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Towards a taxonomically intelligent phylogenetic database

Reference	BB/C004310/1
Principal Investigator / Supervisor	Professor Roderic Page
Co-Investigators / Co-Supervisors
Institution	University of Glasgow
Department	Environmental and Evolutionary Biology
Funding type	Research
Value (£)	149,300
Status	Completed
Type	Research Grant
Start date	01/09/2005
End date	31/08/2008
Duration	36 months

Abstract

TreeBASE (www.treebase.org) is the single largest repository of published phylogenetic trees. A major limitation of this database is the complete lack of controlled vocabularies for either taxon or gene names. This lack of ontologies crippled our ability to query the database effectively. This project will create an annotated version of TreeBASE (www.treebase.org), where each taxon and gene will be linked to a term in a recognised ontology. Existing taxonomic names in TreeBASE will be mapped to names in external databases (eg. NCBI, ITIS, uBio, IPNI) using string matching (exact and approximate) and BLAST searches. Tree matching algorithms will be used to compare different taxonomic classifications obtained from source database, and to develop a consensus classification to support taxonomically intelligent queries. Taxonomically-based tree query methods will be developed using query rewriting techniques. A metric-space index will be developed to support fast queries based on tree similarity. The resulting database and query mechanisms will be made available to users through a web site that uses faceted metadata, and through web service.

Summary

unavailable

Committee	Closed Committee - Genes & Developmental Biology (GDB)
Research Topics	Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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