MetaCyc (MetaCyc.org) is a highly curated, non-redundant reference database of small-molecule metabolism. It contains metabolic pathway and enzyme data that have been experimentally demonstrated in the scientific literature (1
) (). Because MetaCyc contains only experimentally determined pathways and enzymes, and due to its tight integration of data and references, MetaCyc is a uniquely valuable resource in fields including genome analysis, metabolism and metabolic engineering. The metabolic pathways and enzymes in MetaCyc are derived from organisms representing all domains of life ( and ). In the past, microbial and plant metabolism were emphasized, but current curation also focuses on vertebrate metabolism.
Figure 1. An example of a pathway showing omics data pop-ups. Pathways can be displayed at varying levels of detail, and this pathway’s display depicts an intermediate level of detail including enzymes, EC numbers and genes, but no chemical structures. (more ...)
List of species that have more than 15 experimentally elucidated pathways represented in MetaCyc
Table 2. Distribution of pathways in MetaCyc based on the taxonomic classification of associated species. Taxonomic groups (phyla for Bacteria and Archaea, kingdoms for Eukarya) are grouped by domain and are ordered within each domain based on the number of pathways (more ...)
In conjunction with its role as a general reference on metabolism, MetaCyc is used as a reference database for the PathoLogic component of the Pathway Tools software (2
) to computationally predict the metabolic network of any organism having a sequenced and annotated genome (3
). In this automated process, a predicted metabolic network is created in the form of a Pathway/Genome Database (PGDB). BioCyc (BioCyc.org) is a collection of more than 500 organism-specific PGDBs that were generated in this way both at SRI and by other groups. The editing capability of Pathway Tools enables computationally predicted PGDBs to be improved and updated by manual curation. Interested scientists may adopt and curate existing PGDBs through the BioCyc Web site (biocyc.org/intro.shtml#adoption), or create new PGDBs using MetaCyc and Pathway Tools (biocyc.org/download.shtml). More than 80 groups have used Pathway Tools and MetaCyc to create PGDBs for their organisms of interest, including important model organisms such as Saccharomyces cerevisiae
), Arabidopsis thaliana
), Oryza sativa
), Mus musculus
), Bos taurus
), Medicago truncatula
), Dictyostelium discoideum
), Leishmania major
), Chlamydomonas reinhardtii
), several Solanaceae
) and many pathogenic bacteria (14
) (see http://biocyc.org/otherpgdbs.shtml
for a more complete list).
A web server included in Pathway Tools enables the publishing of PGDBs through either the internet or an internal network. The Navigator component of Pathway Tools allows the browsing and analysis of PGDBs either locally or over the Internet. A detailed description of Pathway Tools can be found at http://bioinformatics.ai.sri.com/ptools/
and in (15
PGDBs generated by Pathway Tools and MetaCyc are an excellent platform for the integration of genome information with many other types of data regarding metabolism, regulation, and genetics. They provide powerful tools for analyzing omics datasets from experiments related to gene transcription, metabolomics, proteomics, ChIP-chip analysis, etc. (). The PGDBs accelerate research in many fields including biochemistry, molecular biology, biotechnology, bioinformatics, metabolic engineering and systems biology (16–19
). Both MetaCyc and organism-specific PGDBs can also be used as educational tools.
Figure 2. The omics viewers enable visualization of omics datasets on genome-scale diagrams. The background of this figure shows part of the cellular overview, with gene transcription data superimposed over the enzymatic reactions that are catalyzed by the enzymes (more ...)
During the past 2 years, we again significantly expanded the data content of MetaCyc and BioCyc. We also added supporting enhancements to the Pathway Tools software. The expanded and enhanced databases and software are described in the following sections.