University of Glasgow

Roderic Page

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):  
  

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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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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

![Lp
attenborough](http://lh5.ggpht.com/-pc7jjQCDFwc/UA08X_pc8wI/AAAAAAAABpc/K_1VQRcgziE/lp-attenborough.jpg?imgmax=800 "lp-attenborough.jpg"){border="0"
width="200" style="float:right;"}Half-baked idea time. Thinking about
projects such as the [Earth Microbiome
Project](http://www.earthmicrobiome.org/) and [Genomic
Observatories](http://www.genomicobservatories.org/), the recent
[GBIC2012](http://www.gbic2012.org/) meeting (I\'m still [digesting that
meeting](http://iphylo.blogspot.com/2012/07/post-gbic2012-thoughts.html)),
and mulling over the book [A Vast
Machine](http://www.amazon.com/Vast-Machine-Computer-Climate-Politics/dp/0262013924)
I keep thinking about the possible parallels between climate science and
biodiversity science.  
  
One metaphor from \"A Vast Machine\" is the difference between \"global
data\" and \"making data global\". Getting data from around the world
(\"global data\") is one challenge, but then comes making that data
global:  

> building complete, coherent, and consistent global data sets from
> incomplete, inconsistent, and heterogeneous datasources

  
The focus of [GBIF\'s data portal](http://data.gbif.org) is global data,
bringing together specimen records and observations from all around the
world. This is global data, but one could argue that it\'s not yet ready
to be used for most applications. For example, GBIF doesn\'t give you
the geographic distribution of a given species, merely where it\'s been
recorded from (based on that subset of records that have been
digitised). That\'s a very important start, but if we had for each
species an estimated distribution based on museum records, observations,
published maps, together with habitat modelling, then we\'d be closer to
a dataset that we could use to tackle key questions about the
distribution of biodiversity.  
  
![EMP green
small](http://lh6.ggpht.com/-SXPIMaJzfSk/UA08WjuWlYI/AAAAAAAABpQ/8Tt3GuQNEU0/EMP-green-small.png?imgmax=800 "EMP-green-small.png"){border="0"
width="200" style="float:right;"}But if we continue with the theme that
microbiology is the dark matter of biology, and if we look at projects
like the [Earth Microbiome Project](http://www.earthmicrobiome.org/),
then we could argue that focussing on eukaryote, particularly
macro-eukaryote such as plants, fungi, and animals, may be a mistake. To
use a crude analogy, perhaps we have been focussing on the big phenomena
(equivalent to thunder storms, flash floods, tornados, etc.) rather than
the underlying drivers (equivalent to climatic processes such as those
captured in [global climate
models](http://en.wikipedia.org/wiki/Global_climate_model)). Certainly,
any attempt to model the biosphere is going to have to include the
microbiome, and indeed perhaps the microbiome would be enough to have a
working model of the biosphere?  
  
I\'m simply waving my arms around here (no, really?), but it\'s worth
thinking about whether the macroecology that conservation and
biodiversity focusses on is actually the important thing to consider if
you want to model fundamental biological processes. Might
macro-organisms be like the weather, and the microbiome is like the
climate. As humans we notice the weather, because it is at a scale that
affects us directly. But if the weather is a (not entirely predictable)
consequence of the climate, what is the equivalent of global climate
model for biodiversity?  
  


Half-baked idea time. Thinking about projects such as the Earth Microbiome Project and Genomic Observatories, the recent GBIC2012 meeting (I'm still digesting that meeting), and mulling over the book A Vast Machine I keep thinking about the possible parallels between climate science and biodiversity science.

Microbiome as climate, macrobiome as weather, and a global model of biodiversity

I\'m back from Copenhagen and [GBIC2012](http://www.gbic2012.org). The
meeting spanned three fairly intense days (with the days immediately
before and after also working days for some of us), and was run by a
group of facilitators lead by Natasha Walker, who were [described
us](http://natashafacilitator.wordpress.com/2012/07/05/gbic2012-100-biodiversity-informatics-experts-on-their-way-to-changing-the-game/)
as \"an interesting (and delightfully brainy, if sometimes scatty) group
of academics, researchers, museum managers and people close to
policy\...\". I\'ve attempted to capture tweets about the meeting using
[Storify](http://storify.com/rdmpage/gbic-2012/).  
  
