Title |
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
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Published in |
BMC Bioinformatics, May 2013
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DOI | 10.1186/1471-2105-14-158 |
Pubmed ID | |
Authors |
Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy A Heath, Peter E Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro, Aaron Steele, Greg Jordan |
Abstract |
Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 12 | 29% |
United Kingdom | 6 | 15% |
Hong Kong | 1 | 2% |
France | 1 | 2% |
Spain | 1 | 2% |
Germany | 1 | 2% |
Brazil | 1 | 2% |
Argentina | 1 | 2% |
Ireland | 1 | 2% |
Other | 4 | 10% |
Unknown | 12 | 29% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 20 | 49% |
Members of the public | 17 | 41% |
Science communicators (journalists, bloggers, editors) | 3 | 7% |
Practitioners (doctors, other healthcare professionals) | 1 | 2% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 15 | 10% |
Brazil | 3 | 2% |
Chile | 2 | 1% |
Netherlands | 1 | <1% |
Germany | 1 | <1% |
Cuba | 1 | <1% |
Sweden | 1 | <1% |
France | 1 | <1% |
Belgium | 1 | <1% |
Other | 3 | 2% |
Unknown | 119 | 80% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 45 | 30% |
Student > Ph. D. Student | 27 | 18% |
Student > Master | 13 | 9% |
Professor > Associate Professor | 12 | 8% |
Student > Bachelor | 12 | 8% |
Other | 29 | 20% |
Unknown | 10 | 7% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 74 | 50% |
Computer Science | 20 | 14% |
Environmental Science | 11 | 7% |
Biochemistry, Genetics and Molecular Biology | 7 | 5% |
Engineering | 7 | 5% |
Other | 16 | 11% |
Unknown | 13 | 9% |