Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
Affiliation
Institute for Bioscience and Biotechnology Research (IBBR), Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USANational Evolutionary Synthesis Center, 2024 W. Main St, Durham, NC, 27705, USA
The iPlant Collaborative and EEB Department, University of Arizona, 1657 E Helen St, Tucson, AZ, 85721, USA
Digital Enterprise Research Institute, National University of Ireland, University Road, Galway, Ireland
Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331-3803, USA
Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309-0334, USA
Department of Computer Science, New Mexico State University, MSC CS, Box 30001, Las Cruces, NM, 88003, USA
NCB Naturalis, Einsteinweg 2, Leiden, 2333 CC, the Netherlands
Arnold Arboretum of Harvard University, Boston, MA, 02130, USAInstitute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, PO Box 443051, Moscow, ID, 83844-3051, USAUniversity of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USADepartment of Ecology & Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN, 37996, USADepartment of Computer Science, University of Texas at Austin, Austin, TX, 78701, USACenter for Evolutionary Medicine and Informatics, The Biodesign Institute, and School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USAUC Davis Genome Center, One Shields Ave, Davis, CA, 95618, USADepartment of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USAUniversity of Texas at Austin, BEACON, Austin, TX, USABiology Department, Duke University, Biological Sciences Building, 125 Science Drive, Durham, NC, 27708, USABiodiversity Synthesis Center, Field Museum of Natural History, 1400 S Lakeshore Dr, Chicago, IL, 60605, USADepartment of Ecology and Evolutionary Biology, South University of California Los Angeles, 621 Charles E. Young Dr, Los Angeles, CA, 90095, USAU.C. Berkeley Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USAPaperpile, 34 Houghton Street, Somerville, MA, 02143, USA
Issue Date
2013Metadata
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BioMed CentralCitation
Stoltzfus et al. BMC Bioinformatics 2013, 14:158 http://www.biomedcentral.com/1471-2105/14/158Journal
BMC BioinformaticsRights
© 2013 Stoltzfus et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)Collection Information
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.Abstract
BACKGROUND: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.RESULTS:With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components(2) proof-of-concept pruners and controllers
(3) a meta-API for taxonomic name resolution services
(4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying
(5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes
and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org webcite), and a server image.CONCLUSIONS:Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.