University of Glasgow

Roderic Page

[Hasan Jamil](http://www.cs.wayne.edu/~jamil/) has released
[PhyQL](http://integra.cs.wayne.edu/IIL/softwares/phyql/), a visual
system for querying  
phylogenetic information. To quote from the web site:  

> Popular phylogenetic databases such as TreeBASE, PhyloFinder, TreeFAM
> offer complex text-based web forms for structure queries. Still there
> seems a great need for intelligent visual query formation based on a
> phylogenetic query language for content exploration. PhyQL offers a
> visual query design interface where the user can create simple to
> complex queries based visual query operators. The query language is
> translated to a list of datalog queries, then executed in XSB, an
> extension of Prolog. Separating the application layer from the data
> layer by a logic layer reduces query tools development time. Moreover,
> PhyQL offers interactive tree visualization which is very convenient
> for viewing very large trees.

  
There is also a YouTube screencast:  

  
  
I haven\'t had a chance to play with it yet. PhyQL was originally
described by Jamil et al. \"Querying phylogenies visually\", BIBE 2001
([doi:10.1109/BIBE.2001.974405](http://dx.doi.org/10.1109/BIBE.2001.974405)).


Hasan Jamil has released PhyQL, a visual system for querying phylogenetic information. To quote from the web site:There is also a YouTube screencast:I haven't had a chance to play with it yet. PhyQL was originally described by Jamil et al. "Querying phylogenies visually", BIBE 2001 (doi:10.1109/BIBE.2001.974405).

PhyQL

In the absence of a proper bug reporting system, I\'m going to use this
post to collect errors in the [TBMap
project](http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap/), which maps
taxonomic names in TreeBASE onto names in other databases.  

  

TaxonID

TaxonName

Notes

  

  

T57654

Lycorideae

Erroneously agrep matched to the spider family Lycosidae, this is a
plant tribe.

  

T56449

Ficus uncinata

bad agrep to *Pinus uncinata*

  


In the absence of a proper bug reporting system, I'm going to use this post to collect errors in the TBMap project, which maps taxonomic names in TreeBASE onto names in other databases.TaxonIDTaxonNameNotesT57654LycorideaeErroneously agrep matched to the spider family Lycosidae, this is a plant tribe.T56449Ficus uncinatabad agrep to
<i>
 Pinus uncinata
</i>

TBMap errors

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

PhyQL

TBMap errors

TBMap paper out