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WormBase -- one Web site, many roles

WormBase -- one Web site, many roles. Caenorhabditis elegans. Diverse data (from 3,739 papers). Prior to July, 2006:. 127 phenotype objects in WormBase. three-tiered organization (specialization_of or generalization_of) redundancy existed between terms

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WormBase -- one Web site, many roles

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  1. WormBase -- one Web site, many roles PATO, December 2006

  2. Caenorhabditis elegans PATO, December 2006

  3. Diverse data (from 3,739 papers) PATO, December 2006

  4. Prior to July, 2006: • 127 phenotype objects in WormBase. • three-tiered organization (specialization_of or generalization_of) • redundancy existed between terms • no phenotype term definitions, references • many RNAi experiments annotated to ‘Unclassified’ phenotype term • ‘Not’ phenotype associations were not captured • Phenotype vocabulary was not used for annotation of alleles and transgene objects PATO, December 2006

  5. A controlled and structured vocabulary for phenotypes: • allows complex data queries, and expedites analysis of genes that act in the same processes or pathways. • helps to integrate a massive array of data from many different sources into a common body of knowledge. • provides the option of linking phenotype data with other data in WormBase or with data from other databases. • facilitates communication within and outside of the C. elegans community PATO, December 2006

  6. Expansion of the phenotype ontology, source for term names: • text descriptions in WormBase • free text phenotype descriptions associated with alleles • text associated with RNAi objects annotated to ‘Unclassified’ phenotype • prior phenotype terms in WormBase • GO ontology • WormBase anatomy ontology • Life stage ontology Term names and synonyms reflect the language of researchers. PATO, December 2006

  7. The WormBase phenotype ontology is a pre-coordinated ontology: 1348 terms, ~20% of terms are defined PATO, December 2006

  8. Current term usage: 40% used for annotation 60% not associated with an annotation PATO, December 2006

  9. RNAi-phenotype data: • 272,759 total RNAi-phenotype connections • 63,439 RNAi experiments • 19,692 genes associated with phenotypes via RNAi experiments: • 19,185 genes connected via “Not” associations • 4,577 genes connected directly PATO, December 2006

  10. Allele-phenotype data: • Most phenotype connections are to knockout alleles (NBP). • Ongoing: • Continuing to collect phenotype data from the community. • Starting to annotate early papers describing large collections of mutants -> many high-level phenotype annotations. • Starting to annotate new papers. Currently, 4,401 total allele-phenotype connections to 2585 alleles, defining 1296 genes. PATO, December 2006

  11. Lots of RNAi data -> dense early_embryonic_lethal node: PATO, December 2006

  12. Vague collections of phenotypes present challenges for ontology/annotation: pleiotropic_defects_severe_early_emb: “Often multiple pronuclei, aberrant cytoplasmic texture, drop in overall pace of development, osmotic sensitivity.” complex_phenotype_early_emb “Complex combination of defects that does not match other class definitions.” PATO, December 2006

  13. Looking ahead to an entity-quality compatible schema: • Within OBO-Edit we store relevant GO term names within primary names or synonym names (GO ID stored in relevant dbxref field) • Phenotype ontology is developed using existing anatomy and life stage term names PATO, December 2006

  14. Phenotype data integration: • Phenotype annotations are associated with molecular information for alleles, transgenes, and RNAi objects that permit mapping these objects to the genome. • High-level phenotype annotations associated with RNAi objects are automatically converted to GO terms (RNAi2GO) and associated with gene objects. • Phenotype annotations describing gene regulation (‘transgene_expression_abnormal’) linked with detailed gene regulation information. • Phenotypes linked to life stage and anatomy term PATO, December 2006

  15. RNAi summary on gene page: PATO, December 2006

  16. Sample detailed RNAi report: PATO, December 2006

  17. Sample allele report: PATO, December 2006

  18. Immediate future plans: • Ontology: • Define terms, further refine ontology (expansion will be dictated by community feedback and curation needs) • Solicit more expert community feed-back • Web site: • Enhance phenotype search tools PATO, December 2006

  19. Ontology browser to be integrated into WormBase: http://elbrus.caltech.edu/cgi-bin/igor/ontology/ontology.cgi PATO, December 2006

  20. WormBase = ~30 people, 4 centers Cold Spring Harbor Laboratory Payan Canaran Jack Chen Tristan Fiedler Todd Harris Sheldon McKay Will Spooner Lincoln Stein Washington University at St. Louis Tamberlyn Bieri Darin Blasiar Phil Ozersky John Spieth • California Institute of Technology • Igor Antoshechkin • Carol Bastiani • Juancarlos Chan • Wen Chen • Ranjana Kishore • Raymond Lee • Hans-Michael Müller • Cecilia Nakamura • Andrei Petcherski • Gary Schindelman • Erich Schwarz • Paul Sternberg • Kimberly Van Auken • Daniel Wang • Xiaodong Wang Wellcome Trust Sanger Institute Paul Davis Richard Durbin Michael Han Anthony Rogers Mary Ann Tuli Gary Williams PATO, December 2006

  21. Other acknowledgements: • NIH/NHGRI • C. elegans research community PATO, December 2006

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