GOSAP: Gene Ontology-Based Semantic Alignment of Biological Pathways

A large number of biological pathways have been assembled in later years, and are being stored in databases. Hence, the need for methods to analyse these pathways has emerged. One class of methods compares pathways, in order to discover parts that are evolutionary conserved between species or to discover intra-species similarites. Most previous work has been focused on methods targeted at metabolic pathways utilising the EC enzyme hierarchy. Here, we propose a Gene Ontology (GO) based approach for finding semantic local alignments when comparing paths in biological pathways where the nodes are gene products. The method takes advantage of all three sub-ontologies, and uses a measure of semantic similarity to calculate a match score between gene products. Our proposed method is applicable to all types of biological pathways, where nodes are gene products, e.g. regulatory pathways, signalling pathways and metabolic enzyme-to-enzyme pathways. It would also be possible to extend the method ...

• Type: Journal
• Year: 2008
• Where: IJBRA
• Authors: Jonas Gamalielsson, Björn Olsson
• Keywords: Biological Pathways, Gene, IJBRA 2008, Metabolic Pathways