University of Glasgow

Roderic Page

> [@rdmpage](https://twitter.com/rdmpage)
> [@BioDivLibrary](https://twitter.com/BioDivLibrary)
> [@bouchoutdec](https://twitter.com/bouchoutdec) Why aren\'t you
> creating an iphylo blog what metrics you expect to see so you will not
> be disappointed?
>
> --- Donat Agosti (@myrmoteras) [May 1,
> 2015](https://twitter.com/myrmoteras/status/594151154914693121)

> There are no requirements for signing up. A signature is first and
> foremost a statement of support for open data . Each signatory can
> determine how best to make progress towards the goal. Some
> recommendations are included in the declaration. We hope that
> signatories will become early adopters of the open access approach,
> that they will promote change in their institutions, societies and
> journals, and will position themselves and their institutions as
> leaders. (from <http://www.bouchoutdeclaration.org/faqs/>)

![M13QFZi4](http://lh3.googleusercontent.com/-KBiVfFvubjM/VUzyDYGQuII/AAAAAAAADus/GtUQB590U5o/m13QFZi4.jpeg?imgmax=800 "m13QFZi4.jpeg"){border="0"
width="94" height="107" style="float:right;"}I\'ve put off writing this
post about the [Bouchout
Declaration](http://www.bouchoutdeclaration.org) for a number of
reasons. I attended the meeting that launched the declaration last year,
and from my perspective that was a frustrating meeting. Much talk about
\"Open Biodiversity Knowledge Management\" with nobody seemingly willing
or able to define it (see [The vision thing - it\'s all about the
links](http://iphylo.blogspot.com/2014/06/the-vision-thing-it-all-about-links.html)
for some comments I made before attending the meeting), and as much as
the [signing of the Boechout
Declaration](http://www.bouchoutdeclaration.org/news/messge/bouchout-declaration-successfully-launched/6ebcb917076b38ea5eb57d3fd2c8d4a5/)
provided good theatre, it struck me as essentially an empty gesture.
Public pronouncements are all well and good, but are ultimately of
little value unless backed up by action. We have institutions that have
signed the declaration yet have much of their intellectual output locked
behind paywalls (e.g., [JSTOR Global
Plants](http://iphylo.blogspot.com/2013/02/why-are-botanists-locking-away-their.html)).
So much for being open.

So, since [Donat challenged
me](https://twitter.com/myrmoteras/status/594143276107702272), here\'s
what I\'d like to see happen. I\'d like to see metrics of \"openness\"
that we can use to evaluate just how open the signatories actually are.
These metrics could be viewed as ways to try and persuade institutions
into sharing data and other information, as a league table we can use to
apply pressure, or as a way to survey the field and see what the
impediments are to being open (are they financial, legal, cultural,
resource, etc.).

Below are some of the things I think we could \"score\" the openness of
biodiversity institutions.

#### Is the collection digitised and in GBIF?

Simple criterion that is easy to measure. If an institution has
specimens or other biological material, is data and or metadata on the
collection freely available? What fraction of the collection has been
digitised? How good is that digitsation (e.g., what fraction has been
georeferenced?). We could define digitisation more broadly to include
imaging and sequencing (both are methods of converting analogue
specimens into digital objects).

#### Are the institutional publications digitised? Are they open access?

Some institutions have a history of digitising their in-house
publications and making them freely available online (e.g., the AMNH),
some even make them fully citable with CrossRef DOIs (e.g., the
Australian Museum). But some institutions have, sadly, signed over their
publications to commercial publishers or archives that charge for access
(e.g., Kew\'s publications have been digitised by JSTOR, which limits
their accessibility). As a foot note, I suspect that those institutions
that lost confidence in their in-house publishing operations and
outsourced them are the ones who have ended up loosing control of their
intellectual output, some of which is now closed off (e.g., some of the
NHM London\'s journals are now the property of Cambridge University
Press). Those institutions that maintained a culture of in-house
publishing are the ones at the vanguard of digitising and opening up
those publications.

#### Does the institution take part on the Biodiversity Heritage Library?

There are at least two ways to participate in the [Biodiversity Heritage
Library](http://biodiversitylibrary.org) (BHL), one is by becoming a
member and start scanning books from institutional libraries. The other
is by granting permission to BHL to scan institutional publications. BHL
is often viewed as an archive of \"old\" literature, but in fact it has
some very recent content. Some farsighted organisations have let BHL
scan their journals, contributing to BHL becoming an indispensable
resource for biodiversity research.

#### Do institution staff publish in open access journals?

A while ago I complained about how few new species descriptions were in
open access journals ([The top-ten new species described in 2010 and the
failure of taxonomy to embrace Open Access
publication](http://iphylo.blogspot.com/2011/05/top-ten-new-species-described-in-2010.html)).
A measure of openness is whether an institution encourages its staff to
publish their work in open access journals, and to make their data
freely available as well. Some prefer to chase *Nature* and *Science*
papers, but I\'d like to think we could prioritise openness over journal
impact factor.

These are just some of the more obvious things that could be used to
measure openness. At the same time, it would be useful to develop ways
to show the benefits of being open. For example, I\'ve long argued that
we could develop citation tracking for specimens. This gives researchers
a means to track provenance of information (who said what about the
identity of a specimen), and it also gives institutions a way to measure
the impact of their collections. Doing this at scale is only going to be
possible if collections are digitised, specimens have identifiers of
some sort, and we can text mine the literature and associated data for
those identifiers (in other words, the data and publications need to be
open). So, perhaps on way to help make the case for being open is to
develop metrics that are useful for the institutions themselves.