There will be a document (perhaps several) based on the meeting, but
until then here are a few quick thoughts. Note that the comments below
are my own and you shouldn\'t read into this anything about what
directions the GBIC document(s) will actually take.  
  

## Microbiology rocks

  
Highlight of the first day was [Robert J.
Robbin\'s](http://www.esp.org/rjr/) talk which urged the audience to
consider that life was mostly microbial, that the the things most people
in the room cared about were actually merely a few twigs on the tree of
life, that the tree of life didn\'t actually exist anyway, and many of
the concepts that made sense for multicellular organisms simply didn\'t
apply in the microbial world. Basically it was a homage to Carl Woese
(see also Pace et al. 2012
[doi:10.1073/pnas.1109716109](http://dx.doi.org/10.1073/pnas.1109716109))
and a wake up call to biodiversity informaticians to stop viewing the
world through multicellular eyes. (You can find all the keynotes from
the first day [here](http://www.gbic2012.org/documents.html/)).  
  
![F1
large](http://lh4.ggpht.com/-oF-sNj4wiQM/T_b9ufDofjI/AAAAAAAABeQ/l0AcUL9H-Pw/F1.large.jpg?imgmax=800 "F1.large.jpg"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="600"}

<div>

From Pace, N. R. (1997). A Molecular View of Microbial Diversity and the
Biosphere. Science, 276(5313), 734--740.
[doi:10.1126/science.276.5313.734](http://dx.doi.org/10.1126/science.276.5313.734)

</div>

## Sequences rule

  
The future of a lot of biodiversity science belongs to sequences, from
simple DNA barcoding as a tool for species discovery and identification,
metabarcoding as a tool for community analysis, to comparisons of
metabolic pathways and beyond. The challenge for classical biodiversity
informatics is how to engage with this, and to what extent we should try
and map between, say sequences and classical taxa, or whether it might
make more sense (gasp) to abandon the taxonomic legacy and move on.
Perhaps are more nuanced response is that the point of connection
between sequences and classical biodiversity data is unlikely to be at
the level of taxonomic names (which are mostly tags for collections of
things that look similar) but at the level of specimens and
observations.  
  

## Ontologies considered harmful

  
This is my own particular hobby horse. Often the call would come \"we
need an ontology\", to which I respond read [Ontology is Overrated:
Categories, Links, and
Tags](http://www.shirky.com/writings/ontology_overrated.html). I have
several problems with ontologies. The first is that they are too easy to
make and distract from the real problem. From my perspective a big
challenge is linking data together, that is going from  
  
![a](http://lh6.ggpht.com/-hDCN7_a6py4/T_b9vTqS8nI/AAAAAAAABeY/uHVUD8_5MuA/a.png?imgmax=800 "a.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="390" height="104"}  
  
to  
  
![b](http://lh4.ggpht.com/-_5ym0xM25Pg/T_b9wYL02JI/AAAAAAAABeg/CSgGcKLY5jQ/b.png?imgmax=800 "b.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="390" height="104"}  
  
Let\'s leave aside what \"A\" and \"B\" are (I suspect it matters less
than people think), once we have the link then we can can start to do
stuff. From my perspective, what ontologies give us is basically this:  
  
![c](http://lh3.ggpht.com/-yijoX2Ce3jA/T_b9yIUcJxI/AAAAAAAABeo/6Ff2dyz3Zxs/c.png?imgmax=800 "c.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="390" height="181"}  
  
So now we know the \"type\" of the link (e.g., \"is a part of\", \"cites
approvingly\", etc.). I\'m not arguing that this isn\'t useful to have,
but if you don\'t have the network of links then typing the links
becomes an idle exercise.  
  
To give an example, the web itself can be modelled as simply nodes
connected by links, ignoring the nature of the links between the web
pages. The importance of those links can be inferred later from
properties of the network. To a first approximation this is how Google
works, it doesn\'t ask what the links \"mean\" it simply investigates
the connections to determine how important each web page is. In the same
way, we build citation networks without bothering to ask the nature of
the citation (yes I know there are ontologies for citations, but anyone
willing to bet how widely they\'ll be adopted?).  
  
