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TBMap: a taxonomic perspective on the phylogenetic database TreeBASE.

Roderic D M Page1

  • 1Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow, UK. r.page@bio.gla.ac.uk

BMC Bioinformatics
|May 22, 2007
PubMed
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This study introduces TBMap, a database that maps TreeBASE taxonomic names to external databases, improving phylogenetic data integration and discoverability. It clusters equivalent names, enhancing access to evolutionary relationships.

Area of Science:

  • Bioinformatics
  • Systematics
  • Computational Biology

Background:

  • TreeBASE is a key repository for published organismal phylogenies.
  • Lack of taxonomic consistency hinders integration with external genomic and taxonomic databases.
  • Inconsistent naming conventions limit the utility of phylogenetic knowledge in TreeBASE.

Purpose of the Study:

  • To address taxonomic inconsistencies in TreeBASE.
  • To create a mapping of TreeBASE names to external taxonomic databases.
  • To enable better integration and retrieval of phylogenetic data.

Main Methods:

  • Mapped TreeBASE taxonomic names to IPNI, ITIS, NCBI, and uBio.
  • Constructed a graph of these mappings, including taxonomic synonymies.

Related Experiment Videos

  • Extracted graph components to form 'name clusters' of equivalent taxa.

    • Main Results:

    • Developed the TBMap database, linking TreeBASE names to external taxonomic authorities.
    • Created clusters of equivalent names, grouping synonyms and taxonomic variations.
    • Demonstrated that mapping to NCBI improves TreeBASE information retrieval significantly.

    Conclusions:

    • TBMap provides a crucial mapping and clustering of TreeBASE names.
    • The developed system enables novel queries and visualizations of phylogenetic data.
    • Facilitates enhanced integration of TreeBASE with other biological databases.