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Progress, plans and prospects

NESCent Evolutionary Informatics Working Group. Progress, plans and prospects. Third Meeting, May 19 to 22, 2008, Durham, NC. 2003. CDAT OO database (Mackey, Stoltzfus). 2004. NESCent Evolutionary Informatics Working Group. Bio::NEXUS (Qiu, Stoltzfus). 2005.

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Progress, plans and prospects

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  1. NESCent Evolutionary Informatics Working Group Progress, plans and prospects Third Meeting, May 19 to 22, 2008, Durham, NC

  2. 2003 CDAT OO database (Mackey, Stoltzfus) 2004 NESCent Evolutionary Informatics Working Group Bio::NEXUS (Qiu, Stoltzfus) 2005 Bio::CDAT BioPerl Proposal (Stoltzfus, Vos, Qiu) working group proposal (Stoltzfus, Vos) “Evolutionary Informatics Group” meets in Philly (Stoltzfus, Qiu, Mackey, Vos, and 6 others) 2006 Jon Eisen (“phylogenomics”) Joe Felsenstein (PHYLIP) Mark Holder (GARLI) Sergei Kosakovsky Pond (HyPhy) Sudhir Kumar (MEGA) Paul Lewis (NCL) Aaron Mackey (BioPerl,GMOD) David Maddison (Mesquite) Wayne Maddison (Mesquite) Andrew Rambaut (BEAST) Arlin Stoltzfus (Bio::NEXUS) David Swofford (PAUP*) Rutger Vos (Bio::Phylo) Xuhua Xia (DAMBE) Christian Zmasek (ATV, RIO) NESCent Phyloinformatics Hackathon (incl. Holder, Mackey, Qiu, Stoltzfus, Vos, Lewis, Kosakovsky Pond, Swofford, Zmasek) 2007 First meeting NIH proposal (Stoltzfus, Pontelli, Gupta) Second meeting 2008 CDAO visiting scientists meeting Third meeting 2009 Fourth meeting History Informatics projects and activities of group members NESCent GSoC Projects You are here

  3. Prioritization exercise In spring of 2007, participants ranked 11 proposed items leaders devised coherent plan with suggested tactics

  4. First meeting • May 21-23, 2007, NESCent • Priorities and activities • Supporting current file formats • Substitution model language • Central unifying artefact • New data exchange format • Outreach (funding, community needs)

  5. Central unifying artefact • Implementation as • File format • DB schema • Ontology • Criteria to choose one • Richness • Ease of expression • Tech support for • transfer • storage • query • validation • Extensibility

  6. Tangible Outcomes, period 1 • New data exchange format (wiki) • Detailed proposal • Current formats (wiki) • Use assessment (incomplete) • Examples (incomplete) • Transition Model Language (wiki) • Assessment • Initial results on related technologies • Central Unifying Artefact (wiki, docs, online demos) • NeXML draft • Ontology development strategy (CDAO) • Concept glossary • Ontology-based semantic transformation demos • Project proposal (4-year, ~1.2 M$ NIH RO1) • International team of collaborators • Outreach: not much (broader awareness)

  7. Tangible Outcomes, period 2 • New data exchange format (wiki, nexml.org) • NeXML (Rutger’s talk) • Current formats (wiki) • NA • Transition Model Language (wiki) • NA • Comparative data analysis ontology (wiki, docs, demos) • Analyzed related artefacts • Expanded concept glossary • Developed first draft of CDAO • Started evaluation • Outreach: not much (broader awareness)

  8. Developing an ontology • Define domain by means of use cases • From use cases, identify core concepts and relations, and capture them in glossary • Study related artefacts, including ontologies to be integrated (MAO, PhyloXML, NEXUS) • Formally encode concepts and relations in an ontology language • Evaluate and revise the encoding

  9. NESCent Evolutionary Informatics Working Group 2007 First meeting 2008 Second meeting Ontology session at Evolution 2008 NESCent Phyloinformatics course Third meeting Google Summer-of-Code projects 2009 Woods’ Hole, Mol Evol Workshop Fourth meeting • Ongoing opportunities: • Workshops • Summer-of-code • Funding proposals • NESCent visiting scientist • NESCent hack-a-thon • NESCent working group • NSF meeting proposals • Research proposals 2010 • Timespan of NIH project if funded • Comparative Data Analysis Ontology • Domain-specific language • Workflow construction using reasoning • Services infrastructure for execution 2011 2012 Accomplishing our goals • Some milestones to consider: • Glossary completion • neXML application support • CDAO demonstrations

  10. Activities for this week • Nexml • CDAO

  11. What we will hear about today 9:30 Current state of the NeXML project (Rutger Vos) 11:00 Implementation of NEXML in DAMBE (Xuhua Xia) 11:30 PhyloWS project (Hilmar Lapp) 1:40 Initial implementation of CDAO (Enrico)

  12. This Afternoon 1:40 Ontology talk and discussion Break 3:40 Reconvene to make plans for the week 6:00 Group dinner (Pops)

  13. Other talks this week • Ryan Scherle (repositories, Dryad project) • Jim Leebens-Mack (MIAPA) • Jim Balhoff (phenoscape) • Arlin Stoltzfus (worm evo-devo ontology)

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