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Tutorial: Bridging data and modeling communities: ontologies of cellular networks, pathway databases, and pathway data retrieval tools
From Q-bio
Oliver Ruebenacker (University of Connecticut Health Center) Slides available on http://vcell.org/biopax
- Abstract
- Computational biology has two communities each with a large pool of data and with their own established exchange formats: The modeling community with simulation-oriented formats like Systems Biology Markup Language (SBML, http://sbml.org ), and the community of pathway database users and developers that use ontologies like Biological Pathways eXhange Standard (BioPAX, http://biopax.org ). The goal of this tutorial is to raise awareness among members of both communities about data sources and tools that aim to support both standards. In particulars, the aims of the tutorial are:
- To describe tools specifically designed to manipulate data from multiple pathway databases, or accept data in BioPAX format. The review will include Cytoscape (http://cytoscape.org) and its plug-ins designed to deal with BioPAX data, Patica (http://www.patika.org) and Paxtools (http://www.biopax.org/paxtools), Sybil (http://www.ccam.uchc/mblinov/biopax), BioUML (http://www.biouml.org), and others.
- To discuss difficulties that exists in one-to-one mapping between data and modeling exchange standards (BioPAX as a representataive of ontology, and SBML as a representative of markup languages), and current approaches to overcome this problem.
- We propose to organize this tutorial to be able to provide participants with hands-on experience with retrieving pathway data from databases, visualizing it, and using for modeling. An introduction to the definition and methods of ontology will be followed by an overview of major ontologies used by biological communities, such as Gene Ontology (GO, http://www.geneontology.org), BioPAX ontology (http://www.biopax.org), Systems Biology Ontology (SBO, http://www.ebi.ac.uk/sbo ), and others. Several pathway databases that can serve as the source of data for modelers will reviewed, such as Reactome (http://reactome.org ), Pathway Interaction Database (http://pid.nci.nih.gov/), PANTHER - Protein ANalysis THrough Evolutionary Relationships (http://www.pantherdb.org/), The Cancer Cell Map (http://cancer.cellmap.org/cellmap/), KEGG - Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg), INOH - Integrating Network Objects with Hierarchies (http://www.inoh.org/), the collection of BioCyc databases (http://biocyc.org), and others. We will then specifically cover the ways to retrieve and visualize data, and convert between different data formats.
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