My second complaint is that building ontologies is easy, \"easy\" in the
sense that get a bunch of people together, they squabble for a long time
about terminology, and out comes an ontology. Maybe, if you\'re lucky,
someone will adopt it. The cost of making ontologies, and indeed of
adopting them is relatively low (although it might not seem like it at
the time). The cost of linking data is, I\'d argue, higher, because it
requires that you trust someone else\'s identifiers to the extent that
you use them for things you care about deeply. Consider the citation
network that is emerging from the widespread adoption of DOIs by the
publishing industry. Once people trust that the endpoints of the links
will survive, then the network starts to grow. But without that trust,
that leap of faith, there\'s no network (unless you have enough
resources to build the whole thing internally yourself, which is what
happened with the closed citation network owned by Thomson Reuters).
It\'s much easier to silo the data using unique identifiers than it is
to link to other data (it\'s a variant of the \"not invented here\"
syndrome).  
  
Lastly, ontologies can have short lives. They reflect a certain world
view that can become out of date, or supplanted if the relationships
between things that the ontology cares about can be computed using other
data. For example, biological taxonomy is a huge ontology that is
rapidly being supplanted by phylogenetic trees computed from sequence
(and other) data (compare the classification used by flagship
biodiversity projects like GBIF and EOL with the Pace tree of life shown
above). Who needs an ontology when you can infer the actual
relationships? Likewise, once you have GPS the value of a geographic
ontology (say of place names) starts to decline. I can compute if I\'m
on a mountain simply by knowing where I am.  
  
I\'m not saying ontologies are always bad (they\'re not), nor that they
can\'t be cool (they can be), I\'m just suggesting that they aren\'t the
first thing you need. And they certainly aren\'t a prerequisite for
linking stuff together.  
  

## Google flu trends

  
Perhaps the most interesting idea that emerged was the notion of
intelligently detecting changes in biodiversity (which is the kind of
thing a lot of people want to know) in the way analogous to
[Google.org\'s Flu Trends](http://www.google.org/flutrends/) uses
flu-related search terms to predict flu outbreaks:  
  
Ginsberg, J., Mohebbi, M. H., Patel, R. S., Brammer, L., Smolinski, M.
S., & Brilliant, L. (2008). Detecting influenza epidemics using search
engine query data. Nature, 457(7232), 1012--1014.
[doi:10.1038/nature07634](http://dx.doi.org/10.1038/nature07634)  
  
Could we do something like this for biodiversity data? For various
reasons this suggestion become known at GBIC2012 as the \"Heidorn
paradigm\".  
  

## Thinking globally

  
One challenge for a meeting like GBIC 2012 is scope. There\'s so much
cool stuff to think about. From my perspective, a useful filter is to
ask \"what will happen anyway?\" In other words, there is a lot of stuff
(for example the growth of metabarcoding) that will happen regardless of
anything the biodiversity informatics community does. People will make
taxon-specific ontologies for organismal traits, digitise collections,
assess biodiversity, etc. without necessarily requiring an entity like
GBIF. The key question is \"what won\'t happen at a global scale unless
GBIF (or some other entity) gets involved?\"  
  

## A Vast Machine

![51OttqQDcVL SL500
AA300](http://lh4.ggpht.com/-GM83pvpJdtg/T_b9sH3hCRI/AAAAAAAABeI/zng5aiGH4QQ/51OttqQDcVL._SL500_AA300_.jpg?imgmax=800 "51OttqQDcVL._SL500_AA300_.jpg"){border="0"
width="128" height="128" style="float:right;"}Lastly, in one session Tom
Moritz mentioned a book that he felt we could learn from ([A Vast
Machine: Computer Models, Climate Data, and the Politics of Global
Warming](http://www.amazon.com/Vast-Machine-Computer-Climate-Politics/dp/0262013924)).
The book recounts the history of climatology and its slow transition to
a truly global science. I\'ve started to read it, and it\'s fascinating
to see the interplay between early visions of the future, and the
technology (typically driven by military or large-scale commercial
interests) that made possible the realisation of those visions. This is
one reason why predicting the future is such a futile activity, the
things that have the biggest effect come from unexpected sources, and
effect things in ways it\'s hard to anticipate. On a final note, it took
about a minute from the time from the time Tom mentioned the book to the
time I had a copy from Amazon in the Kindle app on my iPad. Oh that
accessing biodiversity data were that simple.


