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

History CDAT OO database (Mackey, Stoltzfus) Bio::NEXUS (Qiu, Stoltzfus) Bio::CDAT BioPerl Proposal (Stoltzfus, Vos, Qiu) “Evolutionary Informatics Group” meets in Philly (Stoltzfus, Qiu, Mackey, Vos, and 6 others) working group proposal (Stoltzfus, Vos) NESCent GSoC Projects First meeting Second meeting Third meeting Fourth meeting NESCent Evolutionary Informatics Working Group 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) You are here Informatics projects and activities of group members NIH proposal (Stoltzfus, Pontelli, Gupta) NESCent Phyloinformatics Hackathon (incl. Holder, Mackey, Qiu, Stoltzfus, Vos, Lewis, Kosakovsky Pond, Swofford, Zmasek) CDAO visiting scientists meeting

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

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)  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)

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

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)  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)

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)  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)

Developing an ontology 1.Define domain by means of use cases 2.From use cases, identify core concepts and relations, and capture them in glossary 3.Study related artefacts, including ontologies to be integrated (MAO, PhyloXML, NEXUS) 4.Formally encode concepts and relations in an ontology language 5.Evaluate and revise the encoding 1.Define domain by means of use cases 2.From use cases, identify core concepts and relations, and capture them in glossary 3.Study related artefacts, including ontologies to be integrated (MAO, PhyloXML, NEXUS) 4.Formally encode concepts and relations in an ontology language 5.Evaluate and revise the encoding

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

Activities for this week  Nexml  CDAO  Nexml  CDAO

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) 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)

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

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