University of Glasgow

Roderic Page

![F93f2e30d1cca847800e6f3060b8101a](https://lh3.googleusercontent.com/--pRhqTZ9_EE/Vc4EXwMnG7I/AAAAAAAAEA4/V6iPvjQGDh0/f93f2e30d1cca847800e6f3060b8101a.jpg?imgmax=800 "f93f2e30d1cca847800e6f3060b8101a.jpg"){border="0"
width="128" height="128" style="float:right;"} I need more time to
sketch this out fully, but I think a case can be made for a
taxonomy-centric (or, perhaps more usefully, a biodiversity-centric)
clone of PubMed Central.

Why? We already have [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/),
and a European version [Europe PubMed Central](http://europepmc.org/),
and the content of Open Access journals such as ZooKeys appears in both,
so, again, why?

Here are some reasons:

1.  PubMed Central has pioneered the use of XML to archive and publish
    scientific articles, specifically JATS XML. But the biodiversity
    literature comes in all sorts of formats, including several flavours
    of XML (such as SciElo XML, XML from OCR literature such as DjVu,
    ABBYY, and TEI, etc.)
2.  While [Europe PMC](http://europepmc.org/) is doing nice things with
    ORCIDs and entity extraction, it doesn\'t deal with the kinds of
    entities prevalent in the taxonomic literature (such as geographic
    localities, specimen codes, micro citations, etc.). Nor does it deal
    with extracting the core scientific statements that a taxonomic
    paper makes.
3.  Given that much of the taxonomic literature will be derived from OCR
    we need mechanisms to be able to edit and fix OCR errors, as well as
    markup errors in more recent XML-native documents. For example, we
    could envisage having XML stored on GitHub and open to editing.
4.  We need to embed taxonomic literature in our major biodiversity
    databases, rather than have it consigned to ghettos of individual
    small-scale digitisation project, or swamped by biomedical
    literature whose funding and goals may not align well with the
    biodiversity community (Europe PMC is funded primary by medical
    bodies).

I hope to flesh this out a bit more later on, but I think it\'s time we
started treating the taxonomic literature as a core resource that we, as
a community, are responsible for. The NIH did this with biomedical
research, shouldn\'t we be doing the same for biodiversity?


I need more time to sketch this out fully, but I think a case can be made for a taxonomy-centric (or, perhaps more usefully, a biodiversity-centric) clone of PubMed Central. Why? We already have PubMed Central, and a European version Europe PubMed Central, and the content of Open Access journals such as ZooKeys appears in both, so, again, why?

Possible project: A PubMed Central for taxonomy

![ZooBankBanner](http://lh4.ggpht.com/-O7ywE8AEdhU/Td59P6h6zKI/AAAAAAAAA5c/MoyKBhEVeTc/ZooBankBanner.jpg?imgmax=800){border="0"
width="200" height="41" style="float:right;"}Last December I released a
web site called [Australian Faunal Directory on
CouchDB](http://iphylo.org/~rpage/afd/), which was part of my ongoing
exploration of how to build a simple yet useful database of taxonomic
names. In particular, I want to [link names directly to the primary
taxonomic
literature](http://iphylo.blogspot.com/2010/12/linking-taxonomic-databases-to-primary.html).
No longer is it adequate to simply list names, or list names with
mangled bibliographic details (I\'m looking at you, [Catalogue of
Life](http://www.catalogueoflife.org/)). This is the 21st century, so I
expect one click from name to literature, or at the most two (via, say,
a DOI). Nothing else will cut it.  
  
![Couchbase](http://lh6.ggpht.com/-dEznrgUky5Q/Td59Qat6zbI/AAAAAAAAA5g/-i-w1UQmONI/couchbase.png?imgmax=800){border="0"
width="128" height="128" style="float:right;"}The Australian Faunal
Directory (AFD) was an eye opener as it was the first serious use I\'d
made of CouchDB (now [CouchBase](http://www.couchbase.com/)). I\'d
played with [replicating and forking data in 2010: Catalogue of Life and
CouchDB](http://iphylo.blogspot.com/2010/10/replicating-and-forking-data-in-2010.html),
but the AFD project was bigger, and also inspired me to use [web
hooks](http://iphylo.blogspot.com/2011/02/web-hooks-and-openurl-screencast.html)
to make the database editable. Suddenly this stuff started to look easy:
no schema, simple web services, and tiny amounts of code.  
  
**ZooBank**  
So then my attention turned to [ZooBank](http://zoobank.org), which is
\"the official registry of Zoological Nomenclature, according to the
International Commission on Zoological Nomenclature (ICZN).\" ZooBank
was proposed by Polaszek et al. (2005) in a short piece in *Nature* (\"A
universal register for animal names\",
[doi:10.1038/437477a](http://dx.doi.org/10.1038/437477a)). By providing
a registry of names for animals, ultimately it aims to help avoid
embarrassing situations such as the example I recount in my paper on
[BioStor](http://biostor.org)
([doi:10.1186/1471-2105-12-187](http://dx.doi.org/10.1186/1471-2105-12-187)):
a recent paper in *Nature* published the name *Leviathan* for an extinct
sperm whale with a giant bite
([doi:10.1038/nature09067](http://dx.doi.org/10.1038/nature09067)), only
for authors to have to publish an erratum with a new name
([doi:10.1038/nature09381](http://dx.doi.org/10.1038/nature09381)) when
it was discovered that *Leviathan* had already been used for an extinct
mammoth.  
  
