ICSB 2010 Tutorial

= ICSB - BioPAX Tutorial =

Representing pathway data in BioPAX Level 3. The BioPAX ontology (www.biopax.org) is a standard language for formally representing biological pathways. BioPAX enables the exchange and integration of pathway data. This has been a community effort spanning 7 years, culminating in the recent release of BioPAX level 3. With this release, BioPAX now fully supports the representation of metabolic pathways, signal transduction pathways, protein-protein interaction networks, gene regulatory networks and genetic interactions. This tutorial aims to provide a complete overview of BioPAX in order to aid new users and developers into the BioPAX community. The tutorial will give an in-depth review of data representation in BioPAX and is aimed at biologist interested in pathway analysis, computation biologists interested in pathway representation and pathway data providers.

Outline:

 * Introduction to Pathway Data and Data Integration in life sciences
 * Purpose of Data Exchange standards
 * Introduction to OWL
 * BioPAX class/property structure
 * Representing data in BioPAX
 * Metabolic pathways
 * Signaling pathways
 * Protein-protein, molecular interactions
 * Gene regulatory pathways
 * Genetic interactions
 * Annotation Classes in BioPAX
 * Representing States and Reference Molecules
 * Use of Xrefs and Controlled Vocabularies
 * Data Mapping forum/ Bring your own data

Duration: 4 hour, with one break.

Requirements: We recommend, though it is not essential, for participants to bring their own laptop, help will be available at the tutorial to install required software. There will be an opportunity to ask specific mapping questions, please bring any data and parsers that you may be working on.

We have limited funds to reimburse the tutorial costs for some students and post-docs. Please apply with a short cover letter stating your research objectives and interest in BioPAX to anwar@cbio.mskcc.org.

Tutorial Registration