GOPHER, an HPC framework for large scale graph exploration and inference

by Xavier Teruel form BSC

Abstract

Biological ontologies, such as the Human Phenotype Ontology (HPO) and the Gene Ontology (GO), are extensively used in biomedical research to investigate the complex relationship that exists between the phenome and the genome. The interpretation of the encoded information requires methods that efficiently interoperate between multiple ontologies providing molecular details of disease-related features. To this aim, we present GenOtype PHenotype ExplOrer (GOPHER), a framework to infer associations between HPO and GO terms harnessing machine learning and large-scale parallelism and scalability in High-Performance Computing. The method enables to map genotypic features to phenotypic features thus providing a valid tool for bridging functional and pathological annotations. GOPHER can improve the interpretation of molecular processes involved in pathological conditions, displaying a vast range of applications in biomedicine.

Slides

Paper pre-print

About the Speaker

Xavier Teruel received the Computer Engineering degree and the Master on Computer Architecture, Network and Systems at Technical University of Catalonia (UPC) in 2006 and 2008, respectively. Since 2006 Xavier is working as a researcher within the group of Parallel Programming Models in the Computer Science department at the Barcelona Supercomputing Center (BSC). He has participated in several research projects in the framework of the European Union as well as in the OpenMP Language Committee since version 3.0. He spent three years, from 2007 to 2009, collaborating with the IBM XL compiler team in the IBM Markham Laboratory in Toronto, Canada. From 2010 to 2012 he also worked as a part-time lecturer in the Computer Architecture Department at the UPC. His research interests include the areas of operating systems, programming languages, compilers, runtime systems and applications for high-performance computing and multiprocessor systems. He has published several papers in international workshops, conferences and journals in these topics.