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An Ontology for Subcellular Localization

An Ontology for Subcellular Localization. Iwei Yeh and Russ Altman Stanford University. What is Subcellular Localization?. Organelles Membranes Compartments Micro-environments. Why is Subcellular Localization Important?. Function is dependent on context

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An Ontology for Subcellular Localization

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  1. An Ontology for Subcellular Localization Iwei Yeh and Russ Altman Stanford University

  2. What is Subcellular Localization? • Organelles • Membranes • Compartments • Micro-environments

  3. Why is Subcellular Localization Important? • Function is dependent on context • Localization is dynamic and changing • Compartmentalization forms groups which allows for abstraction of concepts (i.e. mitochondria)

  4. Specifying Subcellular Localization: Why is it difficult? • Biological Context • Hard to define boundaries • Dynamic Systems • Distributions of proteins

  5. Assigning Subcellular Localization • Direct assays: in situ hybridation • High-throughput methods • Prediction based on sequence: PSORT predicts proteins in mitochondria, nucleus, peroxisome, chloroplast, ER, vesicles • Bayesian Methods • Natural Language Processing

  6. Gene Ontology Cellular component contains organelles, membranes, cell regions, localized and unlocalized protein complexes

  7. Subcellular Localization Ontology • Cellular Components can be instantiated • Captures spatial relationships • Maps to GO concepts • Uses EcoCyc concepts: Macromolecule, Reaction, Pathway

  8. Membranes

  9. Spaces

  10. Compartments/Organelles

  11. Future Directions • Qualitative modifiers: near the plasma membrane • Temporal modeling: vesicle fusion, how do compartments communicate • Instantiations of compartments with data from various sources (i.e. GO annotations)

  12. Acknowledgements • Peter Karp • Hagai Ginsburg • Burroughs-Wellcome

  13. Thank you yeh@smi.stanford.edu GO in Protégé-2000 available at: http://smi.stanford.edu/projects/helix/gokbms/

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