TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using a special access code.
The current release includes a host of new features and improvements over the previous TreeBASE prototype. New features include:
Richer annotation of metadata (journal DOIs, specimen georeferences, Genbank accession numbers, etc)
A mapping between taxon labels and taxonomic names in uBio and NCBI for improved normalization of names
The ability to visualize and edit trees using Phylowidget
The ability to search on tree topology
Persistent and resolvable URIs for data objects in TreeBASE (i.e. studies, trees, matrices) serve as both globally unique identification numbers and resource locators. These can be included in articles and on researcher's websites, making access to TreeBASE data only a click away
A special URL gives journal editors and reviewers anonymous advanced access to data
Programmatic access to the data using the PhyloWS API. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)
As of early 2010, TreeBASE contains 6,500 trees in 2,500 publications written by 4,500 different authors. These trees have 135,000 distinct taxon labels that map to approximately 60,000 distinct taxa.
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Source/Fonte: TreeBASE Web
Banco de dados de conhecimento filogenético para ser usado tendo em mente este artigo de Doolittle e Bapteste que concluíram que a Árvore da Vida de Darwin já era:
Pattern pluralism and the Tree of Life hypothesis
W. Ford Doolittle* and Eric Bapteste
-Author Affiliations
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
Contributed by W. Ford Doolittle, December 5, 2006 (received for review November 11, 2006)
Abstract
Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.
lateral gene transfer phylogeny
Footnotes
*To whom correspondence should be addressed. E-mail: ford@dal.ca
This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on April 30, 2002.
Author contributions: W.F.D. and E.B. wrote the paper.
The authors declare no conflict of interest.
The authors declare no conflict of interest.
Abbreviations:TOL,Tree of Life;LGT,lateral gene transfer.
