sandy Knapp's "Four New Vining Species of

 Solanum

(Dulcamaroid Clade) from Montane Habitats in Tropical America" doi:10.1371/journal.pone.0010502.

Linnaeus meets the Internet: PLoS + Botany =  #fail

[CrossRef](http://www.crossref.org) has been having some issues with
it\'s OpenURL resolver over the weekend, which means that attempts to
retrieve metadata from a DOI, or to find a DOI from metadata, have been
thwarted. While annoying (see [The dangers of the 'free' cloud: The Case
of
CrossRef](http://bibwild.wordpress.com/2009/04/20/the-dangers-of-the-free-cloud-the-case-of-crossref/)),
in one sense it\'s reassuring that it\'s not just [biodiversity data
providers](http://iphylo.blogspot.com/2008/10/biodiversity-service-status.html)
that are having problems with service availability.


CrossRef has been having some issues with it's OpenURL resolver over the weekend, which means that attempts to retrieve metadata from a DOI, or to find a DOI from metadata, have been thwarted. While annoying (see The dangers of the ‘free’ cloud: The Case of CrossRef), in one sense it's reassuring that it's not just biodiversity data providers that are having problems with service availability.

CrossRef fail - at least we're not alone...

OK, second rant of the day. One of my favourite online specimen
databases is [AntWeb](http://www.antweb.org/). For a while the ability
to harvest data from this database using the venerable DiGIR protocol
hasn\'t been possible, due to various issues at the California Academy
of Sciences. Well, now it\'s back, and \"accessible\" using [TAPIR
(TAPIR - TDWG Access Protocol for Information
Retrieval)](http://www.tdwg.org/dav/subgroups/tapir/1.0/docs/tdwg_tapir_specification_2009-02-05.htm).
Accessible, that is, if you like horrifically over-engineered, poorly
documented standards. OK, at lot of work has gone into TAPIR, there\'s
lots of [great code on
SourceForge](http://sourceforge.net/projects/digir/), and there\'s lots
of documentation, but I\'ve really struggled to get the most basic tasks
done. 
 
For example, let\'s imagine I and want to retrieve the information on
the ant specimen
[CASENT0100367](http://www.antweb.org/specimen.do?name=casent0100367)
(note how trivial this is via a web browser, just append the specimen
name to **http://www.antweb.org/specimen.do?name=**). After much
clenching of teeth struggling with the TAPIR documentation and the TAPIR
client software, I finally found [an email by Markus
Döring](http://lists.tdwg.org/pipermail/tdwg-tapir/2008-April/000493.html)
that gave me the clue. If I\'m going to construct a URL to retrieve this
specimen record, I need to include the URL of an XML document that
serves as a template for the query. Since one doesn\'t exist, I have to
create it and make it accessible to the TAPIR server (i.e., the AntWeb
TAPIR server needs to access it, so I have to place this XML document on
my web server). The template (shown below) lives at
<http://bioguid.info/tapir/dwc_catalog_number.xml>: 

``` prettyprint

 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
 xmlns:xs="http://www.w3.org/2001/XMLSchema" 
 xsi:schemaLocation="http://rs.tdwg.org/tapir/1.0
 http://rs.tdwg.org/tapir/1.0/schema/tapir.xsd
 http://www.w3.org/2001/XMLSchema
 http://www.w3.org/2001/XMLSchema.xsd">
 Scientific name in query
 Query for a Scientific Name. Based on http://rs.tdwg.org/tapir/cs/dwc/1.4/template/dwc_sci_name_range.xml, found in email by Markus Döring http://lists.tdwg.org/pipermail/tdwg-tapir/2008-April/000493.html
 
 
 
 
 
 
 
```

 
Now I can write my query:
[http://www.antweb.org/tapirlink/www/tapir.php/antweb 
op=search 
&start=0 
&limit=1 
&template=http://bioguid.info/tapir/dwc_catalog_number.xml 
&name=casent0100367](http://www.antweb.org/tapirlink/www/tapir.php/antweb?op=search&start=0&limit=1&template=http://bioguid.info/tapir/dwc_catalog_number.xml&name=casent0100367) 
So, the AntWeb server is going to read this query, and call my web
server to get the query template to figure out what I actually want. Am
I the only person who thinks that this is insane? Can anybody imagine
going through these hoops to access a GenBank record, or a PubMed
record? 
 
Perhaps it\'s me, and my obsession with linking individual data records
(rather than harvested lots of records, or federated search). But it
strikes me that harvesting is a simple task and not many people will be
doing it (at least, not on the scale of GBIF), and federated search is a
non-starter as our community can\'t keep data providers online to save
themselves. 
 
In many ways I think TAPIR (and DiGIR before it) missed what for me is
the most basic use case, namely I have a specimen identifier and I want
to get the record for that specimen. These services make it much harder
than it needs to be. It\'s a symptom of our field\'s inability to
deliver simple tools that do basic tasks well, rather than overly
general and highly complex tools that are poorly documented. Of course,
retrieving individual records woud be easy if we have resolvable GUIDs
for specimens, but we\'ve singularly failed to deliver that, so we are
stuck with very clunky tools. There\'s got to be a better way\...

OK, second rant of the day. One of my favourite online specimen databases is AntWeb. For a while the ability to harvest data from this database using the venerable DiGIR protocol  hasn't been possible, due to various issues at the California Academy of Sciences.

Publicaciones de Rogue Scholar

Taylor and Francis Online breaks DOIs - lots of DOIs

Linnaeus meets the Internet: PLoS + Botany = #fail

CrossRef fail - at least we're not alone...

Accessing specimens using TAPIR or, why do we make this so hard?