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

• Localization is dynamic and changing

• Compartmentalization forms groups which allows for abstraction of concepts (i.e. mitochondria)

Specifying Subcellular Localization: Why is it difficult?

• Biological Context

• Hard to define boundaries

• Dynamic Systems

• Distributions of proteins

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

Gene OntologyCellular 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

Membranes

Spaces

Compartments/Organelles

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)

Acknowledgements

• Peter Karp

• Hagai Ginsburg

• Burroughs-Wellcome

Thank you

yeh@smi.stanford.edu

GO in Protégé-2000 available at:

http://smi.stanford.edu/projects/helix/gokbms/