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

This seems to be the season for big, arm-wavy documents about the future
of biodiversity informatics (see [A decadal view of biodiversity
informatics: challenges and
priorities](http://iphylo.blogspot.com/2013/04/a-decadal-view-of-biodiversity.html)).
An equivalent document is being drafted based on the [Global
Biodiversity Informatics Conference (GBIC
2012)](http://www.gbic2012.org/) conference. Writing these documents is
hard work, they have to balance a set of conflicting visions, predict
the future, and communicate a coherent plan to people who either could
help make this happen, or feel they have a stake in the outcome.  
  
Leaving all those constraints behind, and waving arms wildly, here\'s
one take on the future of biodiversity informatics. I see three
themes.  
  
**1. Knowing what we know**  
  
We have a limited grasp of how much we actually know, and crap tools to
summarise this knowledge. I want a Google Analytics for biodiversity
data where I can see at a glance the current state of our knowledge
(e.g., what is the rate of sequencing of environmental samples in the
Mediterranean? How much of Indonesia\'s amphibian fauna is in protected
areas?). These are fairly trivial queries. If Google can analyse web
traffic from sites being hit over a million times per day ( \~ 365
million hits per year) we can do the same thing on GBIF-scale databases.
There is huge scope here for cool visualisation of the growth of our
knowledge, such as this:  
  

::: {.iframe src="http://player.vimeo.com/video/6916985"}
:::

[If biologists were explorers (Mammalia)\...](http://vimeo.com/6916985)
from [Andrew W Hill](http://vimeo.com/andrewxhill) on
[Vimeo](http://vimeo.com).

  
Imagine the GBIF classification like this:  
  

::: {.iframe src="http://player.vimeo.com/video/25344427"}
:::

[filesystem visualisation](http://vimeo.com/25344427) from [wonderful
websolutions](http://vimeo.com/user7391360) on
[Vimeo](http://vimeo.com).

**2. Life stream**  
  
Terrible title, but this is where we monitor change, both \"organic\"
and anthropogenic. This is where we use data mining to do a sentiment
analysis of the biosphere, looking to detect changes such as outbreaks
of disease, invasive species, etc. This builds on 1 but focusses on
change. Imagine a \"news service\" for biology along the lines of tools
available to financial markets (e.g., Silobreaker):  
  

::: {.iframe}
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This is where we interface with decision makers, in the sense that
[Braulio Dias\'s
statement](http://imsgbif.gbif.org/CMS_NEW/get_file.php?FILE=508666625a662054bfa02ffbc4feea)
\"I am convinced that the lack of adequate biodiversity monitoring is at
the heart of our difficulties to make convincing arguments\" is true,
this tackles that question.  
  
**3. Modelling the biosphere**  
  
Time to model all life on Earth (<http://dx.doi.org/10.1038/493295a>) is
our equivalent of a moon shot (oh how I hate that analogy). Purves et
al. have made the case, this is the task that will galvanise people
outside the taxonomy/biodiversity community. This is real megascience
(1. is data collection, 2. is data mining and analysis). Climate
modellers and oceanographers get to do this:  
  

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[Sieh dir dieses Video auf www.youtube.com
an](https://www.youtube.com/watch?v=QwIvYwJXObc){target="_blank"} oder
aktiviere JavaScript, falls es in deinem Browser deaktiviert sein
sollte.
:::
:::
:::

  
  
Can we do the same?


This seems to be the season for big, arm-wavy documents about the future of biodiversity informatics (see A decadal view of biodiversity informatics: challenges and priorities). An equivalent document is being drafted based on the Global Biodiversity Informatics Conference (GBIC 2012) conference.

Thoughts on GBIC 2012 and a vision of the future of biodiversity informatics

Time for more half-baked ideas. There\'s been a lot of discussion on
Twitter about EOL, Linked Data (sometimes abbreviated LOD), and
Wikipedia. Pete DeVries ([@pjd](http://twitter.com/pjd)) is keen on LOD,
and has been asking why TDWG isn\'t playing in this space. I\'ve been
muttering dark thoughts about EOL, and singing the praises of Wikipedia.
On so it goes on. So, here\'s one vision of where we could (?should) be
going with this.  
  
Let\'s imagine that we do indeed want to play in the Linked Data space.
The concern that tends to raised the most is that biodiversity
informatics uses LSIDs as the standard GUID, and this doesn\'t play nice
with Linked Data. This is true, but not life threatening. There are
various hacks (like
[this](http://iphylo.blogspot.com/2009/04/lsids-http-uri-linked-data-and-bioguid.html)
and [this](http://biocol.org/static/webserves.html) that deal with
this).  
  
