The BioCyc database collection is an assortment of organism specific Pathway/ Genome Databases (PGDBs). They provide reference to genome and metabolic pathway information for thousands of organisms. As of December 2016, there are 9300 databases within BioCyc. The list of databases can be found here. SRI International, based in Menlo Park, California, maintains the BioCyc database family.
Categories of Databases within BioCyc:
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.
Software Tools within BioCyc:
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.
Pathway Tools Software:
The Pathway Tools is a comprehensive systems biology software package that underlies BioCyc and enables:
The Pathway Tools software has four main components:
- PathoLogic: Algorithm that takes Genbank entry as input and creates the new PGDB containing the predicted metabolic pathways of an organism.
- Pathway/Genome Navigator: Allows query, visualization, and analysis of PGDBs.
- MetaFlux: Supports development of metabolic flux models.
- Pathway/Genome Editors: Provides interactive editing capabilities for PGDBs.
BioCyc databases rely on Pathway Tools for their initial generation, subsequent updating, and for querying their content. The databases can also be installed locally in conjunction with Pathway Tools.
All BioCyc databases share the same database schema, which facilitates comparisons across the databases.
Use of BioCyc Database Collection 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 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.