The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
By Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, T. A. Holland, I. Keseler, Anamika Kothari, A. Kubo and 10 more. Nucleic Acids Res., 2013
609 citations recorded by the source corpus.
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.
Subfields: Biomedical Engineering, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/baf03356bf3403f0fc111e1b348a77a01ef48899
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Citations in the corpus
- Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “Name Content Website References KEGG Metabolic pathway resource http://kegg.jp Kanehisa et al., 2012 MetaCyc http://metacyc.org Caspi et al., 2012 HumanCyc http://humancyc.org Romero et al., 2005 SMPDB Small Molecule (e.g., drug) Pathway Database http://smpdb.ca Frolkis et al., 2010 HMDB Human…”
- The Transporter Classification Database (TCDB): recent advances (2015, background): “conserved domains KEGG (31) & BioCyc (32) These resources allow transport systems to be linked with metabolomics data EggNOG (33) Multiple alignments and phylogenetic trees containing a protein of interest can be viewed RefSeq (34) Information about a gene source is provided with comments and refere”
- Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community (2019, methodology): “Name to ID conversion Open [41] BiofOmics • Transcriptomics • Proteomics • Metabolomics Biofilm - Experiment library - Data depository Open [113] BioCyc/MetaCyc • Genomics • Proteomics • Metabolomics Unspecified - Online encyclopedia of metabolism - Predicted metabolic pathways in sequenced genomes ”
- Maize Metabolic Network Construction and Transcriptome Analysis (2013, methodology): “In addition, EC numbers were cross-checked with the latest ENZYME release from the Enzyme Nomenclature Database at ExPASy (Schneider et al., 2004), and if available, corresponding EC-formatted MetaCyc (Caspi et al., 2012) cross-references were added.”