The BioCyc

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases s ...

collection is an assortment of organism specific Pathway/Genome Databases (PGDBs) that provide reference to

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...

and metabolic pathway information for thousands of organisms. As of June 2021, there were over 17,800 databases within BioCyc.

SRI International SRI International (SRI) is an American nonprofit scientific research institute and organization headquartered in Menlo Park, California. The trustees of Stanford University established SRI in 1946 as a center of innovation to support economic ...

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based in Menlo Park, California, maintains the BioCyc database family.

Categories of Databases

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 The MetaCyc database 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 ...

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.

Software tools

The BioCyc website contains 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.

Use in Research

Since BioCyc Database family comprises a long list of organism specific databases and also data at different systems level in 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 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.

References

{{reflist Genome databases Biotechnology Metabolism SRI International