Information+Sources+for+models

Information+Sources+for+models - Information Sources for...

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Information Sources for models BCB 570 Julie Dickerson
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Topics Ontologies Data sources for building models of a pathway or system Project 1 Modeling tools
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Activity on Descriptions Describe what you see in the picture
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Ontology Ontology in philosophy (from the Greek ) is the study of the nature of being , existence or reality in general, as well as of the basic categories of being and their relations. Traditionally listed as a part of the major branch of philosophy known as metaphysics , ontology deals with questions concerning what entities exist or can be said to exist, and how such entities can be grouped, related within a hierarchy , and subdivided according to similarities and differences. http://en.wikipedia.org/wiki/Ontology
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Why develop an ontology? To share common understanding of the structure of information To enable reuse of domain knowledge To make domain assumptions explicit To separate domain knowledge from the operational knowledge To analyze domain knowledge http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html
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Ontology Examples Gene Ontology
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is a part of develops from other Directed Acyclic Graph (DAG)
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children
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Type of Ontology Information Source Strength of Evidence
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Strength of Evidence
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Uses Common language for defining gene function and commonalities/differences across organisms Quick links to evidence Often used with BLAST to find a putative gene function via orthology Used to find function of an unannotated gene and to validate experimental results
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Problems People ignore the evidence codes and believe what they read Many evidence codes are weak (electronically inferred) Not really useful for biologists until you get out to the leaves of the tree to specific function
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Other ontologies Plant ontology
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Defining Pathways and Models How do you then describe the mechanisms behind the functional definitions? Need common terms to define reactions, substrates, products, etc. SBML-Systems Biology Markup Language BIOPAX
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SBML From modeling community, for modeling Strong on representation of mathematical relationships Weak on describing the underlying biology
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SBML Concepts The Systems Biology Markup Language ( SBML ) is a computer- readable format for representing models of biochemical reaction networks in software. (sbml.org) SBML is a machine-readable format for representing models
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SBML Model Components Function definition A named mathematical function that may be used throughout the rest of a model. Unit definition A named definition of a new unit of measurement, or a redefinition of an existing SBML default unit. Compartment Type
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This note was uploaded on 03/08/2010 for the course BCB 570 taught by Professor Juliedickerson during the Spring '10 term at Iowa State.

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Information+Sources+for+models - Information Sources for...

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