Progress plans and prospects
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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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Progress plans and prospects

NESCent Evolutionary Informatics Working Group

Progress, plans and prospects

Third Meeting, May 19 to 22, 2008, Durham, NC


History

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


Prioritization exercise

Prioritization exercise

In spring of 2007, participants ranked 11 proposed items

leaders devised coherent plan with suggested tactics


First meeting

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)


Central unifying artefact

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

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)


Tangible outcomes period 2

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)


Developing an ontology

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


Accomplishing our goals

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


Activities for this week

Activities for this week

  • Nexml

  • CDAO


What we will hear about today

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)


This afternoon

This Afternoon

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

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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