University of Glasgow

Roderic Page

[![](http://www.scfbm.org/graphics/interface/header/10118/headsquare.gif){style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](http://www.scfbm.org/graphics/interface/header/10118/headsquare.gif)  
My short note on the [LSID Tester
tool](http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/) has been
published in the Open Access journal [Source Code for Biology and
Medicine](http://www.scfbm.org/). The article has just come out so the
DOI
([doi:10.1186/1751-0473-3-2](http://dx.doi.org/10.1186/1751-0473-3-2))
isn\'t live yet, the direct link is
<http://www.scfbm.org/content/3/1/2/>. Source code for the tester is
available from [Google Code](http://code.google.com/p/lsid-php/).


My short note on the LSID Tester tool has been published in the Open Access journal Source Code for Biology and Medicine. The article has just come out so the DOI (doi:10.1186/1751-0473-3-2) isn't live yet, the direct link is http://www.scfbm.org/content/3/1/2/. Source code for the tester is available from Google Code.

LSID Tester, a tool for testing Life Science Identifier resolution services

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...

Rogue Scholar Beiträge

LSID Tester, a tool for testing Life Science Identifier resolution services

TBMap paper out