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    Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

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    1471-2105-14-158.pdf
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    Author
    Stoltzfus, Arlin
    Lapp, Hilmar
    Matasci, Naim
    Deus, Helena
    Sidlauskas, Brian
    Zmasek, Christian
    Vaidya, Gaurav
    Pontelli, Enrico
    Cranston, Karen
    Vos, Rutger
    Webb, Campbell
    Harmon, Luke
    Pirrung, Megan
    O'Meara, Brian
    Pennell, Matthew
    Mirarab, Siavash
    Rosenberg, Michael
    Balhoff, James
    Bik, Holly
    Heath, Tracy
    Midford, Peter
    Brown, Joseph
    McTavish, Emily Jane
    Sukumaran, Jeet
    Westneat, Mark
    Alfaro, Michael
    Steele, Aaron
    Jordan, Greg
    Show allShow less
    Affiliation
    Institute for Bioscience and Biotechnology Research (IBBR), Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
    National 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, USA
    Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, PO Box 443051, Moscow, ID, 83844-3051, USA
    University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
    Department of Ecology & Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN, 37996, USA
    Department of Computer Science, University of Texas at Austin, Austin, TX, 78701, USA
    Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA
    UC Davis Genome Center, One Shields Ave, Davis, CA, 95618, USA
    Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
    University of Texas at Austin, BEACON, Austin, TX, USA
    Biology Department, Duke University, Biological Sciences Building, 125 Science Drive, Durham, NC, 27708, USA
    Biodiversity Synthesis Center, Field Museum of Natural History, 1400 S Lakeshore Dr, Chicago, IL, 60605, USA
    Department of Ecology and Evolutionary Biology, South University of California Los Angeles, 621 Charles E. Young Dr, Los Angeles, CA, 90095, USA
    U.C. Berkeley Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA
    Paperpile, 34 Houghton Street, Somerville, MA, 02143, USA
    Show allShow less
    Issue Date
    2013
    Keywords
    Phylogeny
    Taxonomy
    Hackathon
    Web services
    Data reuse
    Tree of life
    
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    Show full item record
    Publisher
    BioMed Central
    Citation
    Stoltzfus et al. BMC Bioinformatics 2013, 14:158 http://www.biomedcentral.com/1471-2105/14/158
    Journal
    BMC Bioinformatics
    Rights
    © 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.
    EISSN
    1471-2105
    DOI
    10.1186/1471-2105-14-158
    Version
    Final published version
    Additional Links
    http://www.biomedcentral.com/1471-2105/14/158
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2105-14-158
    Scopus Count
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