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Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

Nadia Anwar1* and Ela Hunt2

Author Affiliations

1 Faculty of Biomedical and Life Sciences, University of Glasgow, UK

2 Computer and Information Sciences, University of Strathclyde, UK

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BMC Evolutionary Biology 2009, 9:93  doi:10.1186/1471-2148-9-93

Published: 8 May 2009



TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory.


We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL webcite

The methodology we developed is scalable and can be applied to new data, as those become available in the future.


Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection.