University of Glasgow

Roderic Page

My [BioStor](http://biostor.org/) project has reached over 13,000
articles, making it a sizeable respository of open access articles on
biodiversity. It\'s still a tiny fraction of what could be extracted
from the [Biodiversity Heritage
Library](http://www.biodiversitylibrary.org) (BHL), but perhaps it\'s
worth taking stock of what\'s there.  
  
**Coverage**  
  
One pleasing discovery is that, despite the 1923 cut-off due to U.S.
copyright, BHL contains a lot of post-1923 articles. Indeed, a sparkline
of the number of articles over time shows that the bulk of the articles
I\'ve extracted from BHL are from the second half of the twentieth
Century. These include journals such as [*Entomological
News*](http://biostor.org/issn/0013-872X), and major herbaria and museum
publications, such as [*Annals of the Missouri Botanical
Garden*](http://biostor.org/issn/0026-6493),
[*Breviora*](http://biostor.org/issn/0006-9698), [*Bulletin of the
British Museum (Natural History).
Zoology*](http://biostor.org/issn/0007-1498), and [*Proceedings of the
United States National Museum*](http://biostor.org/issn/0096-3801).  
  

::: {style="text-align:center;"}
![](http://chart.apis.google.com/chart?chs=360x100&cht=ls&chco=0077CC&chm=B,e6f2fa,0,0.0,0.0&chd=t:0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,8,0,0,7,6,0,9,0,6,0,9,0,0,8,9,0,9,0,0,0,0,12,0,0,5,8,0,6,4,4,4,3,9,0,0,4,5,0,0,5,4,1,5,3,0,0,0,0,4,4,2,4,3,4,0,0,0,6,3,3,3,2,1,3,7,5,3,2,4,3,1,0,3,4,3,4,2,3,2,4,0,4,3,1,4,3,3,3,3,3,1,2,4,4,6,2,5,2,5,4,5,7,10,6,7,8,11,8,12,13,8,11,10,8,9,12,13,16,15,22,27,21,29,22,21,27,18,19,12,8,12,12,17,17,21,19,17,22,24,15,14,18,14,13,26,26,31,29,20,17,21,24,15,19,27,26,26,37,75,45,45,45,62,60,44,54,58,65,75,81,74,87,88,81,56,86,85,74,56,54,67,43,58,63,50,51,44,63,64,77,87,97,95,100,94,62,81,83,79,58,65,76,62,57,73,60,83,44,27,42,26,15,6,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0&chxt=x,y&chxl=0:%7C1750%7C1800%7C1850%7C1900%7C1950%7C2000%7C2050%7C1:%7C%7C278)
:::

  
  
This distribution partly reflects my own biased harvesting of BHL, but
perhaps it also reflects a transition in publishing (from books and
monographs to journals).  
  
**Exhibit**  
  
The interface to BioStor is still pretty rough, but one thing I\'ve had
fun adding is the [SIMILE
Exhibit](http://www.simile-widgets.org/exhibit/) widget to the author
pages. Exhibit enables faceted browsing, so you can filter an author\'s
list of publications by the journal they published, what year the
article was published, and who was a coauthor.  
  

::: {style="text-align:center;"}
![author.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/S03T6vakh7I/AAAAAAAAAlo/yYxcj1qIkhc/author.png?imgmax=800){border="0"
width="400"}
:::

  
  
One use I\'ve found is that you can quickly filter out purely
nomenclatural papers by select an author\'s publications in the
[Bulletin of Zoological
Nomenclature](http://biostor.org/issn/0007-5167).  
  
**Sparklines**  
  
I\'m a fan of sparklines, and I\'m a starting to add some to various
pages. For example, you can now see a graph of how many papers an author
has published over time, the example below is for the prolific [Charles
P Alexander](http://biostor.org/author/10073):  
  

::: {style="text-align:center;"}
![](http://chart.apis.google.com/chart?chs=300x50&cht=ls&chco=0077CC&chm=B,e6f2fa,0,0.0,0.0&chd=t:0,0,0,0,17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,17,17,50,83,50,50,33,50,83,33,100,50,50,50,33,17,33,17,17,17,0,0,0,0,0,0,0,0,0,0,50,17,0,33,33,33,33,50,33,17,50,17,50,0,0,33,33,17,33,50,33,33,0,33,33,33,33,17,0,33,17,33,33,17,0,0,0,0,0,0,0&chxt=x,y&chxl=0:%7C1880%7C1890%7C1900%7C1910%7C1920%7C1930%7C1940%7C1950%7C1960%7C1970%7C1980%7C1:%7C%7C6)
:::

  
  
**Search**  
  
This pretty much sums up search in BioStor at the moment:  
  

::: {style="text-align:center;"}
:::

  
  
**Harvesting**  
  
The rate of growth of BioStor has been pretty steady, partly because I
keep managing to find (or are alerted to, or are given) sources of
bibliographic metadata. I\'m also adding individual papers as I come
across them, either using the [Reference finder
form](http://biostor.org/openurl.php) directly, or by using OpenURL
[from within Endnote](http://biostor.org/endnote.php). But there\'s
still a crying need for large bibliographies that can be harvested.  
  
