University of Glasgow

Roderic Page

> [@rdmpage](https://twitter.com/rdmpage)[@AlexHardisty](https://twitter.com/AlexHardisty)[@proibiosphere](https://twitter.com/proibiosphere)
> Well, take part in the process of clarification!
>
> --- Pensoft Publishers (@Pensoft) [June 10,
> 2014](https://twitter.com/Pensoft/statuses/476448848572067841)

  
I\'ve been involved in a few Twitter exchanges about the upcoming
[pro-iBiosphere
meeting](http://wiki.pro-ibiosphere.eu/wiki/Final_Conference) regarding
the \"Open Biodiversity Knowledge Management System (OBKMS)\", which is
the topic of the meeting. Because for the life of me I can\'t find an
explanation of what \"Open Biodiversity Knowledge Management System\"
is, other than vague generalities and appeals to the magic pixie dust
that is \"Linked Open Data\" and \"RDF\", I\'ve been grumbling away on
Twitter.  
  
So, here\'s my take on what needs to be done. Fundamentally, if we are
going to link biodiversity information together we need to build a
network. What we have (for the most part) at the moment is a bunch of
nodes (which you can think of as data providers such as natural history
collections, databases, etc., or different kinds of data, such as names,
publications, sequences, specimens, etc.).  
  
![1](http://lh3.ggpht.com/-1KAPFoCAkvw/U5gne46fP2I/AAAAAAAADaM/Mbx5XTcWKjo/1.png?imgmax=800 "1.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="300" height="241"}  
We\'d like a network, so that we can link information together, perhaps
to discover new knowledge, to serve as a pathway for analyses that
combine different sorts of data, and so on:  
  
![2](http://lh3.ggpht.com/-kKx-O09ClKQ/U5gnflRsBkI/AAAAAAAADaU/TkaVTX9k8XE/2.png?imgmax=800 "2.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="300" height="241"}  
A network has nodes and links. Without the links there\'s no network.
The fundamental problem as I see it is that we have nodes that have
clear stakeholders (e.g., individual, museums, herbaria, publishers,
database owners, etc.). They often build links, but they are typically
incomplete (they don\'t link to everything that is relevant), and
transitory (there\'s no mechanism to facilitate persistence of the
links). **There is no stakeholder for whom the links are most
important**. So, we have this:  
  
![3](http://lh6.ggpht.com/-lpMCa1B7TM8/U5gngqyDzMI/AAAAAAAADac/6vsdr7yANiM/3.png?imgmax=800 "3.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="300" height="242"}  
This sucks. I think **we need an entity, a project, and organisation,
whatever you want to call it for whom the network is everything**. In
other words, they see the world like this:  
![4](http://lh6.ggpht.com/-_xqqnb-d9iE/U5gnhJkVHyI/AAAAAAAADak/-PFfc1n8s_I/4.png?imgmax=800 "4.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="300" height="237"}  
If this is how you view the world, then your aim is to build that
network. You live or die based on the performance of that network. **You
make sure the links exist, they are discoverable, and that they
persist.** You don\'t have the same interests as the nodes, but clearly
you need to provide value to them because they are the endpoints of your
links. But you also have users who don\'t need the nodes per see, they
need the network.  
  
If you buy this, then you need to think about how to grow the network.
**Are there network effects that you can leverage**, in the same way
CrossRef has with publishers submitting lists of literature cited linked
to DOIs, or in social media where you give access to your list of
contacts to build your social graph?  
  
If the network is the goal, you don\'t just think \"let\'s just stick
HTTP URLs on everything and it will all be good\". You can think like
that if you are a node, because if the links die you can still persist
(you\'ll still have people visiting your own web site). But **if you are
a network and the links die, you are in big trouble**. So you develop
ways to make the network robust. This is one reason why CrossRef uses an
identifier based on indirection, it makes it easier to ensure the
network persists in the face of change in how the nodes serve their
data. What is often missed is that **this also frees up the nodes**,
because they don\'t need to commit to serving a given URL in perpetuity,
indirections shields them from this.  
  
In order to serve users of the network, you want to ensure you can
satisfy their needs rapidly. This leads to things like caching links and
basic data about the end points of those links (think how Google caches
the contents of web pages so if the site is offline you may still find
what you are looking for).  
  
