University of Glasgow

Roderic Page

The journal *Mycokeys* has published the following paper:  
  

> Triebel, D., Hagedorn, G., & Rambold, G. (2012). An appraisal of
> megascience platforms for biodiversity information. MycoKeys, 5(0),
> 45--63.
> [doi:10.3897/mycokeys.5.4302](http://dx.doi.org/10.3897/mycokeys.5.4302)

  
This paper contains a diagram that seems innocuous enough but which I
find worrying:  
  
![MycoKeys 005 045
g001](http://lh3.ggpht.com/-kFqL7VtjBss/UPaPYLjM0kI/AAAAAAAACZU/LBIxEGjA4GA/MycoKeys-005-045-g001.jpg?imgmax=800 "MycoKeys-005-045-g001.jpg"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="450" height="353"}  
  
The nodes in the graph are \"biodiversity megascience platforms\", the
edges are \"cross-linkages and data exchange\". What bothers me is that
if you view biodiversity informatics through this lens then the
relationships among these projects becomes the focus. Not the data, not
the users, nor the questions we are trying to tackle. It is all about
relationships between projects.  
  
I want a different view of the landscape. For example, below is a very
crude graph of the kinds of things I think about, namely kinds of data
and their interrelationship:  
  
![Biodiversity](http://lh6.ggpht.com/-5ZThLyl3MTU/UPaPZBCjaFI/AAAAAAAACZc/VwAmYoXhzlE/biodiversity.png?imgmax=800 "biodiversity.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="423"}  
  
What tends to happen is that this data landscape gets carved up by
different projects, so we get separate databases of taxonomic names,
images, publications, and specimens (these are the \"megascience
platforms\" such as CoL, EOL, GBIF). This takes care of the nodes, but
what about the edges, the links between the data? Typically what happens
is lots of energy is expended on what to call these links, in other
words, the development of the vocabularies and ontologies such as those
curated by [TDWG](http://www.tdwg.org). This is all valuable work, but
this doesn\'t tackle what for me is the real obstacle to progress, which
is creating the links themselves. Where are the \"megascience
platforms\" devoted to linking stuff together?  
  
When we do have links between different kinds of data these tend to be
**within** databases. For example, Genbank explicitly links sequences to
publications in PubMed, and taxa in the NCBI taxonomy database. All
three (sequence, publication, taxon) have identifiers (accession number,
PubMed id, taxon id, respectively) that are widely used outside GenBank
(and, indeed, are the de facto identifiers for the bioinformatics
community). Part of the reason these identifiers are so widely used is
because GenBank is the only real \"megascience platform\" in the list
studied by Triebel et al. It\'s the only one that we can readily do
science with (think BLAST searches, think of the number of databases
that have repurposed GenBank data, or build on NCBI services).  
  
![Genbank](http://lh4.ggpht.com/-XWEcA32ShlY/UPaPaZ4IcPI/AAAAAAAACZk/6POYc11uNFw/genbank.png?imgmax=800 "genbank.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="421"}  
  
Many of the questions we might ask can be formulated as paths through a
diagram like the one above. For example, if I want to do phylogeography,
then I want the path phylogeny -\> sequence -\> specimen -\> locality.
If I\'m lucky the phylogeny is in a database and all the sequences have
been georeferenced, but often the phylogeny isn\'t readily available
digitally, I need to map the OTUs in the tree to sequences, I then need
to track down the vouchers for those sequences, and obtain the
localities for those sequences from, say, GBIF. Each step involves some
degree of pain as we try and map identifiers from one database to those
in another.  
  
![Phylogeography](http://lh5.ggpht.com/-RTdx3GB4lEg/UPaPdO2m8AI/AAAAAAAACZ0/B5ZMf6NdtzU/phylogeography.png?imgmax=800 "phylogeography.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="422"}  
  
If I want to do classical alpha taxonomy I need information on taxonomic
names, concepts, publications, attributes, and specimens. The digital
links between these are tenuous at best (where are the links between
GBIF specimen records and the publications that cite those specimens,
for example?).  
  
![Taxonomy](http://lh5.ggpht.com/-tE7oXO-FmJU/UPaPeAEqwTI/AAAAAAAACZ8/RZuQq6l23_A/taxonomy.png?imgmax=800 "taxonomy.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="422"}  
  
Focussing on so-called \"platforms\" is unfortunate, in my opinion,
because it means that we focus on data and how we carve up
responsibility for managing it (never mind what happens to data that
lacks an obvious constituency). The platforms aren\'t what we should be
focussing on, it is the relationships between data (and no, these are
not the same as the relationships between the \"platforms\").  
  
If I\'d like to see one thing in biodiversity informatics in 2013 it is
the emergence of a \"platform\" that makes the links the centre of their
efforts. Because without the links we are not building \"platforms\", we
are building silos.


The journal
<em>
 Mycokeys
</em>
has published the following paper:  This paper contains a diagram that seems innocuous enough but which I find worrying:    The nodes in the graph are "biodiversity megascience platforms", the edges are "cross-linkages and data exchange". What bothers me is that if you view biodiversity informatics through this lens then the relationships among these projects becomes the focus.

Messaggi di Rogue Scholar

Megascience platforms for biodiversity information: what's wrong with this picture?