An Ontology for Subcellular Localization

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An Ontology for Subcellular Localization

• Iwei Yeh and Russ Altman
• Stanford University

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What is Subcellular Localization?

• Organelles
• Membranes
• Compartments
• Micro-environments

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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)

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Specifying Subcellular Localization Why is it
difficult?

• Biological Context
• Hard to define boundaries
• Dynamic Systems
• Distributions of proteins

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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

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Gene Ontology

• Cellular component contains organelles,
  membranes, cell regions, localized and
  unlocalized protein complexes

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Subcellular Localization Ontology

• Cellular Components can be instantiated
• Captures spatial relationships
• Maps to GO concepts
• Uses EcoCyc concepts Macromolecule, Reaction,
  Pathway

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Membranes
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Spaces
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Compartments/Organelles
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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)

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Acknowledgements

• Peter Karp
• Hagai Ginsburg
• Burroughs-Wellcome

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Thank you

• yeh_at_smi.stanford.edu

GO in Protégé-2000 available at http//smi.stanf
ord.edu/projects/helix/gokbms/