| Title |
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
|
|---|---|
| Published in |
BMC Bioinformatics, May 2013
|
| 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. |
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X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 11 | 32% |
| United Kingdom | 7 | 21% |
| Spain | 1 | 3% |
| Ireland | 1 | 3% |
| Hong Kong | 1 | 3% |
| France | 1 | 3% |
| Germany | 1 | 3% |
| Argentina | 1 | 3% |
| Canada | 1 | 3% |
| Other | 1 | 3% |
| Unknown | 8 | 24% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 16 | 47% |
| Members of the public | 14 | 41% |
| Science communicators (journalists, bloggers, editors) | 3 | 9% |
| Practitioners (doctors, other healthcare professionals) | 1 | 3% |
Mendeley demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 15 | 10% |
| Brazil | 3 | 2% |
| Chile | 2 | 1% |
| Sweden | 1 | <1% |
| Netherlands | 1 | <1% |
| Greece | 1 | <1% |
| United Kingdom | 1 | <1% |
| France | 1 | <1% |
| Spain | 1 | <1% |
| Other | 3 | 2% |
| Unknown | 118 | 80% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 45 | 31% |
| Student > Ph. D. Student | 26 | 18% |
| Student > Master | 13 | 9% |
| Professor > Associate Professor | 13 | 9% |
| Student > Bachelor | 12 | 8% |
| Other | 29 | 20% |
| Unknown | 9 | 6% |
| 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 | 12 | 8% |