If your business depends on the network, then you need to think how you
can create incentives for nodes to join. For example, **what services
can you offer them that make you invaluable to the nodes?** Once you
crack that, then all sorts of things can happen. Take structured markup
as an example. Google is driving this on the web using
[schema.org](http://schema.org). If you want to be properly indexed by
Google, and have Google display your content in a rich form (e.g.,
thumbnails, review ratings, location, etc.) you need to mark up your
page in a way Google understands. **Given that some businesses live or
die based on their Google ranking, there\'s a strong incentive for web
sites to adopt this markup**. There\'s a strong incentive for Google to
encourage markup so that it can provide informative results for its
users (otherwise they might rely on \"social search\" via Facebook and
mobile apps). This is the kind of thing you want the network to aim
for.  
  
In summary, this is my take on where we are at in biodiversity
informatics. The challenge is that the organisations in the room
discussing this are typically all nodes, and I\'d argue that by
definition they aren\'t in a position to solve the problem. **You need
to pivot (ghastly word) and think about it from the perspective of the
network.** Imagine you were to form a company whose mission was to build
that network. How would you do it, how would you convince the nodes to
engage, what value would you offer them, what value would you offer
users of the network? If we start thinking along those lines, then I
think we can make progress.


I've been involved in a few Twitter exchanges about the upcoming pro-iBiosphere meeting regarding the "Open Biodiversity Knowledge Management System (OBKMS)", which is the topic of the meeting. Because for the life of me I can't find an explanation of what "Open Biodiversity Knowledge Management System" is, other than vague generalities and appeals to the magic pixie dust that is "Linked Open Data" and "RDF", I've been grumbling away on Twitter.

The vision thing - it's all about the links

![Unknown](http://lh6.ggpht.com/-hoG9F68aBoA/UvjtfuhfddI/AAAAAAAADQk/QmMlAV8U39E/Unknown.png?imgmax=800 "Unknown.png"){border="0"
width="135" height="135" style="float:right;"}I gave a remote
presentation at a
[proiBioSphere](http://wiki.pro-ibiosphere.eu/wiki/MS12_-_Workshop_on_mark-up_of_biodiversity_literature)
workshop this morning. The slides are below (to try and make it a bit
more engaging than a desk of Powerpoints I played around with Prezi).  
  

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There is a version on Vimeo that has audio as well.  
  

  
I sketched out the biodiversity \"knowledge graph\", then talked about
how mark-up relates to this, finishing with a few questions. The
question that seems to have gotten people a little agitated is the
relative importance of markup versus, say, indexing. As Terry Catapano
pointed out, in a sense this is really a continuum. If we index content
(e.g., locate a string that is a taxonomic name) and flag that content
in the text, then we are adding mark-up (if we don\'t, we are simply
indexing, but even then we have mark-up at some level, e.g. \"this term
occurs some where on this page\"). So my question is really what level
of markup do we need to do useful work? Much of the discussion so far
has centered around very detailed mark-up (e.g., the kind of thing
*ZooKeys* does to each article). My concern has always been how scalable
this is, given the size of the taxonomic literature (in which *ZooKeys*
is barely a blip). It\'s the usual trade off, do we go for breadth (all
content indexed, but little or no mark-up), or do we go for depth
(extensive mark-up for a subset of articles)? Where you stand on that
trade off will determine to what extent you want detailed mark up,
versus whether indexing is \"good enough\".  


I gave a remote presentation at a proiBioSphere workshop this morning. The slides are below (to try and make it a bit more engaging than a desk of Powerpoints I played around with Prezi).  There is a version on Vimeo that has audio as well. I sketched out the biodiversity "knowledge graph", then talked about how mark-up relates to this, finishing with a few questions.

Mark-up of biodiversity literature

I\'ve just come back from a pro-iBiosphere [Workshop at
Leiden](http://wiki.pro-ibiosphere.eu/wiki/Workshops_Leiden_February_2013)
where the role of \"legacy literature\" became the subject of some
discussion. This continued on Twitter as Ross Mounce
([@rmounce](http://twitter.com/rmounce)) and I went back and forth:  

> @[rdmpage](https://twitter.com/rdmpage) but \~700,000 papers were
> published in 2009. Were there even 70,000 published in 1920? 2000-2012
> contains \*a lot\*  
> --- Ross Mounce (@rmounce) [February 13,
> 2013](https://twitter.com/rmounce/status/301774549329010688)

Ross was wondering whether we should invest much effort in extracting
information from legacy literature, suggesting that this literature was
of most interest to taxonomists, whereas other biologists will be more
likely to find what they want from ever growing recent literature. I was
arguing that because many taxa are poorly studied, the chances that you
will find data on your organism in the recent literature is likely to be
low, unless you study an economically or medically important taxon, or a
model organism (many of which fit first categories). My view is based on
papers such as Bob May\'s 1988 paper:  

