title: Biomolecular pathway databases.
abstract: From the database point of view, biomolecular pathways are sets of proteins and other biomacromolecules that represent spatio-temporally organized cascades of interactions with the involvement of low-molecular compounds and are responsible for achieving specific phenotypic biological outcomes. A pathway is usually associated with certain subcellular compartments. In this chapter, we analyze the major public biomolecular pathway databases. Special attention is paid to database scope, completeness, issues of annotation reliability, and pathway classification. In addition, systems for information retrieval, tools for mapping user-defined gene sets onto the information in pathway databases, and their typical research applications are reviewed. Whereas today, pathway databases contain almost exclusively qualitative information, the desired trend is toward quantitative description of interactions and reactions in pathways, which will gradually enable predictive modeling and transform the pathway databases into analytical workbenches.
authors.affiliation: Bioinformatics Institute, Agency for science, Technology, and Research, Singapore.
authors.forename: Hong Sain
authors.initials: HS
authors.lastname: Ooi
authors.forename: Georg
authors.initials: G
authors.lastname: Schneider
authors.forename: Teng-Ting
authors.initials: TT
authors.lastname: Lim
authors.forename: Ying-Leong
authors.initials: YL
authors.lastname: Chan
authors.forename: Birgit
authors.initials: B
authors.lastname: Eisenhaber
authors.forename: Frank
authors.initials: F
authors.lastname: Eisenhaber
mesh_terms: D000818:Animals; D057225:Data Mining; D030541:Databases, Genetic; D030562:Databases, Protein; D006801:Humans; D033181:Information Dissemination; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D012984:Software; D049490:Systems Biology; D018511:Systems Integration; D009626:Terminology as Topic
chemical_list: D011506:Proteins