**Export**  
  
Individual references can be exported in a range of formats, and there
is a RSS feed, but I need to add bulk export (including the ability to
dump the whole database).  
  
**Viewer**  
  
The viewer I [developed
earlier](http://iphylo.blogspot.com/2009/11/bhl-viewer-now-with-go-faster-stripes.html)
is working reasonably well, but could do with sprucing up. I\'m also
toying with using other viewers as well as (or instead of) mine. One
possibility is [iPaper](http://www.scribd.com/developers) (although this
is Flash-based, and I\'d like to avoid Flash wherever possible).  
  
**Taxonomic names**  
  
One thing I\'ve discovered to my horror is just how common it is for the
BHL taxon finder to miss obvious taxonomic names. I need to investigate
this a bit more, but this is potentially a major issue as taxonomic
indexing is one of the primary ways people will find content in
BioStor  
  
**Future**  
  
There\'s still so much to do. For one thing, the
[visualisations](http://iphylo.blogspot.com/2009/10/biodiversity-heritage-library.html)
that originally got me seriously thinking about playing with BHL aren\'t
in BioStor yet. And there\'s a long [to-do
list](http://biostor.uservoice.com/forums/36526-general).


My BioStor project has reached over 13,000 articles, making it a sizeable respository of open access articles on biodiversity. It's still a tiny fraction of what could be extracted from the Biodiversity Heritage Library (BHL), but perhaps it's worth taking stock of what's there.
<b>
 Coverage
</b>
One pleasing discovery is that, despite the 1923 cut-off due to U.S. copyright, BHL contains a lot of post-1923 articles.

BioStor so far

The latest post on the EOL blog ([Biodiversity in a rapidly changing
world](http://blog.eol.org/2008/12/11/biodiversity-in-a-rapidly-changing-world/))
really, really annoys me. It claims that  
  

> The case of the red lionfish exemplfies how EOL can provide
> information for science-based decision making. Red lionfish are native
> to coral reef ecosystems in the Indo-Pacific. Yet, probably due to
> human release of the fish from aquariums, a large population has found
> itself in the waters near the Bahamas.

  
Nope, I suggest it demonstrates just how limited EOL is. If I view the
page for the [red lionfish](http://www.eol.org/taxa/17061533) I get an
out of date map from GBIF that shows a very limited distribution, and
doesn\'t show the introductions in Florida and the Bahamas (I have to
wade through text to find reference to the Florida introduction, and the
page doesn\'t mention the Bahamas!). The blog entry states that  

> In this senerio\[sic\], EOL and its data partners provide up to date
> information about the lionfish, or *pterois*\[sic\] *volitans*, in a
> species page.

  
Well, the GBIF map is old (a more recent map is available from [GBIF
itself](http://data.gbif.org/species/13546738)), the bibliography omits
key references such as [\"Biological invasion of the Indo-Pacific
lionfish Pterois volitans along the Atlantic coast of North
America\"](http://www.int-res.com/articles/meps2002/235/m235p289.pdf)
(useful reading for a \"science-based decision\", one would think). Most
of this information I got from Wikipedia, GBIF, and Google Scholar via
an [iSpecies search](http://ispecies.org/?q=Pterois+volitans).  
  
In other words, EOL in it\'s present state is serving limited, out of
date information. The gap between hype and delivery shows no sign of
narrowing. How can this help \"science-based decision making\"? Surely
there will come a point when people will tire of breathless statements
about how EOL will be useful, and they will start to ask [\"where\'s the
beef?\"](http://en.wikipedia.org/wiki/Where's_the_beef%3F)


The latest post on the EOL blog (Biodiversity in a rapidly changing world) really, really annoys me. It claims thatNope, I suggest it demonstrates just how limited EOL is. If I view the page for the red lionfish  I get an out of date map from GBIF that shows a very limited distribution, and doesn't show the introductions in Florida and the Bahamas (I have to wade through text to find reference to the Florida introduction, and the page doesn't

EOL hyperbole

Some thoughts on the first release of the [Encyclopedia of
Life](http://www.eol.org). I am being deliberately critical. This is a
high profile project with tens of millions of dollars in funding, lots
of people involved, and is accompanied by some of the most overblown
hype in organismal biology. In a sense I think EOL has set itself up by
over promising and under delivering.  
  
