TreeBase
NAR Molecular Biology Database Collection entry number 906
Piel W.H.1 and Miller M.A.2
1Department of Biological Sciences, 608 Cooke, North Campus, University at Buffalo, Buffalo, NY 14260
2Division of Scientific Research and Development, San Diego Supercomputer Center, University of California - San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
2Division of Scientific Research and Development, San Diego Supercomputer Center, University of California - San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
Database Description
TreeBASE is a relational database of phylogenetic information hosted by the State University of New York at Buffalo. TreeBASE is a community resource that stores phylogenetic trees and the data matrices used to generate them from published research papers. We encourage biologists to submit phylogenetic data that are either published or in press, especially if these data were not fully presented in the publication due to space limitations. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Presently TreeBASE is being mirrored at the San Diego Supercomputer Center at UCSD.
Recent Developments
TreeBASE development is now occurring under the auspices of the NSF-sponsored ITR project Cyberinfrastructure for Phylogenetic Research (CIPRES: http://www.phylo.org). As such, it is being redesigned from the ground up through a collaborative research effort by Computer Scientists, Biologists, and Database Developers. The redesigned, version of TreeBASE (codenamed Treebase2) is expected to be released in beta form in early 2006. It will feature a new schema that represents trees explicitly as nodes and edges, making complex tree comparisons possible. It will also permit more complex queries across all data, new administrative forms that simplify the submission process, and a commercial relational Database management system that is SQL compliant. Contact TreeBASE through the curator by email at piel@treebase.org.
Acknowledgements
We are grateful to Drs Michael Donoghue, Junhyong Kim, Brent Mishler, Wayne Maddison, Shirley Cohen, and other members of CIPRES project for their expert advice. TreeBASE is currently supported by the National Science Foundation NSF EF 04-51824; EF 04-51657; and NSF EF 04-51721.
Category: Genomics Databases (non-vertebrate)
Subcategory: Genome annotation terms, ontologies and nomenclature
Go to the abstract in Bioinformatics, 2003, 19, 1162-1168
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