ZooBank is developed and run by [Rich
Pyle](http://hbs.bishopmuseum.org/staff/pylerichard.html), and has some
nice features, such as RDF export (via LSIDs), but like most taxonomic
databases it doesn\'t link directly to the literature. Where are the
DOIs? Where are links to BHL? Where is the ability to add these links?
And why is it almost entirely about fish? (OK, I know the answer to that
one).  
  
**CouchDB**  
But the thing which really got me thinking about using CouchDB to create
a version of ZooBank was Rich Pyle\'s vision of having a distributed
ZooBank, and his insistence on using ugly
[UUIDs](http://en.wikipedia.org/wiki/Universally_unique_identifier) in
ZooBank identifiers (e.g.,
[urn:lsid:zoobank.org:act:6BBEF50E-76B4-42EF-97B1-7029DBCD8257](http://zoobank.org:80/?uuid=6bbef50e-76b4-42ef-97b1-7029dbcd8257)).
As much as they are ugly, Rich has always argued that they make
distributed systems easy because you don\'t need a centralised system to
assign unique identifiers.  
  
Anybody who has played with CouchDB will know that CouchDB uses UUIDs by
default to create identifiers for database documents. It also excels at
data synchronisation, and can run on platforms large and small
(including mobile such as Android and
[iOS](http://blog.couchbase.com/mobile-couchbase-iOS-beta)). This means
a database could be updated on an iPhone or iPad without an Internet
connection, then the data could be synchronised with other databases.
Indeed, I developed this CouchDB clone of ZooBank on my MacBook, then
pointed it at CouchDB running on my server and within minutes had an
exact copy of the database running on the server. This ease of
replication, together with the joy of schema-less design makes CouchDB
seem an obvious fit to ZooBank.  
  
**Demo**  
You can [see the ZooBank on CouchDB demo
here](http://iphylo.org/~rpage/zoobank/). It\'s not a complete copy of
ZooBank, but has most of it. I reuse the UUIDs issued by ZooBank, so
that  
  
[http://zoobank.org:80/?uuid=**6bbef50e-76b4-42ef-97b1-7029dbcd8257**](http://zoobank.org:80/?uuid=6bbef50e-76b4-42ef-97b1-7029dbcd8257)  
  
becomes  
  
[http://iphylo.org/\~rpage/zoobank/**6bbef50e-76b4-42ef-97b1-7029dbcd8257**](http://iphylo.org/~rpage/zoobank/6bbef50e-76b4-42ef-97b1-7029dbcd8257)  
  
As usual it\'s all a bit crude, but has some nice features, such as
links to BHL content with a built in article viewer I wrote for the [AFD
project](http://iphylo.org/~rpage/afd/):  
  
[![Etheostoma](http://lh5.ggpht.com/-ie3tvY9_qEw/Td59RBtyM1I/AAAAAAAAA5k/PU1KM7Ejeg8/etheostoma.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400"
height="340"}](http://iphylo.org/~rpage/zoobank/id/27b8aa5e-c8c4-4c1d-bef2-546f6a8479f4)**What\'s
next?**  
At present only a fraction of the ZooBank references have external
links, I hope to add more in the next few days, using both automatic
scripts and the web hook interface. The search interface needs work, and
being that ZooBank is about nomenclature and not taxonomy, it might be
useful to add a classification (say from the Catalogue of Life) so that
users can navigate around the names (and get a sense of how many are
\*cough\* fish).  
  
At present to display a reference I do one of four things:  

1.  If reference is in BHL I use my article viewer
2.  If there is a freely available PDF online I display that using
    Google Docs PDF viewer
3.  If 1 and 2 don\'t apply, but there is a DOI then I resolve the DOI
    and display the result in an IFRAME (yuck)
4.  If none of 1-3 apply I display a blank rectangle

  
There are a couple ways we could improve this. The first is to enhance
the display of BHL content by making use of the [structure of the source
DjVu
files](http://iphylo.blogspot.com/2010/10/towards-interactive-djvu-file-viewer.html).
Another is to make use of the XML now being made available by the
journal *Zookeys* (see [my blog
post](http://iphylo.blogspot.com/2010/07/zookeys-publishes-articles-of-future.html),
and Pensoft\'s announcement that [*ZooKeys* is now being archived by
PubMed Central](http://www.pensoft.net/news.php?n=56), complete with
taxonomic markup). There are a lot of [*ZooKeys* articles in
ZooBank](http://iphylo.org/~rpage/zoobank/publication_outlet/ZooKeys),
so there\'s a lot of potential for embedding an article viewer that
takes *Zookeys* XML and redisplays it with taxonomic names and
references as clickable links that link to other ZooBank content. That
way we approach the point where taxonomic literature becomes a first
class citizen of a taxonomic database.


Last December I released a web site called Australian Faunal Directory on CouchDB, which was part of my ongoing exploration of how to build a simple yet useful database of taxonomic names. In particular, I want to link names directly to the primary taxonomic literature.

Rogue Scholar Beiträge

Possible project: A PubMed Central for taxonomy

ZooBank on CouchDB: UUIDs, replication, and embedding the literature in taxonomic databases