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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.
The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. The 2018 issue has a list of about 180 such databases and updates to previously described databases. [2] Omics Discovery Index can be used to browse and search several biological databases.
Free abstract & references, Open Access titles, and Subscription Available from BioOne [27] Bioinformatic Harvester: Biology, bioinformatics: A meta search engine for 50 major bioinformatic databases and projects. Free Available from Liebel-Lab KIT Karlsruhe Institute of Technology Book Review Index Online: Book reviews: Subscription Thomson ...
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).
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.
According to the Online Dictionary for Library and Information Science, a pathfinder is "designed to lead the user through the process of researching a specific topic, or any topic in a given field or discipline, usually in a systematic, step-by-step way, making use of the best finding tools the library has to offer.
The Pathway Interaction Database (PID) is a free biomedical database of human cellular signaling pathways. [1] The database contains information about the molecular interactions and reactions that take place in cells, with a particular focus on processes that might be relevant to cancer research and treatment.
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).