University of Glasgow

Roderic Page

![bhlstrip.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/SsN6GxNSkeI/AAAAAAAAAjU/oF-3wq1Yb3M/bhlstrip.png?imgmax=800){border="0"
width="128" align="right"}One thing about the [Encyclopedia of
Life](http://www.eol.org) which bugs me no end is the awful way it
displays the bibliography generated from the [Biodiversity Heritage
Library](http://www.biodiversitylibrary.org) (BHL). The image on the
right shows the bibliography for the frog [*Hyla rivularis* Taylor,
1952](http://www.eol.org/pages/330840). It\'s one long, alphabetical
list of pages. How can a user make sense of this? It\'s even more
annoying because the BHL is one of the cornerstones of EOL, and one
could argue that BHL content is one of the few thing pages EOL offer
that distinguishes them from cheap and cheerful mashups such as
[iSpecies](http://ispecies.org). Can\'t we do something a little
better?  
  
BHL has an API ([documented
here](http://docs.google.com/Doc?id=dgvjvvkz_1x5qbm3)), so I decided to
experiment. As I mentioned in an earlier post ([Biodiversity Heritage
Library, Google books, and metadata
quality](http://iphylo.blogspot.com/2009/09/biodiversity-heritage-library-google.html)),
a key piece of metadata about a bibliographic reference is its date.
This is especially so for the taxonomic literature, where the earliest
reference that contains a name may (depending on how complete BHL
scanning is) be the first description of that name. So, it would be nice
to order the BHL bibliography by date. Turns out it\'s possible to get
dates from quite a few BHL items, providing one fusses with regular
expressions long enough.  
  
So, in principle we could sort BHL content by dates. But, we could go
one better and visualise them. As an experiment, I\'ve put together a
demo that uses the [SIMILE Timeline
widget](http://www.simile-widgets.org/timeline/) to display the BHL
bibliography for a taxon. Here\'s a screenshot of the bibliography for
[*Hyla rivularis*](http://bioguid.info/bhl/?name=Hyla+rivularis):  

::: {style="text-align:center;"}
![bhltimeline.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/SsN-Sa4v9aI/AAAAAAAAAjY/Our9A9D23rQ/bhltimeline.png?imgmax=800){border="0"
width="400"}
:::

  
  
You can generate others at <http://bioguid.info/bhl/>. The demo has been
thrown together in haste, but here\'s what it does:  

1.  Takes a taxon name and tries to find it in uBio. This gives us the
    NamebankID BHL needs
2.  Calls the BHL API and retrieves the bibliography for the NamebankID
    found in step 1
3.  Parses the BHL result, trying to extract dates (often the dates are
    ranges, e.g. 1950-1955)
4.  The previous step generates a JSON document which can be displayed
    by Timeline

  
If you click on an item you get a list of pages, clicking on any those
takes to you to the page in BHL. Items that have a range of dates are
displayed as horizontal lines, items with a well-defined date are shown
as points. Note that my code for working out the date of an item will
probably fail on some items, and some items don\'t have any dates at
all. Hence, not every item in BHL will appear in the timeline.  
  
It would be nice to embellish the results a little (for example, group
pages into articles, refine the dates, etc.) but I think this goes a
little way to demonstrating what can be done. We could also add articles
obtained from other sources (e.g., Google Scholar, PubMed) to the same
display, providing an overview of published knowledge about a taxon.  


One thing about the Encyclopedia of Life which bugs me no end is the awful way it displays the bibliography generated from the Biodiversity Heritage Library (BHL). The image on the right shows the bibliography for the frog
<i>
 Hyla rivularis
</i>
Taylor, 1952. It's one long, alphabetical list of pages. How can a user make sense of this?

Visualising the Biodiversity Heritage Library as a Timeline

::: {style="float:right"}
![zotero_z_32px.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/Sly4gEMkseI/AAAAAAAAAgU/6X6NcZz2Uwg/zotero_z_32px.png?imgmax=800){border="0"
width="32" height="32"}
:::

  
Lately I\'ve become more and more interested in moving data off my
machine(s) and into the cloud. I\'m keen to do this partly to avoid
having data in one place (e.g., a machine at work) when I need it
someplace else (e.g., at home), and there are great tools for doing this
(such as the wonderful [Dropbox](http://www.getdropbox.com//)).  
  
As a developer, the cloud appeals, not so much because of the compute
power that some are salivating over, but because it may free me from
having to create my own software. For example, some time ago I have
created an [OpenURL resolver](http://bioguid.info/openurl) to help me
find articles online. I harvest a bunch of sources, such as CrossRef,
PubMed, some OPAI respositories, etc., but there\'s always times where I
find a reference online that I\'d like to add, and that reference
doesn\'t have an identifier such as a DOI.  
  
Typically I add these manually, or by importing a file. I could write
some interface code to add (and edit) a bibliographic reference (and,
indeed I did [some time back](http://myphpbib.sourceforge.net/)), but
wouldn\'t it be great if somebody else had done this for me?  
  

::: {style="float:right"}
![idisk.png](http://lh3.ggpht.com/_Gct8lVAxKqQ/Sly8avQgH-I/AAAAAAAAAgc/dabYb4GAcBY/idisk.png?imgmax=800){border="0"
width="32" height="32"}
:::

Well, there are some tools out there for handling bibliographies online,
such as [Connotea](http://www.connotea.org),
[Mendeley](http://www.mendeley.com), and [Zotero](http://www.zotero.org)
(a Firefox add-on). Initially I was skeptical of Zotero (and I\'m not a
big Firefox user), but now that I\'m looking for a place to store
obscure papers it\'s rapidly growing on me. I like the fact that I can
add references *in situ*, and that I can upload PDFs (which can be
stored remotely on a WebDAV disk such as an iDisk). But what makes
Zotero even more attractive is that it generates an RSS feed of [my
bibliography](http://www.zotero.org/rdmpage/items), which I can then
harvest just as I harvest other resources.  
  
Using a resource like Zotero saves me the hassle of having to write my
own bibliographic editor, plus I benefit from using a tool that\'s a lot
more polished than one I could make. Because of this, and my [experience
with the Google Spreadsheets
API](http://iphylo.blogspot.com/2009/07/using-google-spreadsheets-and-rss-feeds.html),
I\'m ultimately aiming to never have to write a user interface again. If
I write services, and rely on third parties to make tools that can
either generate services I can use, or consume my services, then my life
becomes a lot simpler.  
  
OK, perhaps I exaggerate. I like making interfaces, such as my [eBio09
entry](http://iphylo.blogspot.com/2009/05/e-biosphere-challenge-visualising.html),
or the [experiment with
SpaceTree](http://iphylo.blogspot.com/2009/06/visualising-taxonomic-classifications.html).
However, I can imagine a situation where I don\'t have to write a **data
entry** interface ever again.


Lately I've become more and more interested in moving data off my machine(s) and into the cloud.

Rogue Scholar Beiträge

Visualising the Biodiversity Heritage Library as a Timeline

Zotero: creating bibliographies in the cloud