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Phenoscape Data Jamboree 2

Phenoscape Data Jamboree 2. Introduction and Goals: Paula Mabee Sept. 28, 2008. Phenoscape Data Roundup. Introduction and Goals: Paula Mabee Sept. 28, 2008. Ontologies. Data. Cowboys & cowgirls:. Jamboree goals:. Curate data Evaluate web interface prototypes

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Phenoscape Data Jamboree 2

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  1. PhenoscapeData Jamboree 2 Introduction and Goals: Paula Mabee Sept. 28, 2008

  2. PhenoscapeData Roundup Introduction and Goals: Paula Mabee Sept. 28, 2008

  3. Ontologies Data

  4. Cowboys & cowgirls:

  5. Jamboree goals: • Curate data • Evaluate web interface prototypes • Project personnel meeting

  6. Curation goals: • Work with taxon experts to annotate characters using ontologies • Feedback on curation workflow and interface • How to make more efficient? • How to make more consistent? • Priorities for next 3-6 months of curation in relation to: • Prioritized use cases • Number of available character X taxon matrices • Original taxonomic scope

  7. Phenoscape.org • History: Communication between zebrafish model organism community and Cypriniformes Tree of Life group through NESCent workshops (2005-2006) • NSF-DBI to Mabee, Vision, and Westerfield (June 1, 2007) • Goal: Create curated, ontology-based evolutionary phenotype database that maps to genetic databases • Generalizablesystem: Prototype with ostariophysan fishes

  8. Shared ontologies & syntaxconnects models to humansa Model organism Human Ontology Mutant Gene Mutant Gene Mutant or Missing Protein Mutant or Missing Protein Ontology Mutant Phenotype (disease) Mutant Phenotype

  9. Ontology Shared ontologies & syntaxconnects models to other speciesa Zebrafish Multiple fish species Mutant Gene Candidate genes Mutant or Missing Protein ? Natural Phenotypes Mutant Phenotype

  10. Zebrafish: Mutagenesis produces phenotypes Mutagenesis Phenotype 1 Phenotype 3 no tail mutant Halpern et al. (1993) Cell Halpern et al. (1993) Cell

  11. Phenotypes mapped to genes • sox9ahi1134 • sox9ahi1134 • edn1 • sox9ahi1134; lockjaw • val • edn1 • she, stu, edn1-MO • Maxilla: size reduction • Dentary: size reduction • Retroarticular: loss • Opercle: size reduction; loss • Ceratohyal: shape change • Branchiostegals: number decrease • Branchiostegals: shape change

  12. Evolutionary phenotypes Mutation, Gene Flow, Selection, Drift Species A Morphology Species B Morphology Species C Morphology

  13. Evolutionary phenotypesGenetic bases of morphology unknown Mutation, Gene Flow, Selection, Drift ? Species A Morphology Species B Morphology Species C Morphology

  14. Needs analysis use cases: • Phenoscape designed to meet top-priority questions/needs of the community concerning development and evolution of morphology, e.g. • Find genes underlying morphological characters (Which ones? How many?) • Discover patterns of correlation across genes and morphology • Formulate models of morphological evolution; data mining and discovery • Phenotypic BLAST to discover similar phenotypes and taxa

  15. Prototype with Ostariophysan fishes (zebrafish) Ostariophysi & outgroups Mayden et al. 2008 (unpublished)

  16. Phenoscape priorities (yr. 1) • Develop ontologies for evolutionary work • Develop curation tools (Phenote -> Phenex) • Refine syntax for evolutionary characters • Curate phenotypes (characters)

  17. Phenoscape ontologies New: Cloned: Taxonomic Rank Ontology (8->31 terms) Teleost Taxonomy Ontology (36,060 terms; 38,000 synonyms) Teleost Anatomy Ontology (2233 terms; 387 skeletal) Zebrafish Anatomy Ontology (2196 terms; 310 skeletal) Existing: Phenotype and Trait Ontology (1,075 terms) Evidence Code Ontology Spatial Ontology (106 terms) 19 June 2008

  18. Entity Quality Caudal fin Reduced (size) AO Anatomy Ontology: Quality Ontology: PATO no tail mutant Entity-Quality (EQ) syntax

  19. AO PATO Systematic characters can also be described usingEntity-Quality (EQ) syntax Character State Character Entity Attribute Value Caudal fin size reduced Entity Quality

  20. Curate evolutionary phenotypes from free-text • This is not a computable format • These data cannot be easily compared across taxa • These data cannot be linked to developmental genetics • These data cannot be reasoned across

  21. Curation needs: • Data entry tool: Phenex • List of ranked papers: 76 “A” papers • Manual data entry (non-expert): • Pdf (1/2 scanned) • Taxon list (manual entry) • Character matrix (manual entry) • Free text character description (manual entry)

  22. Curation needs: 4. E/Q ontology recoding of characters and states • This workshop

  23. Curation of ichthyological data: proposed Original NSF grant estimate (2006)

  24. Jamboree goal: ~1,530,165 EQ annotations

  25. Acknowledgements • NSF for Phenoscape funding (Mabee, Vision, Westerfield) NSF-DBI0641025 • National Evolutionary Synthesis Center NSF EF-0423641 • NIH HG002659 (to Monte Westerfield) • Phenoscape project: Hilmar Lapp, Wasila Dahdul, Peter Midford, Jim Balhoff, • ZFIN: Monte Westerfield, Melissa Haendel • Cypriniformes Tree of Life (NSF 0431290), colleagues and students (Mayden, Miya, Saitoh, He, Coburn, Arratia, Simon, Conway, Grey, Engeman, Bogutskya, Hilton, Aspinwall); Deep Fin RCN • Suzanna Lewis, Chris Mungall (Lawrence Berkeley National labs) • National Center for Biomedical Ontology

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