Difference between revisions of "2009 Grant Renewal Workshop"
From phenoscape
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''Note that this agenda is still in draft stage and may change before the meeting.'' | ''Note that this agenda is still in draft stage and may change before the meeting.'' | ||
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=== Tuesday, Apr. 27, 2009 === | === Tuesday, Apr. 27, 2009 === | ||
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'''Afternoon:''' | '''Afternoon:''' | ||
| − | * | + | * EQ support by all involved model organism databases |
| − | * | + | * Ontology building |
| − | + | * Legacy character transformation | |
| − | * | + | There are [[Phenoscape Grant Renewal Workshop/Notes#Tuesday_afternooon|notes from the discussion]]. |
| − | + | ||
=== Wednesday, Apr. 28, 2009 === | === Wednesday, Apr. 28, 2009 === | ||
| − | '''Specific goals and approaches''' | + | '''Specific goals and approaches''' |
| − | # Expand taxonomic coverage of Phenoscape to Vertebrata; vertebrate evolutionary skeletal phenotypes associated with skeletal phenotypes and associated data from MODs. | + | # 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 | #* Expand/develop anatomy ontologies for multispecies ontologies and MODs to cover skeleton | ||
#** Teleosts: expand as required for annotation of euteleost matrices (year 1) | #** Teleosts: expand as required for annotation of euteleost matrices (year 1) | ||
| Line 44: | Line 37: | ||
#** Amphibanat | #** Amphibanat | ||
#** XenBase: AO done | #** XenBase: AO done | ||
| − | #** Amniotes: develop from mammal anatomy ontology core | + | #** Amniotes: develop from mammal anatomy ontology core |
#** Mouse (done) | #** Mouse (done) | ||
#* Develop taxonomy ontologies for vertebrates | #* Develop taxonomy ontologies for vertebrates | ||
| Line 55: | Line 48: | ||
#** Amphibanat: curation needs? | #** Amphibanat: curation needs? | ||
#** XenBase: expand to cover skeletal mutants/knockouts | #** XenBase: expand to cover skeletal mutants/knockouts | ||
| − | #** Amniotes: prioritize and curate key papers | + | #** Amniotes: prioritize and curate key papers |
#** Mouse (done) | #** Mouse (done) | ||
| − | #* Add developmental time in consistent schema across MODs to support new evo-devo queries | + | #* Add developmental time in consistent schema across MODs to support new evo-devo queries |
#** ZFIN (done) | #** ZFIN (done) | ||
#** XenBase (done) | #** XenBase (done) | ||
#** Mouse (needs to be done as per discussions) | #** Mouse (needs to be done as per discussions) | ||
#* Add evolutionary time to support new evo-devo queries; reference evo time to taxonomy ontologies | #* Add evolutionary time to support new evo-devo queries; reference evo time to taxonomy ontologies | ||
| − | #** Teleosts: need to add to TTO | + | #** Teleosts: need to add to TTO |
| − | #** Amphibanat: need to add | + | #** Amphibanat: need to add |
| − | #** Amniotes: need to add | + | #** Amniotes: need to add |
#* Synchronize multispecies anatomy ontologies with corresponding MODs | #* Synchronize multispecies anatomy ontologies with corresponding MODs | ||
#** Teleosts + ZFIN (done) | #** Teleosts + ZFIN (done) | ||
| Line 77: | Line 70: | ||
#* Map annotations on phylogenies; | #* Map annotations on phylogenies; | ||
# Specific goal associated with images/morphbank? | # Specific goal associated with images/morphbank? | ||
| − | # Expand database and web interface tools in support of the scientific goals | + | # Expand database and web interface tools in support of the scientific goals |
#* expansion of existing db to handle another 30 million annotations? | #* expansion of existing db to handle another 30 million annotations? | ||
#* two obds? | #* two obds? | ||
| − | # Analytical tools/reasoner to search for correlations across phenotypes, genes, intersections, on trees, particular | + | # Analytical tools/reasoner to search for correlations across phenotypes, genes, intersections, on trees, particular |
# Collaborations | # Collaborations | ||
#* Vertnet? | #* Vertnet? | ||
Revision as of 13:58, 29 April 2009
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
- 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
- Expand/develop anatomy ontologies for multispecies ontologies and MODs to cover skeleton
- 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;
- Specific goal associated with images/morphbank?
- Expand database and web interface tools in support of the scientific goals
- expansion of existing db to handle another 30 million annotations?
- two obds?
- Analytical tools/reasoner to search for correlations across phenotypes, genes, intersections, on trees, particular
- 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 |
