Cluster-based Graph Algorithms for Biological Ontologies

Lawrence Berkeley National Laboratory Computer Science/Mathematics, 2013-14

Liaison(s): Dr. Melissa Haendel, Dr. Chris Mungall, Dr. Nicole Washington ’99
Advisor(s): Andrew J. Bernoff
Students(s): Ki Wan Gkoo, Spencer Harris, Marina Johnson (PM), Ileane O’Leary, Kyle Roskamp

Researchers catalog large volumes of data into biological ontologies, graphs that denote relation- ships between biological descriptors, such as indicating that cystic fibrosis affects the lungs. The Monarch Initiative developed a program that utilizes ontologies to compare genetic diseases across species. This Clinic focuses on designing and implementing a faster algorithm via thresholding, a method of reducing the required calculations by only looking at data that meets a given level of significance, which naturally lends itself to parallel computation.