Before continuing, I should point out that I am involved in EOL in an
advisory capacity, but not in actually making anything. Some of the
tools I\'ve blogged about have made there way into EOL, such as
[Pygmybrowse](http://iphylo.blogspot.com/2007/10/pygmybrowse-revisited.html)
and reference parsing (see David Shorthouse\'s [excellent
work](http://ispiders.blogspot.com/2007/08/gimme-that-scientific-paper-part-iii.html)
on this).  
  
**Lack of content**  
I think the first release of EOL should have, at a minimum, provided at
least as much information that I can get from
[iSpecies](http://ispecies.org) and
[Wikipedia](http://en.wikipedia.org/wiki/Main_Page). Other projects,
such as [Freebase](http://www.freebase.com), have pre-populated their
databases with content from Wikipedia and other sources. Why didn\'t
EOL? If the argument is that they want authenticated content, then this
doesn\'t wash. Their authenticated content is minimal, and waiting for
authentication will, in my view, cripple EOL.  
  
**Exemplars are incomplete**  
The first release contains 25 exemplars. Pages for these taxa  

> \...show the kind of rich environment, with extensive information, to
> which all the species pages will eventually grow. The information on
> the exemplar pages has been authenticated (endorsed) by the scientists
> whose names are listed on these pages.

Well, I hope this isn\'t the standard EOL aspires to. The pages are
incomplete and not interlinked. One of the 25 chosen exemplars is
*Anolis carolinensis*. EOL lists its distribution as:  

> Widely-distributed throughout the southeastern United States: North
> Carolina to Key West, Florida, and west to southest Oklahoma and
> central Texas.

  
However, the GBIF map EOL displays shows lots of dots in Hawaii:  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSWON42LcyYMaIA6HvaH2N_9cKYNivk8cJnFiHg70F7tdqIRnxXM7RBpzUjG59qhfDqjFgX4kaYOmoB6US2yWb881jHm3YgDFMl3pXv1vbncMBpFPYr8pqU_h6AhhQ9GfglrRF/s320/draw.pl.png){#BLOGGER_PHOTO_ID_5171338706800824850
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSWON42LcyYMaIA6HvaH2N_9cKYNivk8cJnFiHg70F7tdqIRnxXM7RBpzUjG59qhfDqjFgX4kaYOmoB6US2yWb881jHm3YgDFMl3pXv1vbncMBpFPYr8pqU_h6AhhQ9GfglrRF/s1600-h/draw.pl.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
The EOL account is silent on this interesting distribution pattern. It
will come as no suprise that the [Wikipedia
account](http://en.wikipedia.org/wiki/Carolina_Anole) of the same
species tells us that it has been introduced into Hawaii. Wikipedia 1,
EOL 0.  
  
**Links**  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiIS6ywUhyphenhyphenMb-1ud4UixVuaqiqaSaR43juINdxyA-o3R5gvlgbCOPeIYKkjI6ZjbpiafZG-VVjwWkzn8HtliEMn1pXrUXAITPxc869qM1lzQtdEDL6vr5c97NHga_iKVLSmPDQ/s200/LocalImage.jpeg){#BLOGGER_PHOTO_ID_5171347322505220658
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiIS6ywUhyphenhyphenMb-1ud4UixVuaqiqaSaR43juINdxyA-o3R5gvlgbCOPeIYKkjI6ZjbpiafZG-VVjwWkzn8HtliEMn1pXrUXAITPxc869qM1lzQtdEDL6vr5c97NHga_iKVLSmPDQ/s1600-h/LocalImage.jpeg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
If two pages talk about species that are ecologically associated, then
surely those pages should be linked? Among the exemplars is *Pissodes
strobi*, the white pine weevil. In the EOL account, among the hosts
listed is *Pinus strobus*, another exemplar taxon. The accounts of these
two taxa **are not linked**. No hyperlink, nothing. The reader has no
idea that there is an exemplar account for *Pinus strobus*. Furthermore,
when reading the account for *Pinus strobus* there is no indication that
it is host to the white pine weevil.  
Surely the point of having all this information in one place is so that
it can be linked together?  
  
**BHL**  
EOL also exposes some limitations of the [Biodiversity heritage
Library](http://www.biodiversitylibrary.org/). Consider the exemplar
page for *Pinus strobus* L. The \"L.\" indicates that this species was
described by Linnaeus. Among the many references listed by BHL, none are
by Linnaeus. What gives?  
  