> MAY, R. M. (1988). How Many Species Are There on Earth? Science,
> 241(4872), 1441-1449.
> [doi:10.1126/science.241.4872.1441](http://dx.doi.org/10.1126/science.241.4872.1441)

In table 3 May lists the average number of papers per species in the
period 1978-1987 across various taxonomic groups. Mammals averaged 1.8
papers per species, beetles averaged 0.01. This means that if you study
a beetle species you have a 1/100 chance (on average) of finding a paper
on your species in any given year (assuming all beetles are equal, which
is clearly false). At this point perhaps we should define \"legacy
literature\". In many ways the issue is not so much the age of the
literature, but whether the literature was \"born digital\", that is,
whether from it\'s authoring to publication the document has been in
digital form, so the output is in a format (e.g., HTML, XML, or PDF that
contains the document text) from which we can readily extract and mine
the text. In contrast, documents that have been digitised from a
physical medium (e.g., scans of pages) are less tractable because the
text has to be extracted by
[OCR](http://en.wikipedia.org/wiki/Optical_character_recognition), and
error-prone process. Given these errors is the effort worth it. At this
point I should say that BHL is not using the best OCR technology
available (my own experience suggests that [ABBYY
Online](http://www.abbyyonline.com/) is much better), and our community
is not making use of [research on automating OCR
correction](http://www.mendeley.com/groups/752871/ocr-optical-character-recognition/papers/)).
But the question is worth asking. In an effort to answer it, I\'ve done
a quick analysis of the PanTHERIA database:  

> Jones, K. E., Bielby, J., Cardillo, M., Fritz, S. A., O Dell, J.,
> Orme, C. D. L., & Purvis, A. (2009). PanTHERIA: a species-level
> database of life history, ecology, and geography of extant and
> recently extinct mammals. (W. K. Michener, Ed.)Ecology, 90(9),
> 2648-2648.
> [doi:10.1890/08-1494.1](http://dx.doi.org/10.1890/08-1494.1)

PanTHERIA is a database assembled by Kate Jones
([@ProfKateJones](http://twitter.com/ProfKateJones)) and colleagues for
comparative biologists (not taxonomists), and collects fundamental
biological data about the best studied animal group on the planet (see
May\'s paper above). In the metadata for the database there is a list of
the 3143 publications they consulted to populate the database. Below is
a table showing the distribution of the year in which these publications
appeared:  
  

|                 |              |
|-----------------|--------------|
| Decade starting | Publications |
| 1840            | 1            |
| 1860            | 1            |
| 1890            | 1            |
| 1900            | 10           |
| 1910            | 4            |
| 1920            | 14           |
| 1930            | 48           |
| 1940            | 61           |
| 1950            | 114          |
| 1960            | 295          |
| 1970            | 527          |
| 1980            | 865          |
| 1990            | 1019         |
| 2000            | 183          |

![Pantheria](http://lh5.ggpht.com/-dUEegSNzxJM/URy3ZtjGV3I/AAAAAAAACbw/YyRd_5nkyWM/pantheria.png?imgmax=800 "pantheria.png"){border="0"
height="348"
style="display: block; margin-left: auto; margin-right: auto;"
width="450"} The bulk of the papers came from the second half of the
20th century, and many of these are \"legacy\" in the sense that they
are in archives like JSTOR, and hence the PDFs are based on scanned
images and OCR. The oldest papers are from the 19th century, which is
legacy by anyone\'s definition. My interpretation of this data is that
even for a well-studied group such as mammals, the basic
organismal-level data sought by comparative biologists is in the
\"legacy\" literature. My suspicion is that if we attempt to build
PanTHERIA-style databases for other, less well-studied taxa, the data
(if it exists at all) will be found not in the modern literature (where
the focus has long since moved on from the organism to genomics and
system biology) but in the corpus of taxonomic and ecological literature
that are being scanned and stored in digital archives.  
  
**Update**  
I\'ve put the articles cited as data sources by the PanTHERIA database
in a [Mendeley
group](http://www.mendeley.com/groups/3069321/pantheria/overview/).


I've just come back from a pro-iBiosphere Workshop at Leiden where the role of "legacy literature" became the subject of some discussion.

Messaggi di Rogue Scholar

The vision thing - it's all about the links

Mark-up of biodiversity literature

Does the legacy biodiversity literature matter?