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Integrating Neuronal Information in WormBase

~ Raymond Lee ~. Integrating Neuronal Information in WormBase. Database of Caenorhabditis elegans and related nematodes. Why Caenorhabditis elegans. Small free-living round worm, easy to breed and study in the lab. Simple nervous system, 302 or 381 neurons.

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Integrating Neuronal Information in WormBase

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  1. ~ Raymond Lee ~ Integrating Neuronal Information in WormBase

  2. Database of Caenorhabditis elegans and related nematodes

  3. WhyCaenorhabditis elegans • Small free-living round worm, easy to breed and study in the lab. • Simple nervous system, 302 or 381 neurons. • Fully sequenced 100Mb genome, 30% genes have human orthologs. (http://inparanoid.cgb.ki.se/)

  4. Challenges We Face information KNOWLEDGE information information information

  5. Goals To Achieve • Comprehensive • Integrated • Accessible • Standardized

  6. Cells C. elegans Literature Physiology Genes

  7. Comprehensive Information • Gene expression. • Neuronal anatomy (schematics, also see WormAtlas). • Neuronal connection (incomplete). • Neuronal cell function (starting).

  8. Integrated Data • Low-level integration: data type connections specified in models of an object-oriented database. • High-level integration: collated WWW views of major aspects, such as Gene, Sequence, Cell and Function.

  9. Cell and Anatomy View

  10. Cell Report

  11. Standardization • Allows inter-operability • Allows better knowledge transfer.

  12. Standardization in WormBase • Shared software tools, familiar interface: GMOD • Shared vocabulary: Gene Ontology, Sequence Ontology, Anatomy Ontology(WB-specific so far).

  13. Why Ontology? • Controlled vocabulary and Semantics • A hierarchical classification scheme that helps data acquisition and searching

  14. Anatomy Ontology: Goals • Organize cell and anatomy knowledge such that the knowledge is more accessible and computer-friendly. • Use it to annotate cell- and anatomy-based experimental results.

  15. ASEL in Anatomy Ontology

  16. Query Utilizing Ontology • What genes are expressed in the left but not in the right amphid neurons? • What genes are found in amphid but not other neurons?

  17. Easy Access • Web-based, user-friendly interface. • Multiple query tools. • Downloadable data sets. • Package for local installation. • Open-source, open-access software.

  18. Literature Search Tool: Textpresso • Full text search. • Category search.

  19. Categories Locus let-7 lsy-6 LIN-41 PATHWAY precursor upstream cascade descendants GENE Neuron EMS HSN AB ASE REGULATION CELL repress enhanced up-regulate inhibition

  20. Q: What genes are expressed in the ASEL neuron? • Keyword search – there is no good query • Category search is better: “gene” + “ASEL”

  21. Q: What genes are expressed in the ASEL neuron? • Keyword search – there is no good query • Category search is better: “gene” + “ASEL” + “express*” Even Better!

  22. www.wormbase.org • Comprehensive • Integrated • Accessible • Standardized

  23. WormBasers Jack Chen Todd Harris Lincoln Stein Payan CanaranIgor Antoshechkin Carol Bastiani Juancarlos Chan Wen Chen Eimear Kenny Ranjana Kishore Raymond Lee Hans-Michael Muller Cecilia Nakamura Andrei Petcherski Erich Schwarz   Paul Sternberg Kimberly Van Auken Daniel Wang Tamberlyn Bieri Darin Blasiar John Spieth Keith Bradnam Chao-Kung Chen  Paul Davis Richard Durbin  Dan Lawson Phil Ozersky   Anthony Rogers Jonathan  Hodgkin (CGC) Theresa Stiernagle (CGC) Funded by US-NIH and British MRC

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