ArticleNucleic acids research2021
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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101 citing papers in PubMed.
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- BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation.Bioinformatics (Oxford, England) · 2026Article
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
- Hypergraph learning with multi-dimensional metabolite feature extractions and static-dynamic attention mechanisms to fill missing reactions in metabolic networks.Briefings in bioinformatics · 2026Article
- MechFind: a computational framework for de novo prediction of enzyme mechanisms.Nature communications · 2026Article
- Predicting enzyme-compound associations for enzyme-catalysed reactions.Journal of cheminformatics · 2026Article
- Metabolite names and identifiers: how far are we from interoperability?Metabolomics : Official journal of the Metabolomic Society · 2026Article
- LumbriCyc: towards metabolic modelling of earthworms.NPJ systems biology and applications · 2026Article
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
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- KG-Microbe: Building modular and scalable knowledge graphs for microbiome and microbial sciences.GigaScience · 2026Article
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.mSystems · 2026Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).
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