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NCI-Nature Pathway Interaction Database; Netpath: curated resource of signal transduction pathways in humans; 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 ...
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
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.
Pathways can also turn genes on and off, or spur a cell to move. [1] Some of the most common biological pathways are involved in metabolism, the regulation of gene expression and the transmission of signals. Pathways play a key role in advanced studies of genomics. Most common types of biological pathways: [1] Metabolic pathway; Genetic pathway
WikiPathways is originally built using MediaWiki software, [4] a custom graphical pathway editing tool (PathVisio [5]) and integrated BridgeDb [6] databases covering major gene, protein, and metabolite systems. WikiPathways was founded in 2008 by Thomas Kelder, Alex Pico, Martijn Van Iersel, Kristina Hanspers, Bruce Conklin and Chris Evelo.
Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use.
The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database.
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.