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Building a C. elegans Cell and Anatomy Ontology

Building a C. elegans Cell and Anatomy Ontology. What is it good for? What knowledge is there? What are the practical issues? Progress and future plans. Raymond Lee. November 2002. A Nobel Prize for Worms!. Sydney Brenner. John E. Sulston. H. Robert Horvitz. Cells.

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Building a C. elegans Cell and Anatomy Ontology

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  1. Building a C. elegans Cell and Anatomy Ontology • What is it good for? • What knowledge is there? • What are the practical issues? • Progress and future plans. Raymond Lee November 2002

  2. A Nobel Prize for Worms! Sydney Brenner John E. Sulston H. Robert Horvitz

  3. Cells C. elegans Research Genes Behavior

  4. Goals • Organize cell and anatomy knowledge into an ontology so that the knowledge is more accessible and computer-friendly. • Use the ontology to annotate cell- and anatomy-based experimental results.

  5. Building a C. elegans Cell and Anatomy Ontology • What is it good for? • What knowledge is there? • What are the practical issues? • Progress and future plans. Raymond Lee November 2002

  6. Anatomy Pictures from WormAtlas.org

  7. Neural Anatomy Schematic of nerve bundles in the head Neural Circuit [White et al., 1986; WormAtlas.org]

  8. Cells and Nuclei [Leon Avery] [Albertson and Thomson, 1975] [Ron Ellis]

  9. Follow Cells With Green Fluorescent Proteins in a Live Animal [WormAtlas.org]

  10. AB.alaaaa l r r l l r AB.alaaaalal; AINL AB.alaaaalpp; ILshL AB.alaaaarlp; RMEL AB.alaaaarrp; RMER Development and Cell Lineage Time [Drawing from Nick Rhind]

  11. Building a C. elegans Cell and Anatomy Ontology • What is it good for? • What knowledge is there? • What are the practical issues? • Progress and future plans. Raymond Lee November 2002

  12. LINEAGE ORGAN AB.plpaappaa Amphid Sensilla TYPE POSITION Neuron Left Lateral Ganglion FUNCTION Sense Noxious Stimuli Adopt a Directed Acyclic Graph Structure ASHL

  13. MS.paapaaa Lineage P0 P1’ EMS MS MS.p P P P P P P P MS.pa MS.paa MS.paap MS.paapa MS.paapaa MS.paapaaa Organ pharynx terminal bulb M1 MS.paapaaa Cell Type neuron motor neuron M1 MS.paapaaa MS.paapaaa i i i i i terminal bulb corpus isthmus

  14. A Few Tricks • Treat cell lineage as a relationship of nuclei. • A nucleus is PART_OF a cell; Two or more nuclei are PART_OF a syncytium. • Sexual dimorphism is coded in relation types: DESC_HERM and DESC_MALE. • Indeterminacy is represented by indeterminate-state nodes.

  15. i i i i Z4.aaa(5L) D D AC nucleus Cell P Z1.ap Z4.aaa Z4.apa Z4.aap Z4.app anchor cell P Z1.ppp AC nucleus Lineage P Z1.paa Z1.ppa Z1.pap Z4.pa Z1.p Z1.pp 5R Z1.ppp H Z1.ppp(5R) D D AC nucleus Z4.a Z4.aa Z4.aaa H anchor cell Z1.ppx/Z4.aax Z1.ppx/Z4.aax (5L) D Z4.aaa(5L) D D AC nucleus Z1.ppx/Z4.aax (5R) D Z1.ppp(5R) 5L D D AC nucleus Z4.apa Z1.ap Z4.app Z4.aap Z4.aaa Z1.paa Z1.ppa Z1.pap Z4.pa Z1.ppp [Kimble and Hirsh, 1979]

  16. Progress and Plans • 5000+ nodes and relationships, expect 15,000 to call it ‘complete’. • Focus on cell group terms that are of immediate utility in WormBase (e.g. for gene expression annotation). • Collaborate with WormAtlas and GMODs to develop high-level terms for comparative anatomy. • Integration with life stage ontology. • Include information on other nematodes.

  17. Building a C. elegans Cell and Anatomy Ontology • What is it good for? • What knowledge is there? • What are the practical issues? • Progress and future plans. Raymond Lee November 2002

  18. Acknowledgements • WormBase ConsortiumDrs. Sylvia Martinelli, Paul Sternberg • GeneOntology Consortium • WormAtlas Group • The Worm Research Community

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