Plant and Animal Genome XXI Conference

January 11 - 16, 2013

PIR Workshop: Knowledge Mining Tools for Proteins, Complexes and PTMs

In the post-genome era, researchers are systematically tackling gene functions and complex regulatory processes by studying organisms on a global scale; however, a major challenge lies in the voluminous, complex, and dynamic data being maintained in heterogeneous sources including databases, ontologies and literature. As technology increasingly provides with better means to identify and characterize protein post-translational modifications and macromolecular complexes, formal representation of these is key to allow intelligent queries. Therefore, advanced computational methods, coupled with the use of ontologies and literature mining tools are needed for integration, mining, comparative analysis, representation, and functional interpretation of data. The workshop will focus on resources that either provide or utilize information about PTMs and complexes in the biological context: i)MaizeGDB will present strategies for pathway curation and data sharing; ii) P3DB, database providing a resource of protein phosphorylation data from multiple plants; iii) RLIMS-P and eFIP, text mining tools for phosphorylated proteins; iv) protein ontology, an ontology for the formal representation and annotation of protein forms and protein complexes; and v) iPTMnet, a framework for integrating text mining, data mining, data analysis and visualization tools, and ontologies to explore and discover PTM networks in system biology context.