1. Progress, plans and prospects Second Meeting, Nov. 12 to 14, 2007, Durham, NC NESCent Evolutionary Informatics Working Group

2. History 2008 2006 2004 2007 2005 2003 2009 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) NIH proposal (Stoltzfus, Pontelli, Gupta) NESCent Phyloinformatics Hackathon (incl. Holder, Mackey, Qiu, Stoltzfus, Vos, Lewis, Kosakovsky Pond, Swofford, Zmasek) 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

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)  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)  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. 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

8. Accomplishing our goals 2011 2009 2007 2010 2008 2012 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 complete: Glossary completion Transition model language Comparative Data Analysis Ontology Current stds: translation and validation Ontology session at Evolution 2008 Google Summer-of-Code projects NESCent Phyloinformatics course Woods’ Hole, Mol Evol Workshop

9. Activities for this week  Ontology-related  Use cases - clarify, document, add instances & references  Glossary - continue with concepts, start on instances  Related artefacts - identify, retrieve, start studying  Outreach  Identify 2008 opportunities, make plans for workshops and sessions on evoinfo, interoperability and ontologies  Current standards  library of annotated examples, with pathologies  Transition model language  Funding proposal for pilot projects  Ontology-related  Use cases - clarify, document, add instances & references  Glossary - continue with concepts, start on instances  Related artefacts - identify, retrieve, start studying  Outreach  Identify 2008 opportunities, make plans for workshops and sessions on evoinfo, interoperability and ontologies  Current standards  library of annotated examples, with pathologies  Transition model language  Funding proposal for pilot projects

10. What we will hear about today 9:20 SPAN project proposal (20 min each plus 20 min discussion)  9:20 Integrating Ontologies and Web services in Phylogenetic Workflow Development (Pontelli)  9:40 Problem Solving in Evolutionary Analysis with Web Services and DSLs (Gupta) 10:20 Break 10:40 Additional talks (20 min plus 20 min discussion each)  10:40 Extending MAO (Thompson)  11:20 NeXML (Vos)  12:00 Towards a description language for substitution models (Midford, Kosakovsky Pond) 12:40 Lunch 1:40 get back to work 9:20 SPAN project proposal (20 min each plus 20 min discussion)  9:20 Integrating Ontologies and Web services in Phylogenetic Workflow Development (Pontelli)  9:40 Problem Solving in Evolutionary Analysis with Web Services and DSLs (Gupta) 10:20 Break 10:40 Additional talks (20 min plus 20 min discussion each)  10:40 Extending MAO (Thompson)  11:20 NeXML (Vos)  12:00 Towards a description language for substitution models (Midford, Kosakovsky Pond) 12:40 Lunch 1:40 get back to work

11. What we won’t hear about  pPOD core data model  TreeBase II schema  FIGENIX expert system  pPOD core data model  TreeBase II schema  FIGENIX expert system

12. This Afternoon 1:40 Admonition (Stoltzfus, Vos) 2:00 Work session: organize into task-specific groups and begin work 3:20 Break (20 min) 3:40 Work session 4:40 Stand-ups and discussion (goals and planned activities) 5:40 Adjourn for the day 6:00 Group dinner (venue to be announced) 1:40 Admonition (Stoltzfus, Vos) 2:00 Work session: organize into task-specific groups and begin work 3:20 Break (20 min) 3:40 Work session 4:40 Stand-ups and discussion (goals and planned activities) 5:40 Adjourn for the day 6:00 Group dinner (venue to be announced)

13. Suggested activities  Ontology-related  Use cases - clarify, document, add instances & references  Glossary - continue with concepts, start on instances  Related artefacts - identify, retrieve, start studying  Outreach  Identify 2008 opportunities, make plans for workshops and sessions on evoinfo, interoperability and ontologies  Current standards  library of annotated examples, with pathologies  Transition model language  Funding proposal for pilot projects  Ontology-related  Use cases - clarify, document, add instances & references  Glossary - continue with concepts, start on instances  Related artefacts - identify, retrieve, start studying  Outreach  Identify 2008 opportunities, make plans for workshops and sessions on evoinfo, interoperability and ontologies  Current standards  library of annotated examples, with pathologies  Transition model language  Funding proposal for pilot projects What do I think is important? Where is my expertise? Where is my commitment?

14. Your charge 1.Note activities  Use cases - clarify, document, add instances & references  Glossary - continue with concepts, start on instances  Related artefacts - identify, retrieve, start studying  Outreach - identify 2008 opportunities, make plans  Current standards - document use and misuse  Transition model language - pilot projects, funding 2.Self-organize into groups  Ideally, 2 to 4 people per group  Your choice should reflect your expertise and priorities 3.Rapid assessment, then get to work  Summarize problem, set goals in terms of tangible outcomes  Consume caffeinated beverages  Work towards tangible outcomes  Discuss results and challenges with others  Put your work on the wiki 1.Note activities  Use cases - clarify, document, add instances & references  Glossary - continue with concepts, start on instances  Related artefacts - identify, retrieve, start studying  Outreach - identify 2008 opportunities, make plans  Current standards - document use and misuse  Transition model language - pilot projects, funding 2.Self-organize into groups  Ideally, 2 to 4 people per group  Your choice should reflect your expertise and priorities 3.Rapid assessment, then get to work  Summarize problem, set goals in terms of tangible outcomes  Consume caffeinated beverages  Work towards tangible outcomes  Discuss results and challenges with others  Put your work on the wiki

15. This Afternoon 1:40 Admonition (Stoltzfus, Vos) 2:00 Work session: organize into task-specific groups and begin work 3:20 Break (20 min) 3:40 Work session 4:40 Stand-ups and discussion (goals and planned activities) 5:40 Adjourn for the day 6:00 Group dinner (venue to be announced) 1:40 Admonition (Stoltzfus, Vos) 2:00 Work session: organize into task-specific groups and begin work 3:20 Break (20 min) 3:40 Work session 4:40 Stand-ups and discussion (goals and planned activities) 5:40 Adjourn for the day 6:00 Group dinner (venue to be announced)

16. Groups and targets 1.Group topic (wiki page)  Target 1  Target 2 2.Group topic (wiki page)  Target 1  Target 2 3.Group topic (wiki page)  Target 1  Target 2 4.Group topic (wiki page)  Target 1  Target 2 5.Group topic (wiki page)  Target 1  Target 2 1.Group topic (wiki page)  Target 1  Target 2 2.Group topic (wiki page)  Target 1  Target 2 3.Group topic (wiki page)  Target 1  Target 2 4.Group topic (wiki page)  Target 1  Target 2 5.Group topic (wiki page)  Target 1  Target 2