University of Glasgow

Roderic Page

[Rutger Vos](http://twitter.com/rvosa) asked on Twitter [\"What would
people want/expect from taxon searching on
TreeBASE?\"](http://twitter.com/rvosa/statuses/1265099825). This is a
good question, and one which motivated the work I did on
[TBMap](http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap/) (see
[doi:10.1186/1471-2105-8-158](http://dx.doi.org/10.1186/1471-2105-8-158)),
which developed a mapping between TreeBASE taxa and other databases. In
that paper I published [a table showing the effectiveness of string and
hierarchical queries of
TreeBASE](http://www.biomedcentral.com/1471-2105/8/158/table/T2). A
string query returned just the studies that included the query term, a
hierarchical query returned all studies that contained taxa that descend
from a given node in the NCBI taxonomy.  
  
A hierarchical query can be visualised as a range query. For example,
the diagram below shows a classification where the descendants of Node A
correspond to the range 1-8 (this is a simplification of visitation
numbers, see my [earlier
post](http://iphylo.blogspot.com/2007/01/phylocode.html), and also Chen
et al.
[doi:10.1186/1471-2148-8-90](http://dx.doi.org/10.1186/1471-2148-8-90)).
The three trees can be represented as the ranges 3-8, 6-7, and 2-4,
respectively. To find trees for the taxon corresponding to Node A we
look for trees whose range intersects 1-8, to find trees corresponding
to Node B we look for trees whose range intersects 1-5.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiidDoAccQRNA0cEhAzMsJyjaf7sL-LpZRfdBxuyXFSYI1djfd46PnSCJ_3tjYj0uLYQm4SZbW9QdtD3apnuIJag_SmFmsHLlIk8Alp1NzvTJCyn1NSq-HrFZzJbZaBH6TGIKTm/s400/treesearch.jpg){#BLOGGER_PHOTO_ID_5308336107089860050
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 345px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiidDoAccQRNA0cEhAzMsJyjaf7sL-LpZRfdBxuyXFSYI1djfd46PnSCJ_3tjYj0uLYQm4SZbW9QdtD3apnuIJag_SmFmsHLlIk8Alp1NzvTJCyn1NSq-HrFZzJbZaBH6TGIKTm/s1600-h/treesearch.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
This approach retrieves a list of all trees that include a given taxon,
but potentially this list could be very large (for example, a query for
all plant trees could return 1000\'s of trees). So the question becomes
how to order these trees? Some ideas:  

1.  order by the number of taxa in the tree.
2.  order by the size of the range (\"span\") of the tree.
3.  order by set inclusion.

  
Ordering by size seems attractive, but will favour trees with more taxa
over those with a greater taxonomic spread (which is favoured by
ordering by the span of the tree). I used span in my [challenge
entry](http://iphylo.blogspot.com/2008/11/challenge-entry.html) to
display papers with related taxa.  
  
What I have in mind for ordering by set inclusion is constructing a
directed graph where each node represents a tree, and a pair of nodes
(*x*, *y*) is connected by an edge *x* → *y* if the taxa in tree *y* are
nested inside the taxa in tree *x*. We could also introduce some
additional nodes corresponding to nodes in the classification. If we
then [topologically
sort](http://en.wikipedia.org/wiki/Topological_sorting) the graph we
have a linear order for the trees. Given that this order could be
pre-computed independently of any queries (in much the same way that
PageRank is), it could make for faster queries.  
  
It would be useful to explore these and other ordering criteria. Perhaps
the best approach would be some measure which combines one or more
criteria, in which case we might want to use some form of rank
aggregation (see [iSpecies clones, and taxonomic
intelligence](http://iphylo.blogspot.com/2008/07/ispecies-clones-and-taxonomic.html)
for some links to the relevant literature).


Rutger Vos asked on Twitter "What would people want/expect from taxon searching on TreeBASE?". This is a good question, and one which motivated the work I did on TBMap (see doi:10.1186/1471-2105-8-158), which developed a mapping between TreeBASE taxa and other databases. In that paper I published a table showing the effectiveness of string and hierarchical queries of TreeBASE.

What would people want/expect from taxon searching on TreeBASE?

Nice paper by Robert Huber and Jens Klump has appeared in *Computers &
Geosciences* entitled \"Charting taxonomic knowledge through ontologies
and ranking algorithms\"
([doi:10.1016/j.cageo.2008.02.016](http://dx.doi.org/10.1016/j.cageo.2008.02.016)).
The paper is not open access, but you can get some background from the
post [How TaxonRank
works](http://stratigraphynet.blogspot.com/2008/01/how-taxonrank-works.html).
Here\'s the abstract.  
  

> Since the inception of geology as a modern science, paleontologists
> have described a large number of fossil species. This makes fossilized
> organisms an important tool in the study of stratigraphy and past
> environments. Since taxonomic classifications of organisms, and
> thereby their names, change frequently, the correct application of
> this tool requires taxonomic expertise in finding correct synonyms for
> a given species name. Much of this taxonomic information has already
> been published in journals and books where it is compiled in carefully
> prepared synonymy lists. Because this information is scattered
> throughout the paleontological literature, it is difficult to find and
> sometimes not accessible. Also, taxonomic information in the
> literature is often difficult to interpret for non-taxonomists looking
> for taxonomic synonymies as part of their research.  
>   
> The highly formalized structure makes Open Nomenclature synonymy lists
> ideally suited for computer aided identification of taxonomic
> synonyms. Because a synonymy list is a list of citations related to a
> taxon name, its bibliographic nature allows the application of
> bibliometric techniques to calculate the impact of synonymies and
> taxonomic concepts. TaxonRank is a ranking algorithm based on
> bibliometric analysis and Internet page ranking algorithms. TaxonRank
> uses published synonymy list data stored in TaxonConcept, a taxonomic
> information system. The basic ranking algorithm has been modified to
> include a measure of confidence on species identification based on the
> Open Nomenclature notation used in synonymy list, as well as other
> synonymy specific criteria.  
>   
> The results of our experiments show that the output of the proposed
> ranking algorithm gives a good estimate of the impact a published
> taxonomic concept has on the taxonomic opinions in the geological
> community. Also, our results show that treating taxonomic synonymies
> as part of on an ontology is a way to record and manage taxonomic
> knowledge, and thus contribute to the preservation our scientific
> heritage.


Nice paper by Robert Huber and Jens Klump has appeared in
<i>
 Computers &amp; Geosciences
</i>
entitled "Charting taxonomic knowledge through ontologies and ranking algorithms" (doi:10.1016/j.cageo.2008.02.016). The paper is not open access, but you can get some background from the post How TaxonRank works. Here's the abstract.

Messages de Rogue Scholar

What would people want/expect from taxon searching on TreeBASE?

Charting taxonomic knowledge