University of Glasgow

Roderic Page

NESCent, EOL, and BHL have put together a [research
sprint](http://eol.org/info/nescent_EOL_BHL):  

> We invite participants for an event that will pioneer the mining of
> the Encyclopedia of Life (<http://eol.org>) and the Biodiversity
> Heritage Library (<http://www.biodiversitylibrary.org>) to address
> outstanding and novel questions about the ecology and evolution of
> biodiversity. We aim to identify questions and data for which
> biologists may lack informatics skills and resources to address or
> analyze successfully; and symmetrically, to guide informaticians to
> pressing ecological and evolutionary questions. We seek to make actual
> discoveries through joint activities and to test the "computability"
> of major biodiversity databases.

Since I won\'t be applying to participate I thought I\'d sketch some
possible ideas here.  
  

#### Co-occurrence of taxon names as proxy for ecological associations

  
Some time ago I noted that if you build a \"tag tree\" for taxonomic
names in a BHL document you can get some interesting patterns, such as
the names of hosts and their parasites occurring together. For example,
searching BioNames for the rodent genus
[Praomys](http://bionames.org/search/Praomys) turns up papers with
fleas, lice and cestodes. This suggests ways to mine BHL for ecological
association data. It could be done by looking for general patterns of
co-occurrence, or perhaps in a more targeted fashion (e.g., find all
pages that have mammal and insect names together). Perhaps we could
develop weighting schemes based on taxonomy whereby the co-occurrence of
taxonomically unrelated groups is flagged as possibly significant (at
the same time we\'d want to avoid false positives such as tables of
contents and indices).  
  

#### Mining article titles for ecological associations

  
Another approach is to try and interpret the text itself. Keeping with
the host-parasite theme, often descriptions of new parasite species are
of the form \"new species x from y\". Here are some examples I use in my
[Phyloinformatics
course](http://iphylo.org/~rpage/phyloinformatics/course/datamining/index.html#wordtrees):  
  

  
  
Wordtrees are a great way to visualise these sentences and get insights
into how to parse them (the word tree for the text above is
[here](http://www.jasondavies.com/wordtree/?source=a5b87fdf171e5b65b926cfd2864d2ed0&phrase-line=1&prefix=from%20the).  
  
![Wordtree](http://lh3.ggpht.com/-Ikmk71RYSiU/Uk2inqVLfEI/AAAAAAAADEU/P0k5arvOqnU/wordtree.png?imgmax=800 "wordtree.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="304"}

#### Geography

  
There is a lot of geographic data in BHL, which could potentially fill
in gaps in geographic databases such as GBIF (which feeds into EOL).
Even extracting latitude and longitude pairs from the OCR text can be
enough to build some interesting maps.  
  

#### Image extraction

  
Another approach is to extract images from BHL, ideally with the
associated caption. This would be a way to quickly build an image
database, a lot of taxonomic papers have illustrations of taxa, so this
would be a quick way to get that information. It might be possible to do
some clever parsing of the figure caption to extract not only taxon
names but also other data. For example if the caption mentions a scale
bar you could very quickly classify organisms into size categories (a
1mm scale bar versus a 1cm or 1m scale bar tells you something about the
size of the organism).  
  

#### Data extraction

  
Complementing the idea of image extraction, how about a tool that
identifies tables in BHL OCR text? These tables are potentially sources
of useful data, if they can be pulled out and indexed by taxon name (for
example) then they could be analysed further. BHL OCR of tables tends to
be poor, but the OCR could be redone on just the table, and/or the table
could be edited manually (perhaps with the help of crowd sourcing).  
  


NESCent, EOL, and BHL have put together a research sprint:Since I won't be applying to participate I thought I'd sketch some possible ideas here.
<strong>
 Co-occurrence of taxon names as proxy for ecological associations
</strong>
Some time ago I noted that if you build a "tag tree" for taxonomic names in a BHL document you can get some interesting patterns, such as the names of hosts and their parasites occurring together.

Thoughts on the NESCent-EOL-BHL Research Sprint

[![](https://www.nescent.org/wg/summit/images/summit_logo.gif){style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 100px;"
border="0"}](https://www.nescent.org/wg/summit/images/summit_logo.gif){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Last week I was at [NESCent\'s](http://www.nescent.org) 2008 [Community
Summit](http://www.nescent.org/community_summit/Main_Page). As part of
that meeting a few of us had a breakout group on \"Biodiversity and
phylogenetics\". [Brian O\'Meara](http://treetapper-dev.blogspot.com/)
took some [spectacularly thorough
notes](http://www.nescent.org/community_summit/CommunitySummit_Phylogenetics),
including the pithy:  
  
S\[wofford\]: What?  
  
[Julia Clarke](http://www.meas.ncsu.edu/faculty/clarke/Clarke.htm) and I
were advocating data mining, not entirely successfully. At one point I
started ranting about **post-phylogenetics** (i.e., what do do when
we\'ve basically got the tree of life). For a brief moment I thought
this might be a cool new term to use, although Googling finds that [W.
Ford Doolittle](http://doolittle.biochem.dal.ca/) has used it in the
title of talks given at the Wenner-Gren Foundations International
Symposium at Stockholm in 2003, and at Penn State in 2006. However, the
2006 talk title (Postphylogenetics: The Tree of Life in the Light of
Lateral Gene Transfer) suggests a different meaning (i.e., there isn\'t
a tree of life to be found). I prefer to think of it in the same sense
as \"postgenomics\" \-- now that we have all this information, how can
we make the best use of it?


Last week I was at NESCent's 2008 Community Summit. As part of that meeting a few of us had a breakout group on "Biodiversity and phylogenetics". Brian O'Meara took some spectacularly thorough notes, including the pithy:S[wofford]: What? Julia Clarke and I were advocating data mining, not entirely successfully.

Messages de Rogue Scholar

Thoughts on the NESCent-EOL-BHL Research Sprint

Postphylogenetics