PhyQL

Hasan Jamil has released 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).

TBMap errors

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.

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

TBMap paper out

My paper on mapping TreeBASE names to other databases is out as provisional PDF on the BMC Bioinformatics web site (doi: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 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...