But, the real concern (I think) is that we need a way to link our stuff
to the rest of the Linked Data cloud. That is, wherever possible we need
to **reuse** existing identifiers. In the LOD diagram below (for the
latest version see [here](http://linkeddata.org/))
[DBpedia.org](http://dbpedia.org) is key to linking much of this
together, and major players (such as the
[BBC](http://derivadow.com/2009/06/11/interesting-semantic-web-stuff/))
are now using DBpedia.org to [make
connections](http://derivadow.files.wordpress.com/2009/06/eswc2009-bbc-dbpedia-2.pdf).  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3TgLEfnov-sT62v30YeoprIGiW6lOs70p30pgvT7ccXppUCc1zMzAgH9nMMf_FsdypbyzUdcVCE68UOJILvjWnFtT9uiGHBAYFfRCppXh_OrlXJCBLNIzxVRDdf5pSJYekebH/s400/lod-datasets_2009-03-05-scaled.png){#BLOGGER_PHOTO_ID_5323331608339372786
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 305px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3TgLEfnov-sT62v30YeoprIGiW6lOs70p30pgvT7ccXppUCc1zMzAgH9nMMf_FsdypbyzUdcVCE68UOJILvjWnFtT9uiGHBAYFfRCppXh_OrlXJCBLNIzxVRDdf5pSJYekebH/s1600-h/lod-datasets_2009-03-05-scaled.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
DBpedia.org is based on Wikipedia, so I think you can see where this is
going. There are some 120,000+ taxon pages in Wikipedia, so that\'s some
120,000+ identifiers in DBpedia.org that others interested in organisms
can (and will) use to refer to taxa. Given the centrality of Wikipedia
and DBpedia to LOD, why don\'t we adopt DBpedia.org URIs as the default
GUID for our taxa? At present we have numerous, competing identifiers
(e.g., NCBI tax ids, ITIS tsn\'s, Catalogue of Life LSIDs, uBio
NameBankID\'s, plus LSIDs from various nomenclators). For users this is
a mess \-- which one do I use? Deciding requires dealing with issues
(such as the difference between nomenclatural codes, and between
taxonomic names and concepts, etc., that frankly, nobody outside our
community cares about.  
  
So, if we want to play with LOD, we need to make our identifiers play
nice (straightforward), and we should think seriously about adopting
DBpedia.org URIs as the default GUID for taxa.  
  
Now, where does this leave EOL? Well, frankly, it should get out of the
business of making web pages for taxa, because Wikipedia owns that space
already. Their pages are fewer, but often much more detailed than the
corresponding EOL page, and Wikipedia [reacts faster to new
discoveries](http://blog.eol.org/2008/05/29/sos-state-of-observed-species/).
Wikipedia supports community editing, versioning, and quite
sophisticated tools for handling biblographic references.  
  
There\'s plenty of scope for userful tools and services for EOL to
develop, but I think the real game is elsewhere. Now, Wikipedia is far
from perfect. It\'s basically semi-structured text with a God-awful
template language, and it would benefit greatly from more structure
(e.g., as could be provided by Semantic Mediawiki), but I think we
should think about building upon it. We could build our own (and my
experiments over at [itaxon.org](http://itaxon.org/wikidev/) explore
this), but the big challenge is getting a community around a project,
and if David Shorthouse\'s pronouncement that [The Community is
Dead](http://ispiders.blogspot.com/2009/06/community-is-dead.html) is
correct, then maybe we should get on board with the community that
already exists. Perhaps what EOL should be doing is talking to
Wikipedia, improving the existing templates for taxon pages, and
creating bots to automatically populate Wikipedia with more taxon pages.


Time for more half-baked ideas. There's been a lot of discussion on Twitter about EOL, Linked Data (sometimes abbreviated LOD), and Wikipedia. Pete DeVries (@pjd) is keen on LOD, and has been asking why TDWG isn't playing in this space. I've been muttering dark thoughts about EOL, and singing the praises of Wikipedia. On so it goes on. So, here's one vision of where we could (?should) be going with this.

Messaggi di Rogue Scholar

The vision thing - it's all about the links

Thoughts on GBIC 2012 and a vision of the future of biodiversity informatics

EOL, Wikipedia, TDWG, LinkedData, and the Vision Thing