Biomolecular pathway databases.
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.
Ooi
Hong Sain
HS
Bioinformatics Institute, Agency for science, Technology, and Research, Singapore.
Schneider
Georg
G
Lim
Teng-Ting
TT
Chan
Ying-Leong
YL
Eisenhaber
Birgit
B
Eisenhaber
Frank
F
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
D011506:Proteins