University of Glasgow

Roderic Page

More for my own benefit than anything else I\'ve decided to list some of
the things I plan to work on this year. If nothing else, it may make
sobering reading this time next year.  
  

### A knowledge graph for biodiversity

  
Google\'s introduction of the [\"knowledge
graph\"](http://googleblog.blogspot.co.uk/2012/05/introducing-knowledge-graph-things-not.html)
gives us a happy phrase to use when talking about linking stuff
together. It doesn\'t come with all the baggage of the \"semantic web\",
or the ambiguity of \"knowledge base\". The diagram below is my mental
model of the biodiversity knowledge graph (this comes from
<http://dx.doi.org/10.7717/peerj.190>, but I sketched most of this for
my Elsevier Challenge entry in 2008, see
<http://dx.doi.org/10.1038/npre.2008.2579.1>).  
  
![Fig 1
1x](http://lh4.ggpht.com/-MX9kBSX_D1w/Utal03QKkdI/AAAAAAAADPU/Nj5FKlnNY1E/fig-1-1x.jpg?imgmax=800 "fig-1-1x.jpg"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="560" height="442"}  
  
Parts of this knowledge graph are familiar: **articles** are published
in **journals**, and have **authors**. Articles cite other articles
(represented by a loop in the diagram below). The topology of this graph
gives us citation counts (number of times an article has been cited),
impact factor (citations for articles in a given journal), and
author-based measures such as the H-index (a function of the
distribution of citations for each article you have authored). Beyond
simple metrics this graph also gives us the means to track the
provenance of an idea (by following the citation trail).  
  
![Publication](http://lh6.ggpht.com/-WUOaVg858iI/Utal10382RI/AAAAAAAADPc/zIlho6gu5K4/publication.png?imgmax=800 "publication.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="300"}  
  
The next step is to grow this graph to include the other things we care
about (e.g., taxa, taxon names, specimens, sequences, phylogenies,
localities, etc.).  
  

### BioNames

  
I spent a good deal of last year building
[BioNames](http://bionames.org) (for background see my [blog
posts](http://iphylo.blogspot.co.uk/search?q=bionames) or read the paper
in PeerJ <http://dx.doi.org/10.7717/peerj.190>). BioNames represents a
small corner of the biodiversity knowledge graph, namely taxonomic names
and their associated publications (with added chocolately goodness of
links to taxon concepts and phylogenies). In 2014 I\'ll continue to
clean this data (I seem to be forever cleaning data). So far BioNames is
restricted to animal names, but now that the plant folks have relaxed
their previously [restrictive licensing of plant
data](http://iphylo.blogspot.com/2010/12/plant-list-nice-data-shame-it-not-open.html)
(see [post on TAXACOM](http://markmail.org/message/tutrhtmtklodof36))
I\'m looking at adding the million or so plant names (once I\'ve linked
as many as possible to digital identifiers for the corresponding
publications).  
  

### Spatial indexing

  
Now that I\'ve become [more involved in
GBIF](http://iphylo.blogspot.com/2013/10/what-can-global-biodiversity.html)
I\'m spending more time thinking about spatial indexing, and our ability
to find biodiversity data on a map. There\'s a great Google ad that
appeared on UK TV late last year. In it, Julian Bayliss recounts the use
of Google Earth to discover of virgin rainforest (the \"Google forest\")
on [Mount Mabu](http://en.wikipedia.org/wiki/Mount_Mabu) in
Mozambique.  
  

  
  
It\'s a great story, but I keep looking at this and wondering \"how did
we **know** that we **didn\'t know** anything about Mount Mabu?\" In
other words, can we go to any part of the world and see what we know
about that area? GBIF goes a little way there with its specimen
distribution maps, which gives some idea of what is now known from Mount
Mabu (although the map layers used by GBIF are terrible compared to what
Google offers).  
  
![Mabu](http://lh6.ggpht.com/-NUxoBUzRgJ0/Utal3NR_AAI/AAAAAAAADPk/x4OdQteuW30/mabu.png?imgmax=800 "mabu.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="560" height="379"}  
  
But I want to be able to see all the specimens now known from this
region (including the new species that have been discovered, e.g. see
<http://dx.doi.org/10.1007/s12225-011-9277-9> and
<http://dx.doi.org/10.1080/21564574.2010.516275>). Why can\'t I have a
list of publications relevant to this area (e.g., species descriptions,
range extensions, ecological studies, conservation reports)? What about
DNA sequences from material in this region (e.g., from organismal
samples, DNA barcodes, metagenomics, etc.)? If GBIF is to truly be a
\"Global Biodiversity Information Facility\" then I want it to be able
to provide me with a lot more information than it currently does. The
challenge is how to enable that to happen.  


More for my own benefit than anything else I've decided to list some of the things I plan to work on this year. If nothing else, it may make sobering reading this time next year. A knowledge graph for biodiversity   Google's introduction of the "knowledge graph" gives us a happy phrase to use when talking about linking stuff together.

Messaggi di Rogue Scholar

What I'll be working on in 2014: knowledge graphs and Google forests