The MetaCyc database of metabolic pathways and enzymes
By Ron Caspi, Richard Billington, Carol A. Fulcher, I. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E. Midford, Quang Ong, W. Ong and 3 more. 2017
846 citations recorded by the source corpus.
Abstract MetaCyc (https://MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains more than 2570 pathways derived from >54 000 publications, making it the largest curated collection of metabolic pathways. The data in MetaCyc is strictly evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. MetaCyc is also used as a knowledge base for generating thousands of organism-specific Pathway/Genome Databases (PGDBs), which are available in the BioCyc (https://BioCyc.org) and other PGDB collections. This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
Subfields: Molecular Biology
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In Molecular Biology
- Markus Krummenacker
- Peter D. Karp
- Ron Caspi
- Suzanne M. Paley
- Cholsoon Jang
- Li Chen
- I. Keseler
- Maria Sorokina
Citations in the corpus
- The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “GO imports subsets of these external ontologies that include information about anatomical structures, cell types, chemicals and taxonomic groupings: Uberon (14), Protein Ontology (15), Plant Ontology (16) (23) and MetaCyc (24).”
- The reactome pathway knowledgebase (2019, neutral): “org link next to an event of interest (3) opens an e-mail message (4) pre-populated with the event’s details with slots to accommodate personal details.”
- Review on natural products databases: where to find data in 2020 (2020, background): “The two major and most comprehensive databases for metabolites covering most of the domains of life are KEGG [48] and MetaCyc [49].”
- BRENDA in 2019: a European ELIXIR core data resource (2018, background): “protein sequences (UniProt, (13)), 3D structures (PDB, (14)), KEGG and MetaCyc pathways (15,16), genome annotations in the Genome Explorer (17) and links to PubMed (18) for the literature references.”
- Metabolomics and isotope tracing (2018, methodology): “To facilitate this process, we routinely ‘‘get to know’’ any unfamiliar metabolite that shows an interesting concentration or labeling change by examining its structure, checking its production and consumption routes using a pathway database like KEGG or MetaCyc (Kanehisa et al., 2016; Caspi et al.,”
- The MetaCyc database of metabolic pathways and enzymes - a 2019 update (2019, background): “Since the 2018 Nucleic Acids Research publication (2), we added 184 new base pathways (pathways composed of reactions only, where no portion of the pathway is designated as a subpathway) and 5 superpathways (pathways composed of at least one base pathway plus additional reactions or pathways), and u”