Genomic annotation, enrichment and prediction of concepts in diverse biomedical ontologies



For the past several years, we have been developing tools to aid researchers in the interpretation of genomic and proteomic high throughput experimental datasets. To this end, we have, in collaboration with the NCBO, developed tools for the annotation of curated text describing genes and proteins.  Using these annotations we have developed web-based and Cytoscape tools for visualization, enrichment analysis, and prediction of concepts from a diverse library of biomedical ontologies. Simultaneously, we served as the assessing group for the first Critical Assessment of Function Annotation (CAFA) that evaluated how well researchers predict future Gene Ontology terms that are experimentally validated.  In this talk, I will give an overview of the status of CAFA and I will describe possible paths toward utilizing other ontologies such as concepts from human diseases.  I will also describe our tools and some of the successes that have come from their use.



Dr. Sean Mooney is a group leader in the fields of computational biology and bioinformatics, and manages an active NIH funded laboratory. He received his PhD from UCSF in 2001 under Prof. Teri Klein and did an American Cancer Society Fellowship under Prof. Russ Altman at Stanford. In addition to collaborative activities in bioinformatics, his primary research interests focus on building and applying computational models to understand how genes and genetic variation alters phenotype or causes disease at the protein level.   He also has an interest in developing new tools for understanding high thoughput experimental datasets. He is currently an Associate Professor and Director of Bioinformatics at the Buck Institute for Research on Aging in Novato California.