Well, the [IPNI
record](http://www.ipni.org:80/ipni/idPlantNameSearch.do?id=263339-1&back_page=%2Fipni%2FeditSimplePlantNameSearch.do%3Ffind_wholeName%3DPinus%2Bstrobus%26output_format%3Dnormal)
reveals that this species was described on p. 1001 of *Species
Plantarum*. BHL has digitised *Species Plantarum*, and [page
1001](http://www.biodiversitylibrary.org/page/359007) has *Pinus
strobus*:  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqRDeekLWSoXeurJbONJtafbMMQz5bn-x4WgTWB0y5UVCdQb8fNhV7WYtdwegAKQ5qV9NBJL8HbL9qbrUgq3YU8C6ko-PCRcQjpjEeOS3qeX9vgprhFtMYYNLdpoGzfiNLv8n6/s320/strobus.jpg){#BLOGGER_PHOTO_ID_5171353103531201090
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqRDeekLWSoXeurJbONJtafbMMQz5bn-x4WgTWB0y5UVCdQb8fNhV7WYtdwegAKQ5qV9NBJL8HbL9qbrUgq3YU8C6ko-PCRcQjpjEeOS3qeX9vgprhFtMYYNLdpoGzfiNLv8n6/s1600-h/strobus.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
Now, BHL relies on uBio\'s tools to extract names, and Linnaeus didn\'t
make this easy (the specific epithet *strobus* is in the right hand
margin, separate from *Pinus*), but one would have thought that for the
exemplar taxa an effort would have been made to link Linnaean names to
BHL content \-- what better place to showcase the link between a name
and its publication? It\'s quite easy to do, given that
[IPNI](http://www.ipni.org) has page numbers for plant names. Just map
page numbers to BHL URLs, and you\'re done.  
  
**Inconsistency**  
Going down the taxonomic hierarchy weird things happen. When viewing the
plant genus *Morus* if I can see a picture of *Morus nigra* (presumably
this is \"authenticated\" content). If I drill down to the species
*Morus nigra*, I\'m told there is no authenticated content for this
species. Either the image is *Morus nigra* or it isn\'t. If it is, why
not show it, if it isn\'t, why claim that it is?  
  
  
  
**Logos**  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOYAvReMxHErInnV38TkmSnbBlTx0EwHlddHMNbOouYUaRTApILdL-T8R34QQZ7BlXAqgqBCRpVbt9YBT4-cFztsGEGHM9gIdcdHYga9A-A64f7gh1HRQ1alNppG6wCP657rWx/s200/bhl_logo.gif){#BLOGGER_PHOTO_ID_5171334948704440834
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOYAvReMxHErInnV38TkmSnbBlTx0EwHlddHMNbOouYUaRTApILdL-T8R34QQZ7BlXAqgqBCRpVbt9YBT4-cFztsGEGHM9gIdcdHYga9A-A64f7gh1HRQ1alNppG6wCP657rWx/s1600-h/bhl_logo.gif){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Way too much space is devoted to logos of various contributors, BHL
being the worst offender (it doesn\'t help that the BHL content is
incomplete, lacking links for Linnaean names). **I don\'t care about
logos**. Contributors may care about getting their logos displayed, but
users couldn\'t care less. They get in the way. On some pages, there\'s
more screen space devoted to logos than information (e.g., the page for
[*Apomys datae*](http://www.eol.org/taxa/16985004)). This is, frankly,
ridiculous, and reflects a warped set of priorities.  
  
What\'s worse, all these logos are associated with links that take
people **away** from EOL. Hence EOL becomes little more than a
collection of web links to other sites.  
  
**Search**  
The search is based on the [Catalogue of
Life](http://www.catalogueoflife.org/annual-checklist/2007/search.php),
and inherits the same problems. For example, if I search for \"Morus\" I
get a list in alphabetical order of taxonomic names that contain the
string \"morus\". The two names that are **an exact match** occur as
items three and four on the list \-- they should be first and second.  
  
It gets worse if I search on \"Tyrannosaurus rex\". EOL doesn\'t do
dinosaurs, and so doesn\'t contain anything on *T. rex*, but the search
results tell me that **The following 116 search results contain
\'Tyrannosaurus rex\'**. Nope, none of them do.  
  
The search engine is poorly done, it fails to rank results sensibly,
incorrectly reports what it does find, and has no support for spelling
mistakes.  
  
**Authenticated content**  
This is probably the thing that, if left as it is, will strangle EOL.
The insistence on \"authenticated (endorsed)\" content places a severe
brake on what EOL can offer.  
  
**It\'s a web site**  
EOL\'s web site has no mechanism for people to extract data (e.g., RSS
feeds, microformats, links to RDF, etc.). It\'s intended to be read by
humans, not machines. This greatly diminishes its utility.  
  
So, I\'ve got that off my chest. The first release was always going to
be a disappointment, especially given the hype. What frustrates me,
however, is just how far the first release is from what it could have
been.  
  
The real question is how much the issues I\'ve raised are things which
are easy to fix given time, or whether they reflect underlying problems
with the way the project is conceived.


Some thoughts on the first release of the Encyclopedia of Life. I am being deliberately critical. This is a high profile project with tens of millions of dollars in funding, lots of people involved, and is accompanied by some of the most overblown hype in organismal biology.

Rogue Scholar Beiträge

BioStor so far

EOL hyperbole

Encyclopedia of Life - first impressions