University of Glasgow

Roderic Page

Déjà vu is a scary thing. [Four years
ago](http://iphylo.blogspot.com/2007/02/treebase-name-mapping.html) I
released a mapping between names in TreeBASE and other databases called
[TBMap](http://darwin.zoology.gla.ac.uk/~rpage/tbmap/) (described here:
[doi:10.1186/1471-2105-8-158](http://dx.doi.org/10.1186/1471-2105-8-158)).
Today I find myself releasing yet another mapping, as part of my [NCBI
to Wikipedia](http://iphylo.org/linkout) project. By embedding the
mapping in a wiki, it can be edited, so the kinds of problems I
encountered with TbMap, recounted
[here](http://iphylo.blogspot.com/2006/11/homonyms-and-ubios-data-model-yet-more.html),
[here](http://iphylo.blogspot.com/2007/01/joys-of-mapping-names-in-treebase.html),
and [here](http://iphylo.blogspot.com/2008/02/tbmap-errors.html). The
mapping in and of itself isn\'t terribly exciting, but it\'s the
starting point for some things I want to do regarding how to visualise
the data in TreeBASE.  
  
Because TreeBASE 2 has issued new identifiers for its taxa (see
[TreeBASE II makes me pull my hair
out](http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html)),
and now contains its own mapping to the NCBI taxonomy, as a first pass
I\'ve taken their mapping and added it to <http://iphylo.org/linkout>.
I\'ve also added some obvious mappings that TreeBASE has missed. There
are a lot more taxa which could be added, but this is a start.  
  
The TreeBASE taxa that have a mapping each get their own page with a URL
of the form `http://iphylo.org/linkout/`, e.g.
<http://iphylo.org/linkout/TB2:Tl257333>. This page simply gives the
name of the taxon in TreeBASE and the corresponding NCBI taxon id. It
uses a Semantic Mediawiki template to generate a statement that the
TreeBASE and and NCBI taxa are a \"close match\". If you go to the
corresponding page in the wiki for the NCBI taxon (e.g.,
<http://iphylo.org/linkout/Ncbi:448631>) you will see any corresponding
TreeBASE taxa listed there. If a mapping is erroneous, we simply need to
edit the TreeBASE taxon page in the wiki to fix it. Nice and simple.  
  
At the time of writing the initial mapping is still being loaded (this
can take a while). I\'ll update this post when the uploading has
finished.


Déjà vu is a scary thing. Four years ago I released a mapping between names in TreeBASE and other databases called TBMap (described here: doi:10.1186/1471-2105-8-158). Today I find myself releasing yet another mapping, as part of my NCBI to Wikipedia project. By embedding the mapping in a wiki, it can be edited, so the kinds of problems I encountered with TbMap, recounted here, here, and here.

TreeBASE meets NCBI, again

My paper on mapping [TreeBASE](http://www.treebase.org) names to other
databases is out as provisional PDF on the *BMC Bioinformatics* [web
site](http://www.biomedcentral.com/1471-2105/8/158/abstract)
([doi:10.1186/1471-2105-8-158](http://dx.doi.org/10.1186/1471-2105-8-158)
\-- not working yet).  
  
The abstract:  

> TreeBASE is currently the only available large-scale database of
> published organismal phylogenies. Its utility is hampered by a lack of
> taxonomic consistency, both within the database, and with names of
> organisms in external genomic, specimen, and taxonomic databases. The
> extent to which the phylogenetic knowledge in TreeBASE becomes
> integrated with these other sources is limited by this lack of
> consistency.  
> Taxonomic names in TreeBASE were mapped onto names in the external
> taxonomic databases IPNI, ITIS, NCBI, and uBio, and graph G of these
> mappings was constructed. Additional edges representing taxonomic
> synonymies were added to G, then all components of G were extracted.
> These components correspond to \"name clusters\", and group together
> names in TreeBASE that are inferred to refer to the same taxon. The
> mapping to NCBI enables hierarchical queries to be performed, which
> can improve TreeBASE information retrieval by an order of magnitude.  
> TBMap database provides a mapping of the bulk of the names in TreeBASE
> to names in external taxonomic databases, and a clustering of those
> mappings into sets of names that can be regarded as equivalent. This
> mapping enables queries and visualisations that cannot otherwise be
> constructed. A simple query interface to the mapping and names
> clusters is available at:
> <http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap>  

  
The [TBMap](http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap) web site
needs some work, it\'s really only intended to document the mapping.
Once I\'ve tweaked and updated the mapping, I hope to use it in my
forthcoming all-sining, all-dancing, phylogeny database\...


My paper on mapping TreeBASE names to other databases is out as provisional PDF on the
<i>
 BMC Bioinformatics
</i>
web site (doi:10.1186/1471-2105-8-158 -- not working yet).The abstract:The TBMap web site needs some work, it's really only intended to document the mapping. Once I've tweaked and updated the mapping, I hope to use it in my forthcoming all-sining, all-dancing, phylogeny database...

Messages de Rogue Scholar

TreeBASE meets NCBI, again

TBMap paper out