ReviewBriefings in bioinformatics2014
Reconciliation of metabolites and biochemical reactions for metabolic networks.
Review in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed.
- Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.mSystems · 2026Article
- MetaNetX: a bridge between metabolic resources for enhanced curation and multi-omics data harmonization.Nucleic acids research · 2026Article
- Validated antimalarial drug target discovery using genome-scale metabolic modeling.Antimicrobial agents and chemotherapy · 2025Article
- Article
- An overview of graph databases and their applications in the biomedical domain.Database : the journal of biological databases and curation · 2021Article
- gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.Genome biology · 2021Article
- MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.Nucleic acids research · 2021Article
- Article
- Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling.Metabolites · 2019Article
- Genome-Scale Metabolic Reconstruction ofFrontiers in microbiology · 2019Article
- Combining multiple functional annotation tools increases coverage of metabolic annotation.BMC genomics · 2018Article
- Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.Nature communications · 2018Article
- Metabolomics in Plant Priming Research: The Way Forward?International journal of molecular sciences · 2018Review
- A Genome-Scale Metabolic Model forFrontiers in microbiology · 2018Article
- A review of computational tools for design and reconstruction of metabolic pathways.Synthetic and systems biotechnology · 2017Review
- Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- A review of parameters and heuristics for guiding metabolic pathfinding.Journal of cheminformatics · 2017Review
- Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production.BMC systems biology · 2017Article
- ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network.Plant physiology · 2017Article
- Updates in Rhea - an expert curated resource of biochemical reactions.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-scale metabolic network reconstructions are now routinely used in the study of metabolic pathways, their evolution and design. The development of such reconstructions involves the integration of information on reactions and metabolites from the scientific literature as well as public databases and existing genome-scale metabolic models. The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic network reconstructions. In this work, we discuss some of the major difficulties encountered in the mapping and reconciliation of metabolic resources and review three recent initiatives that aim to accelerate this process, namely BKM-react, MetRxn and MNXref (presented in this article). Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources. By reducing the time required for manual curation of metabolite and reaction discrepancies, these resources aim to accelerate the development and application of high-quality genome-scale metabolic network reconstructions and models.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.