Phylotastic! Making tree-of-life knowledge accessible, reusable andconvenient

BMC Bioinformatics

Arlin Stoltzfus²²  Hilmar Lapp⁷  Naim Matasci⁵  Helena Deus¹⁸  Brian Sidlauskas²¹  Christian M Zmasek¹⁶  Gaurav Vaidya¹⁰  Enrico Pontelli¹⁵  Karen Cranston⁷  Rutger Vos⁸  Campbell O Webb²  Luke J Harmon²³  Megan Pirrung¹³  Brian O'Meara¹⁷  Matthew W Pennell²³  Siavash Mirarab¹⁹  Michael S Rosenberg¹²  James P Balhoff⁷  Holly M Bik¹  Tracy A Heath²⁰  Peter E Midford⁷  Joseph W Brown²³  Emily Jane McTavish⁶  Jeet Sukumaran¹¹  Mark Westneat⁴  Michael E Alfaro³  Aaron Steele¹⁴  Greg Jordan⁹ 

[1] UC Davis Genome Center, One Shields Ave, Davis, CA, 95618, USA

[2] Arnold Arboretum of Harvard University, Boston, MA, 02130, USA

[3] Department of Ecology and Evolutionary Biology, South University ofCalifornia Los Angeles, 621 Charles E. Young Dr, Los Angeles, CA, 90095,USA

[4] Biodiversity Synthesis Center, Field Museum of Natural History, 1400 SLakeshore Dr, Chicago, IL, 60605, USA

[5] The iPlant Collaborative and EEB Department, University of Arizona, 1657 EHelen St, Tucson, AZ, 85721, USA

[6] University of Texas at Austin, BEACON, Austin, TX, USA

[7] National Evolutionary Synthesis Center, 2024 W. Main St, Durham, NC, 27705,USA

[8] NCB Naturalis, Einsteinweg 2, Leiden, 2333 CC, the Netherlands

[9] Paperpile, 34 Houghton Street, Somerville, MA, 02143, USA

[10] Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, Boulder, CO, 80309-0334, USA

[11] Biology Department, Duke University, Biological Sciences Building, 125Science Drive, Durham, NC, 27708, USA

[12] 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

[13] University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045,USA

[14] U.C. Berkeley Museum of Vertebrate Zoology, University of California, 3101Valley Life Sciences Building, Berkeley, CA, 94720, USA

[15] Department of Computer Science, New Mexico State University, MSC CS, Box30001, Las Cruces, NM, 88003, USA

[16] Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, LaJolla, CA, 92037, USA

[17] Department of Ecology & Evolutionary Biology, 569 Dabney Hall, Universityof Tennessee, Knoxville, TN, 37996, USA

[18] Digital Enterprise Research Institute, National University of Ireland,University Road, Galway, Ireland

[19] Department of Computer Science, University of Texas at Austin, Austin, TX,78701, USA

[20] Department of Integrative Biology, University of California, Berkeley, CA,94720-3140, USA

[21] Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall,Corvallis, OR, 97331-3803, USA

[22] Institute for Bioscience and Biotechnology Research (IBBR), Biosystems andBiomaterials Division, National Institute of Standards and Technology,Gaithersburg, MD, 20899, USA

[23] Institute for Bioinformatics and Evolutionary Studies (IBEST), University ofIdaho, PO Box 443051, Moscow, ID, 83844-3051, USA

关键词: Tree of life;    Data reuse;    Web services;    Hackathon;    Taxonomy;    Phylogeny;   

Others  :  1087877
DOI  :  10.1186/1471-2105-14-158

 received in 2013-01-18, accepted in 2013-04-30,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Stoltzfus et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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