Open Tree of Life
Type of site | Taxonomic catalogue |
|---|---|
| Available in | English |
| URL | opentreeoflife.org |
| Commercial | no |
| Registration | not required |
Content license | BSD 2-clause (FreeBSD)[1] |
The Open Tree of Life is an on-line phylogenetic tree of life – a collaborative effort, funded by the NSF AVAToL #1208809.[2] The first draft, including 2.3 million species, was released in September 2015.[3]The Interactive graph allows the user to zoom in to taxomonic classifications, phylogenetic trees, and information about a node. Clicking on a species will return it's source and reference taxonomy.
Approach
The project uses a supertree approach to generate a single phylogenetic tree (served at https://tree.opentreeoflife.org/) from a comprehensive Taxonomy_(biology) and a curated set of published phylogenetic estimates.
The taxonomy is a combination of several large classifications produced by other projects; it is combination is created using a software tool called "smasher" (its source code is in this repository https://github.com/OpenTreeOfLife/reference-taxonomy ). The resulting taxonomy (the Open Tree Taxonomy, OTT) can be browsed at https://tree.opentreeoflife.org/taxonomy/browse.
The set of phylogenetic estimates are curated via a web application (at https://tree.opentreeoflife.org/curator). Any user with a GitHub login is permitted to curate a tree. Curation activities include:
- uploading a tree from a published paper or an archival data store such as TreeBASE.
- rerooting the tree. This is often necessary many phylogenetic methods estimate unrooted trees which are subsequently rooted by other means (see Computational_phylogenetics). The rooting of these trees in supplementary information for publications and in data stores is frequently incorrect.
- associating the tip labels of a tree to the open tree taxonomy to make it feasible to compare different phylogenetic hypotheses.
The curated data store is available for use by others as git repository. All software produced by the project is available under open source licenses; see http://opentreeoflife.github.io/ for links to the code, data, and documentation.
History
The project was started in June of 2012 with a three-year NSF award to researchers at ten universities. In 2015, a two-year supplemental award was made to researchers at three institutions.
References
- Hinchliff, C. E.; Smith, S. A.; Allman, J. F.; Burleigh, J. G.; Chaudhary, R.; Coghill, L. M.; Crandall, K. A.; Deng, J.; Drew, B. T.; Gazis, R.; Gude, K.; Hibbett, D. S.; Katz, L. A.; Laughinghouse, H. D.; McTavish, E. J.; Midford, P. E.; Owen, C. L.; Ree, R. H.; Rees, J. A.; Soltis, D. E.; Williams, T.; Cranstonk, K. A. (2015). "Synthesis of phylogeny and taxonomy into a comprehensive tree of life". Proceedings of the National Academy of Sciences. Early Edition. doi:10.1073/pnas.1423041112.
- ^ https://raw.githubusercontent.com/OpenTreeOfLife/opentree/master/LICENSE.txt
- ^ "Assembling, Visualizing, and Analyzing the Tree of Life | NSF - National Science Foundation". www.nsf.gov. Retrieved 2016-02-11.
- ^ "First comprehensive tree of life shows how related you are to millions of species"[1]