title: Pathway databases: making chemical and biological sense of the genomic data flood.
abstract: Pathway databases are a means to systematically associate proteins with their functions and link them into networks that describe the reaction space of an organism. Here, the Reactome Knowledgebase provides a convenient example to illustrate strategies used to assemble such a reaction space based on manually curated experimental data, approaches to semiautomated extension of these manual annotations to infer annotations for a large fraction of a species' proteins, and the use of networks of functional annotations to infer pathway relationships among variant proteins that have been associated with disease risk through genome-wide surveys and resequencing studies of tumors.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, MSB 390, New York, NY 10016, USA. deustp01@med.nyu.edu
authors.forename: Peter
authors.initials: P
authors.lastname: D'Eustachio
mesh_terms: D000818:Animals; D030562:Databases, Protein; D023281:Genomics / Q000379:methods*; D006801:Humans; D051188:Knowledge Bases; D053858:Metabolic Networks and Pathways; D009154:Mutation; D060066:Protein Interaction Maps; D020543:Proteome / Q000235:genetics / Q000378:metabolism*
chemical_list: D020543:Proteome