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Phenotype Annotation Tool and Ontologies at dictyBase

Phenotype Annotation Tool and Ontologies at dictyBase. Phenotype/PATO 2003. Phenotype Ontology. 420 Phenotype Terms 1780 Phenotype Annotations 470 Genes with Phenotype Annotation(s). Phenotypes. Strains. Phenotypes. Strains. Phenotypes. Strains.

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Phenotype Annotation Tool and Ontologies at dictyBase

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  1. Phenotype Annotation Tool and Ontologies at dictyBase

  2. Phenotype/PATO 2003

  3. Phenotype Ontology • 420 Phenotype Terms • 1780 Phenotype Annotations • 470 Genes with Phenotype Annotation(s)

  4. Phenotypes Strains Phenotypes Strains Phenotypes Strains Previous Phenotype Representation in dictyBase Gene

  5. New Phenotype Representation in dictyBase Gene Gene Gene Strain Phenotype Phenotype Phenotype

  6. Strain and Phenotype Displayon the Gene Page

  7. Phenotype and Strain Details Page

  8. Development of a NewPhenotype Annotation Tool • Developed in collaboration with NCBO • Similar in functionality to Phenote • Web-based tool that can be accessed from any computer

  9. Features of the NewPhenotype Annotation Tool • Runs on top of the Chado database schema • Uses terms from ontologies in .obo format for phenotype annotation • Auto-completes ontology terms similar to Google Suggest • Built using Web 2.0 technologies such as AJAX

  10. Phenotype Annotation Tool

  11. Phenotype Annotation Tool Enter Strain Name

  12. Phenotype Annotation Tool Retrieve Existing Phenotype Annotations

  13. Phenotype Annotation Tool

  14. Phenotype Annotation Tool Enter Phenotype Term Navigate Parent and Child Terms. Click to Populate Phenotype Field

  15. Phenotype Annotation Tool Retrieve Reference by ID or Author Name

  16. Phenotype Annotation Tool

  17. Phenotype Annotation Tool Add Annotation To List

  18. Phenotype Annotation Tool Commit Annotations To Database

  19. Phenotype Annotation Tool

  20. Resulting Phenotype Displayon the Gene Page

  21. Phenotype Annotation Tool Edit Existing Phenotype Annotation

  22. Phenotype Annotation Tool

  23. Phenotype Annotation Tool

  24. Additional Ontologies Assay Environment

  25. Future Directions • Dissection of Dicty phenotype ontology terms to fit PATO Entity-Quality model • Collaboration with other groups on PATO and phenotype-related ontologies (e.g., genetic context, environmental conditions) • Provide phenotype annotation tool to GMOD as open-source software

  26. Principal Investigators Rex Chisholm Warren Kibbe Software Developers Eric Just Sohel Merchant Curators Petra Fey Pascale Gaudet Karen Pilcher Funding NIH GO Consortium Acknowledgements

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