I guess I would have been much more enthusiastic about the Bouchout
Declaration if these sort of things had been in place at the start.
Anyone can sign a document. Ideas are cheap, execution is everything.


I've put off writing this post about the Bouchout Declaration for a number of reasons. I attended the meeting that launched the declaration last year, and from my perspective that was a frustrating meeting.

Putting some bite into the Bouchout Declaration

![BHL Small
Logo](http://lh5.ggpht.com/-LcQpbQwPu9g/VJqbux9nTZI/AAAAAAAADoI/GXaYEKUl0Jk/BHL_Small_Logo.jpg?imgmax=800 "BHL_Small_Logo.jpg"){border="0"
width="128" height="102" style="float:right;"}One of my guilty pleasures
on a Sunday morning is browsing new content on [the Biodiversity
Heritage Library (BHL)](http://biodiversitylibrary.org). Indeed, so
addicted am I to this that I have an [IFTTT.com](http://ifttt.com) feed
set to forward the BHL RSS feed to my iPhone (via the [Pushover
app](https://pushover.net/). So, when I wake most Sunday mornings I have
a red badge on Pushover announcing fresh BHL content for me to browse,
and potentially add to [BioStor](http://biostor.org).  
  
But lately, there has been less and less content that is suitable for
BioStor, and this reflects two trends that bother me. The first, [which
I\'ve blogged about
before](http://iphylo.blogspot.com/2014/04/breaking-biodiversity-heritage-library.html),
is that an increasing amount of BHL content is not hosted by BHL itself.
Instead, BHL has links to external providers. For the reasons I\'ve
given earlier, I find this to be a jarring user experience, and it
greatly reduces the utility of BHL (for example, this external content
is not taxonomically searchable).  
  
The other trend that worries me is that recently BHL content has been
dominated by a single provider, namely the U.S. Department of
Agriculture. To give you a sense of how dominant the USDA now is, below
is a chart of the contribution of different sources to BHL over time.  
  
![Chart
annotated](http://lh4.ggpht.com/-GbzHrWjUzQs/VJqaQ6Pm18I/AAAAAAAADn8/MGEUYbpI77o/chart-annotated.png?imgmax=800 "chart-annotated.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="500"}  
  
I built this chart by querying the BHL API and extracting data on each
item in BHL (source code and raw data available on
[github](https://github.com/rdmpage/bhl-contributors)). Unfortunately
the API doesn\'t return information on what each item was scanned, but
because the identifier for each item (its ItemID) is an increasing
integer, if we order the items by their integer ID then we order them by
the date they were added. I\'ve binned the data into units of 1000 (in
other words, every item with an ItemID \< 1000 is in bin 0, ItemIDs 1000
to 1999 are in bin 1, and so on). The chart shows the top 20
contributors to BHL, with the Smithsonian as the number one
contributor.  
  
The chart shows a number of interesting patterns, but there are a couple
I want to highlight. The first is the noticeable spikes representing the
addition of externally hosted material (from the American Museum of
Natural History Library and the Biblioteca Digital del Real Jardin
Botanico de Madrid). The second is the recent dominance of content from
the USDA.  
  
Now, to be fair, I must acknowledge that I have my own bias as to what
BHL content is most valuable. My own focus is on the taxonomic
literature, especially original descriptions, but also taxonomic
revisions (useful for [automatically extracting
synonyms](http://iphylo.blogspot.com/2014/11/automatically-extracting-possible.html)).
Discovering these in BHL is what motivated me to build
[BioStor](http://biostor.org), and then [BioNames](http://bionames.org),
the later being a database that aims to link every animal taxon name to
its original description. BioNames would be much poorer if it wasn\'t
for BioStor (and hence BHL).  
  
If, however, your interest is agriculture in the United States, then the
USDA content is obviously a potential goldmine of information on topics
such as past crop use, pricing policies, etc. But this a topic that is
both taxonomically narrow (economically important organisms are a tiny
fraction of biodiversity), and, by definition, geographically narrow.  
  
To be clear, I don\'t have any problem with BHL having USDA content as
such, it\'s a tremendous resource. But I worry that lately BHL has been
pretty much **all** USDA content. There is still a huge amount of
literature that has yet to be scanned. I\'d like to see BHL actively
going after major museums and libraries that have yet to contribute. I
especially want to see more post-1923 content. BHL has managed to get
post-1923 content from some of its contributors, it needs a lot more. On
obvious target is those institutions that signed the [Bouchout
Declaration](http://www.bouchoutdeclaration.org/declaration/). If
you\'ve signed up to providing \"free and open use of digital resources
about biodiversity\", then let\'s see something tangible from that -
open up your libraries and your publications, scan them, and make them
part of BHL. I\'m especially looking at European institutions who (with
some notable exceptions) really should be doing a lot better.  
  
It\'s possible that the current dominance of USDA content is a temporary
phenomenon. Looking at the chart above, BHL acquires content in a fairly
episodic manner, suggesting that it is largely at the mercy of what its
contributors can provide, and when they can do so. Maybe in a few months
there will be a bunch of content that is taxonomically and
geographically rich, and I will be spending weekends furiously
harvesting that content for BioStor. But until then, my Sundays are not
nearly as much fun as they used to be.  


One of my guilty pleasures on a Sunday morning is browsing new content on the Biodiversity Heritage Library (BHL). Indeed, so addicted am I to this that I have an IFTTT.com feed set to forward the BHL RSS feed to my iPhone (via the Pushover app. So, when I wake most Sunday mornings I have a red badge on Pushover announcing fresh BHL content for me to browse, and potentially add to BioStor.

Messaggi di Rogue Scholar

Putting some bite into the Bouchout Declaration

I'm worried about the Biodiversity Heritage Library (BHL)