The BioCyc database collection is an assortment of organism specific Pathway/Genome Databases (PGDBs) that provide reference to genome and metabolic pathway information for thousands of organisms. As of July 2023, there were over 20,040 databases within BioCyc. SRI International , based in Menlo Park, California, maintains the BioCyc database family.
7-1255: 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. The other important Tier 1 database is HumanCyc which contains around 300 metabolic pathways found in humans. The remaining five databases include, EcoCyc ( E. coli ), AraCyc ( Arabidopsis thaliana ), YeastCyc ( Saccharomyces cerevisiae ), LeishCyc ( Leishmania major Friedlin ) and TrypanoCyc ( Trypanosoma brucei ). Tier 2: Databases that were computationally predicted but have received moderate manual curation (most with 1–4 months curation). Tier 2 Databases are available for manual curation by scientists who are interested in any particular organism. Tier 2 databases currently contain 43 different organism databases. Tier 3: Databases that were computationally predicted by PathoLogic and received no manual curation. As with Tier 2, Tier 3 databases are also available for curation for interested scientists. The ontological resource contains
14-426: A living system, the usage in research has been in a wide variety of context. Here, two studies are highlighted which show two different varieties of uses, one on a genome scale and other on identifying specific SNPs ( Single Nucleotide Polymorphisms ) within a genome. AlgaGEM AlgaGEM is a genome scale metabolic network model for a compartmentalized algae cell developed by Gomes de Oliveira Dal’Molin et al. based on
21-461: A variety of software tools for searching, visualizing, comparing, and analyzing genome and pathway information. It includes a genome browser, and browsers for metabolic and regulatory networks . The website also includes tools for painting large-scale ("omics") datasets onto metabolic and regulatory networks, and onto the genome. Since BioCyc Database family comprises a long list of organism specific databases and also data at different systems level in
28-476: A visual display that includes the structures of all components. The reactions are balanced and include EC numbers , reaction direction, predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds, and computed Gibbs free energy . All objects in MetaCyc are clickable and provide easy access to related objects. For example, the page for L-lysine lists all of
35-988: Is often used as an extensive online encyclopedia of metabolism. In addition, MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced genomes; it has been used to perform pathway predictions for thousands of organisms, including those in the BioCyc Database Collection . MetaCyc is also used in metabolic engineering and metabolomics research. MetaCyc includes mini reviews for pathways and enzymes that provide background information as well as relevant literature references. It also provides extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, and, when available, kinetic constants. MetaCyc data on metabolites includes chemical structures, predicted Standard energy of formation, and links to external databases. Reactions in MetaCyc are presented in
42-424: Is one of the largest metabolic pathways and enzymes databases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information about chemical compounds, reactions, metabolic pathways and enzymes. The data have been curated from more than 58,000 publications. MetaCyc has been designed for multiple types of uses. It
49-676: The Chlamydomonas reinhardtii genome. It has 866 unique ORFs, 1862 metabolites, 2499 gene-enzyme-reaction-association entries, and 1725 unique reactions. One of the Pathway databases used for reconstruction is MetaCyc. SNPs The study by Shimul Chowdhury et al. showed association differed between maternal SNPs and metabolites involved in homocysteine, folate, and transsulfuration pathways in cases with Congenital Heart Defects (CHDs) as opposed to controls. The study used HumanCyc to select candidate genes and SNPs. MetaCyc The MetaCyc database
#149850