TreeBASE was a repository of

phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...

data published in

scientific journal In academic publishing, a scientific journal is a periodical publication intended to further the progress of science, usually by reporting new research. Content Articles in scientific journals are mostly written by active scientists such as s ...

s. In phylogenetic studies, research data are collected or generated, such as comparative observations (e.g. character state matrices or

multiple sequence alignment Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutio ...

s) made on a set of

taxa In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular nam ...

metadata Metadata is "data that provides information about other data", but not the content of the data, such as the text of a message or the image itself. There are many distinct types of metadata, including: * Descriptive metadata – the descriptive ...

about these taxa, and the

phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

s that are inferred to best describe the evolutionary relationships between the taxa.

Mission

The purpose of the TreeBASE project was to provide stable records and identifiers for these data, so that other workers can refer to their deposited data in their publication, and other scientists can locate the data and use them to verify the original research or to include or extend them in further analyses.

History and funding

The project was started in 1994, with funding from the US

National Science Foundation The National Science Foundation (NSF) is an independent agency of the United States government that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National I ...

. After this prototype, a redesign was initiated under the CIPRES project. This new version was released in March 2010 and has been supported by, among others, the pPOD project, which funded the addition of a RESTful web service interface with CQL search facilities, and

National Evolutionary Synthesis Center The United States National Evolutionary Synthesis Center (NESCent) is a scientific research center in Durham, North Carolina. Known by its acronym NESCent (which rhymes with “crescent”), the center’s goal is to promote collaborative, cross-di ...

(NESCent), which hosted the database and web server. Starting in Winter 2010, TreeBASE was reorganized and became associated with the Phyloinformatics Research Foundation In 2022, TreeBASE was taken offline due to security issues which were unable to be fixed with project resources; the future of the database is uncertain.

References

Bibliographic databases and indexes Academic publishing {{science-stub