Stoltzfus_EvoIO_2010

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

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

Fireplug conforming to NFPA Standard (1905)
An interop disaster story
Seck & Evans, 2004. NISTIR 7158
The Great Baltimore Fire of 1904

The Oakland Firestorm of 1991
Image: wikipedia
standards are voluntary
Seck & Evans, 2004. NISTIR 7158
Oakland conforms to standard

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

EvoIO “stack”

Character-state data model
(widely used model underlying CDAO and neXML)

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

neXML
formally defined syntax
OTS tools to validate
extensible
versioned

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

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
Evolutionary Informatics Working Group
Phyloinformatics VoCamp (Montpellier, Fr)

2009 Data resource interop hackathon
Image: Hilmar Lapp

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

Stack development
Arlin
Karen
Interop targets
Hilmar
Sheldon
Enrico
Rutger
Nico
How to get involved
www.evoio.org

Extra slides
Not used, due to time limitations

Organizational values
Flexible task-specific groups
Heavy use of electronic collaboration tools
Open-source code
Open development teams
Consensus decision-making
Flexible leadership
Coffee

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 . . .

Stoltzfus_EvoIO_2010

by Arlin Stoltzfus on Jul 02, 2010

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Stoltzfus_EvoIO_2010 — Presentation Transcript