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Presentation on the EvoIO collaborative (evoio.org) given by Arlin Stoltzfus June 29, 2010, at the iEvoBio conference in Portland, OR (USA).

Presentation on the EvoIO collaborative (evoio.org) given by Arlin Stoltzfus June 29, 2010, at the iEvoBio conference in Portland, OR (USA).

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    Stoltzfus_EvoIO_2010 Stoltzfus_EvoIO_2010 Presentation Transcript

    • June 29, 2010 iEvoBio
      EvoIO
      Community-driven standards for sustainable interoperability
      www.evoio.org
      Arlin Stoltzfus
      National Institute of Standards and Technology, Gaithersburg, MD arlin@umd.edu
      Karen Cranston
      Field Museum of Natural History, Chicago, IL 50506
      Hilmar Lapp
      National Evolutionary Synthesis Center (NESCent), Durham, NC 27705
      Sheldon McKay
      Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
      Enrico Pontelli
      Department of Computer Science, New Mexico State University, Las Cruces, NM 88003
      Rutger Vos
      University of Reading, Reading, RG6 6BX, United Kingdom
      Nico Cellinese
      University of Florida, Florida Museum of Natural History, Gainesville, FL 32611
    • June 29, 2010 iEvoBio
      Outline
      • an interop disaster story
      • the EvoIO “stack”
      • neXML (data format)
      • phyloWS (web services)
      • CDAO (ontology)
      • process (organization, strategy, hackathons)
      • implementations
      • how to get involved
    • June 29, 2010 iEvoBio
      Fireplug conforming to NFPA Standard (1905)
      An interop disaster story
      Seck & Evans, 2004. NISTIR 7158
      The Great Baltimore Fire of 1904
    • June 29, 2010 iEvoBio
      The Oakland Firestorm of 1991
      Image: wikipedia
      standards are voluntary
      Seck & Evans, 2004. NISTIR 7158
      Oakland conforms to standard
    • June 29, 2010 iEvoBio
      Lessons
      Interoperability standards are developed by stakeholders
      • organize in response to problem
      • collectively develop the solution
      Standards are voluntary
      • compliance is a business decision
      To further the goal of interoperability
      • mitigate costs of compliance
      • enhance benefits of compliance
    • June 29, 2010 iEvoBio
      EvoIO “stack”
    • June 29, 2010 iEvoBio
      Character-state data model
      (widely used model underlying CDAO and neXML)
    • June 29, 2010 iEvoBio
      Specification:
      Study use-cases to clarify scope
      Choice of representation:
      Choose language and development tools
      Ontology refinement
      Conceptualization:
      • Identify terms from use cases, artefacts
      • Build concept glossary
      • Classify key concepts and relations
      Implementation:
      Formalize the concepts and relations using the chosen language and tools
      Evaluation:
      Test the ontology for its ability to represent data called for in the use cases, and to support reasoning
      CDAO development
      Some CDAO concepts and relations in regard to trees
    • June 29, 2010 iEvoBio
      neXML
      • formally defined syntax
      • OTS tools to validate
      • extensible
      • versioned
    • June 29, 2010 iEvoBio
      PhyloWS URL API
      Subdomain for
      any phylogenetic
      resource
      Subdomain for
      PhyloWS API
      http://purl.org/phylo/treebase/phylows/study/TB2:S1787
      Permanent URL
      resolver domain
      Subdomain
      for TreeBASE
      Object ID
    • June 29, 2010 iEvoBio
      2007
      2008
      2009
      2010
      2011
      Process
      Planning meeting (Philly)
      Phylohackathon (Durham)
      WG1
      neXML
      WG2
      DB interop hackathon (Durham)
      CDAO (Durham)
      WG3
      PhyloWS (Tokyo)
      Google Summer-of-Code
      WG4
      Google Summer-of-Code
      Evolutionary Informatics Working Group
      Phyloinformatics VoCamp (Montpellier, Fr)
      Google Summer-of-Code
    • June 29, 2010 iEvoBio
      2009 Data resource interop hackathon
      Image: Hilmar Lapp
    • June 29, 2010 iEvoBio
      Jim Balhoff
      National Evolutionary Synthesis Center, Durham, NC
      Rutger Vos
      University of Reading, Reading, RG6 6BX, United Kingdom
      Vivek Gopalan
      Bioinformatics and Computational Biosciences Branch (BCBB), NIAID
      Brandon Chisham
      New Mexico State University, Las Cruces, NM
      Implementations
      Nexml IO implementations
      • Bio::Phylo, BioPerl, HIVQuery (Perl)
      • DAMBE (C)
      • Mesquite, TreeBase (Java) *
      • Phenex (Java via XMLbeans)
      • DendroPy (Python)
      • NCL (C++)
      • BioRuby (Ruby)
      PhyloWS
      • Phylr
      • TreeBase2
      • Bio::Phylo (ToLWeb and TimeTree via screen-scraping)
      CDAO
      • Nexplorer3
      • CDAO-store
      • translations
    • June 29, 2010 iEvoBio
      Stack development
      Arlin
      Karen
      Interop targets
      Hilmar
      Sheldon
      Enrico
      Rutger
      Nico
      How to get involved
      www.evoio.org
    • June 29, 2010 iEvoBio
      Extra slides
      Not used, due to time limitations
    • June 29, 2010 iEvoBio
      Organizational values
      Flexible task-specific groups
      Heavy use of electronic collaboration tools
      Open-source code
      Open development teams
      Consensus decision-making
      Flexible leadership
      Coffee
    • June 29, 2010 iEvoBio
      The hackathon model
      Before the event
      Organizers develop theme
      Organizers recruit participants
      At the event, day 1
      Initial presentations, group discussion
      Participants self-organize around “pitches”
      At the event, after day 1
      Participants work on project goals
      After the event . . .