2009 Grant Renewal Workshop

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Phenotype Grant Renewal Workshop

A workshop hosted by the National Evolutionary Synthesis Center (NESCent)


Location and Date

Venue: National Evolutionary Synthesis Center (NESCent) (directions, also see information for visitors)

Date: April 28-29, 2009

Organizers: Paula Mabee, Monte Westerfield, Todd Vision

Introduction

The goal of this workshop is to discuss plans for a renewal of the Phenoscape NSF grant, to be submitted in July 2009. Specific aims of the renewal are to be determined by the workshop participants. An initial list includes creating the informatics tools necessary to integrate and mediate between different concepts of homology, extending the systematics legacy data transformation to all vertebrates, and laboratory case-studies for following up specific hypotheses generated by the expanding knowledge base.

Agenda

Note that this agenda is still in draft stage and may change before the meeting.

Tuesday, Apr. 27, 2009

Afternoon:

  • EQ support by all involved model organism databases
  • Ontology building
  • Legacy character transformation

There are notes from the discussion.

Wednesday, Apr. 28, 2009

Specific goals and approaches

  1. Expand taxonomic coverage of Phenoscape to Vertebrata; vertebrate evolutionary skeletal phenotypes associated with skeletal phenotypes and associated data from MODs.
    • Expand/develop anatomy ontologies for multispecies ontologies and MODs to cover skeleton
      • Teleosts: expand as required for annotation of euteleost matrices (year 1)
      • ZFIN (done)
      • Amphibanat
      • XenBase: AO done
      • Amniotes: develop from mammal anatomy ontology core
      • Mouse (done)
    • Develop taxonomy ontologies for vertebrates
      • Teleosts: TTO done
      • Amphibanat: TO status?
      • Amniotes: need to create for extinct archosaurs + birds & croc + mammals
    • Annotate skeletal diversity for vertebrates
      • Teleosts: curate euteleost matrices (year 1)
      • ZFIN: back-curate skeletal phenotypes
      • Amphibanat: curation needs?
      • XenBase: expand to cover skeletal mutants/knockouts
      • Amniotes: prioritize and curate key papers
      • Mouse (done)
    • Add developmental time in consistent schema across MODs to support new evo-devo queries
      • ZFIN (done)
      • XenBase (done)
      • Mouse (needs to be done as per discussions)
    • Add evolutionary time to support new evo-devo queries; reference evo time to taxonomy ontologies
      • Teleosts: need to add to TTO
      • Amphibanat: need to add
      • Amniotes: need to add
    • Synchronize multispecies anatomy ontologies with corresponding MODs
      • Teleosts + ZFIN (done)
      • Amphibanat + XenBase (will be done before grant begins)
      • Amniotes + mammals
    • Align three multispecies anatomy ontologies (fishes, amphibian, amniotes)
      • create general vertebrate reference ontology (to which each multisp ontology maps)
      • create homology table for vertebrate skeletal structures
  2. Add new use cases based on referencing to time-based ontologies and phylogenies
    • Developmental time: Predict when in development a particular evolutionary phenotype might arise. Given some phenotypic evolutionary variation (e.g. presence/absence of scales in fishes), find out their developmental origin (cell lineage) and timing of development (when in zebrafish they form relative to other structures?)
    • Evolutionary time: Determine when a phenotype and its variant arose (e.g. when did scales arise and when were they lost?). Requires phylogeny, referencing taxa in taxonomy ontology to time.
    • Map annotations on phylogenies;
  3. Specific goal associated with images/morphbank?
  4. Expand database and web interface tools in support of the scientific goals
    • expansion of existing db to handle another 30 million annotations?
    • two obds?
  5. Analytical tools/reasoner to search for correlations across phenotypes, genes, intersections, on trees, particular
  6. Collaborations
    • Vertnet?
    • Mesquite
    • TreeBASE
    • Morphbank
    • MOD collabs?

Logistics

  • For long-distance participants, the hotel is the Millennium Hotel (2800 Campus Walk Ave, Durham, NC 27705; tel. (919) 383-8575)
  • For dining & entertainment, NESCent is right across from Ninth Street
  • For the venue, NESCent is in the historic Erwin Mills building (directions)

Reading

  • Within the Phenoscape project, we have been tagging interesting references about phenotype and taxonomy ontologies by using the tag "phenoscape" on Connotea. Everyone is welcome to suggest references by using this tag.

Participants

Members of Phenoscape are in bold font.

Name Institution
Judy Blake The Jackson Laboratory
Wasila Dahdul Phenoscape, and Department of Biology, University of South Dakota
Hilmar Lapp Phenoscape, and NESCent
Suzi Lewis Berkeley Bioinformatics and Ontology Project
John Lundberg Phenoscape, and Department of Ichthyology, Academy of Natural Sciences
Paula Mabee Phenoscape, and Department of Biology, University of South Dakota
Anne Maglia Missouri University of Science and Technology
Peter Midford Dept. of Ecology and Evolutionary Biology, University of Kansas
Paul Sereno University of Chicago
Todd Vision Phenoscape, NESCent, and Department of Biology, University of North Carolina at Chapel Hill
Peter Vize Department of Biology, University of Calgary
Monte Westerfield Phenoscape, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon