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Reactome is a free online database of biological pathways. [ 1 ] [ 2 ] [ 3 ] It is manually curated and authored by PhD-level biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases.
KEGG PATHWAY Database (Univ. of Kyoto) MANET database (University of Illinois) Reactome: navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory)
All pathways have an open license and can be freely used. Reactome is a free and manually curated online database of biological pathways. NCI-Nature Pathway Interaction Database is a free biomedical database of human cellular signaling pathways (new official name: NCI Nature Pathway Interaction Database: Pathway, synonym: PID).
Using the web-interface of the database, one can perform overrepresentation analysis, based on biochemical pathways or on neighbourhood-based entity sets (NESTs) that constitute sub-networks of the overall interaction network containing all physical entities around a central one within a "radius" (number of interactions from the center).
Based on the manual curation done, BioCyc database family is divided into 3 tiers: Tier 1: Databases which have received at least one year of literature based manual curation. Currently there are seven databases in Tier 1. Out of the seven, MetaCyc is a major database that contains almost 2500 metabolic pathways from many organisms.
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