Post GBIC2012 thoughts

![Earth russia large verge medium
landscape](http://lh3.ggpht.com/-3ZW58gMrvlI/T-1zzEyRdKI/AAAAAAAABdA/S7gQl41P1h0/earth-russia_large_verge_medium_landscape.jpg?imgmax=800 "earth-russia_large_verge_medium_landscape.jpg"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="550"}  
  
Next week I\'m in Copenhagen for [GBIC](http://www.gbic2012.org/), the
Global Biodiversity Informatics Conference. The goal of the conference
is to:  

> \...convene expertise in the fields of biodiversity informatics,
> genomics, earth observation, natural history collections, biodiversity
> research and policy needed to set such collaboration in motion.

  
The collaboration referred to is the agreement to mobilise data and
informatics capability to met the [Aichi Biodiversity
Targets](http://www.cbd.int/sp/targets/).  
  
I confess I have mixed feelings about the upcoming meeting. There will
be something like 100 people attending the conference, with backgrounds
ranging from pure science to intergovernmental policy. It promises to be
interesting, but whether a clear vision of the future of biodiversity
informatics will emerge is another matter.  
  
GBIC is part of the process of \"planet management\", a phrase that\'s
been around for a while, but I only came across in the Bowker\'s essay
\"Biodiversity Datadiversity\"^1^:  
  
Bowker, G. C. (2000). Biodiversity Datadiversity. Social Studies of
Science, 30(5), 643--683.
[doi:10.1177/030631200030005001](http://dx.doi.org/10.1177/030631200030005001)  
  
Bowker\'s essay is well worth a read, not least for the choice quotes
such as:  
  

> Each particular discipline associated with biodiversity has its own
> incompletely articulated series of objects. These objects each enfold
> an organizational history and subtend a particular temporality or
> spatiality. They frequently are incompletely articulated with other
> objects, temporalities and spatialities --- often legacy versions,
> when drawing on non-proximate disciplines. **If one wants to produce a
> consistent, long-term database of biodiversity-relevant information
> the world over, all this sounds like an unholy mess**. At the very
> least it suggests that global panopticons are not the way to go in
> biodiversity data. (p. 675, emphasis added)

  
and  

> I have not, in general, questioned the mania to name which is rife in
> the circles whose work I have described. **There is no absolutely
> compelling connection between the observation that many of the world's
> species are dying and the attempt to catalogue the world before they
> do.** If your house is on ﬁre, you do not necessarily stop to
> inventory the contents before diving out the window. However, as Jack
> Goody (1977) and others have observed, list-keeping is at the heart of
> our body politic. It is also, by extension, at the heart of our
> scientific strategies. Right or wrong, it is what we do. (p. 676,
> emphasis added)

  
Given that I\'m a fan of the notion of a \"global panopticon\", and
spend a lot of time fussing with lists of names, I find Bowker\'s views
refreshing. Meantime, roll on GBIC2012.  
  

------------------------------------------------------------------------

  
1. Bowker cites Elichirigoity as a source of the term \"planet
management\":  
  
Fernando Elichirigoity (1999), Planet Management: Limits to Growth,  
Computer Simulations, and the Emergence of Global Spaces (Evanston, IL:
Northwestern  
University Press). ISBN 0810115875 (Google Books
[oP3wVnKpGDkC](http://books.google.co.uk/books?id=oP3wVnKpGDkC)).  
  
From the limited Google preview, and the review by Edwards, this looks
like an interesting book:  
  
Edwards, P. (2000). Book Review:Planet Management: Limits to Growth,
Computer Simulation, and the Emergence of Global Spaces Fernando
Elichirigoity. Isis, 91(4), 828.
[doi:10.1086/385020](http://dx.doi.org/10.1086/385020) ([PDF
here](http://pne.people.si.umich.edu/PDF/elichirigoity.pdf))


Next week I'm in Copenhagen for GBIC, the Global Biodiversity Informatics Conference. The goal of the conference is to:The collaboration referred to is the agreement to mobilise data and informatics capability to met the Aichi Biodiversity Targets.I confess I have mixed feelings about the upcoming meeting. There will be something like 100 people attending the conference, with backgrounds ranging from pure science to intergovernmental policy.

Rogue Scholar Beiträge

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

Microbiome as climate, macrobiome as weather, and a global model of biodiversity

Post GBIC2012 thoughts

Planet management, GBIF, and the future of biodiversity informatics