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

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. HeathPeter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E. Alfaro, Aaron Steele, Greg Jordan

Research output: Contribution to journalArticle

22 Scopus citations

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), 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.

Original languageEnglish (US)
Article number158
JournalBMC bioinformatics
Volume14
DOIs
StatePublished - May 13 2013

Keywords

  • Data reuse
  • Hackathon
  • Phylogeny
  • Taxonomy
  • Tree of life
  • Web services

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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    Stoltzfus, A., Lapp, H., Matasci, N., Deus, H., Sidlauskas, B., Zmasek, C. M., Vaidya, G., Pontelli, E., Cranston, K., Vos, R., Webb, C. O., Harmon, L. J., Pirrung, M., O'Meara, B., Pennell, M. W., Mirarab, S., Rosenberg, M. S., Balhoff, J. P., Bik, H. M., ... Jordan, G. (2013). Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC bioinformatics, 14, [158]. https://doi.org/10.1186/1471-2105-14-158