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

Persistent Link:
http://hdl.handle.net/10150/610243
Title:
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
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
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
Issue Date:
2013
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
Keywords:
Phylogeny; Taxonomy; Hackathon; Web services; Data reuse; Tree of life
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2105/14/158

Full metadata record

DC FieldValue Language
dc.contributor.authorStoltzfus, Arlinen
dc.contributor.authorLapp, Hilmaren
dc.contributor.authorMatasci, Naimen
dc.contributor.authorDeus, Helenaen
dc.contributor.authorSidlauskas, Brianen
dc.contributor.authorZmasek, Christianen
dc.contributor.authorVaidya, Gauraven
dc.contributor.authorPontelli, Enricoen
dc.contributor.authorCranston, Karenen
dc.contributor.authorVos, Rutgeren
dc.contributor.authorWebb, Campbellen
dc.contributor.authorHarmon, Lukeen
dc.contributor.authorPirrung, Meganen
dc.contributor.authorO'Meara, Brianen
dc.contributor.authorPennell, Matthewen
dc.contributor.authorMirarab, Siavashen
dc.contributor.authorRosenberg, Michaelen
dc.contributor.authorBalhoff, Jamesen
dc.contributor.authorBik, Hollyen
dc.contributor.authorHeath, Tracyen
dc.contributor.authorMidford, Peteren
dc.contributor.authorBrown, Josephen
dc.contributor.authorMcTavish, Emily Janeen
dc.contributor.authorSukumaran, Jeeten
dc.contributor.authorWestneat, Marken
dc.contributor.authorAlfaro, Michaelen
dc.contributor.authorSteele, Aaronen
dc.contributor.authorJordan, Gregen
dc.date.accessioned2016-05-20T09:02:02Z-
dc.date.available2016-05-20T09:02:02Z-
dc.date.issued2013en
dc.identifier.citationStoltzfus et al. BMC Bioinformatics 2013, 14:158 http://www.biomedcentral.com/1471-2105/14/158en
dc.identifier.doi10.1186/1471-2105-14-158en
dc.identifier.urihttp://hdl.handle.net/10150/610243-
dc.description.abstractBACKGROUND: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 componentsen
dc.description.abstract(2) proof-of-concept pruners and controllersen
dc.description.abstract(3) a meta-API for taxonomic name resolution servicesen
dc.description.abstract(4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and queryingen
dc.description.abstract(5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodesen
dc.description.abstractand (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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2105/14/158en
dc.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)en
dc.subjectPhylogenyen
dc.subjectTaxonomyen
dc.subjectHackathonen
dc.subjectWeb servicesen
dc.subjectData reuseen
dc.subjectTree of lifeen
dc.titlePhylotastic! Making tree-of-life knowledge accessible, reusable and convenienten
dc.typeArticleen
dc.identifier.eissn1471-2105en
dc.contributor.departmentInstitute for Bioscience and Biotechnology Research (IBBR), Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USAen
dc.contributor.departmentNational Evolutionary Synthesis Center, 2024 W. Main St, Durham, NC, 27705, USAen
dc.contributor.departmentThe iPlant Collaborative and EEB Department, University of Arizona, 1657 E Helen St, Tucson, AZ, 85721, USAen
dc.contributor.departmentDigital Enterprise Research Institute, National University of Ireland, University Road, Galway, Irelanden
dc.contributor.departmentDepartment of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331-3803, USAen
dc.contributor.departmentSanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USAen
dc.contributor.departmentDepartment of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309-0334, USAen
dc.contributor.departmentDepartment of Computer Science, New Mexico State University, MSC CS, Box 30001, Las Cruces, NM, 88003, USAen
dc.contributor.departmentNCB Naturalis, Einsteinweg 2, Leiden, 2333 CC, the Netherlandsen
dc.contributor.departmentArnold Arboretum of Harvard University, Boston, MA, 02130, USAen
dc.contributor.departmentInstitute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, PO Box 443051, Moscow, ID, 83844-3051, USAen
dc.contributor.departmentUniversity of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USAen
dc.contributor.departmentDepartment of Ecology & Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN, 37996, USAen
dc.contributor.departmentDepartment of Computer Science, University of Texas at Austin, Austin, TX, 78701, USAen
dc.contributor.departmentCenter for Evolutionary Medicine and Informatics, The Biodesign Institute, and School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USAen
dc.contributor.departmentUC Davis Genome Center, One Shields Ave, Davis, CA, 95618, USAen
dc.contributor.departmentDepartment of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USAen
dc.contributor.departmentUniversity of Texas at Austin, BEACON, Austin, TX, USAen
dc.contributor.departmentBiology Department, Duke University, Biological Sciences Building, 125 Science Drive, Durham, NC, 27708, USAen
dc.contributor.departmentBiodiversity Synthesis Center, Field Museum of Natural History, 1400 S Lakeshore Dr, Chicago, IL, 60605, USAen
dc.contributor.departmentDepartment of Ecology and Evolutionary Biology, South University of California Los Angeles, 621 Charles E. Young Dr, Los Angeles, CA, 90095, USAen
dc.contributor.departmentU.C. Berkeley Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USAen
dc.contributor.departmentPaperpile, 34 Houghton Street, Somerville, MA, 02143, USAen
dc.identifier.journalBMC Bioinformaticsen
dc.description.collectioninformationThis 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.en
dc.eprint.versionFinal published versionen
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