ArticleNucleic acids research2024
PathBank 2.0-the pathway database for model organism metabolomics.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- MetaboGraph: A Framework for Metabolomics and Lipidomics Annotation and Pathway Network Analysis.Analytical chemistry · 2026Article
- Decoding the Metabolic Signatures of Neurodegeneration Diseases: Advances in Mass Spectrometry-Based Metabolomics.Metabolites · 2026Review
- Analyses of plasma multi-omic data across ancestries identify novel pathways implicated in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- MiMeDB 2.0: the Human Microbial Metabolome Database for 2026.Nucleic acids research · 2026Article
- Metabolomics Data Analysis with the HMDB.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- HUBMet: an integrative database and analytical platform for human blood metabolites and metabolite-protein associations.Genome biology · 2025Article
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- Short-term dietary methionine restriction with high fat diet counteracts metabolic dysfunction in male mice.Physiological reports · 2025Article
- Plasma metabolomics signatures predict COVID-19 patient outcome at ICU admission comparable to clinical scores.Scientific reports · 2025Article
- HCDT 2.0: A Highly Confident Drug-Target Database for Experimentally Validated Genes, RNAs, and Pathways.Scientific data · 2025Article
- Mechanisms of Homoarginine: Looking Beyond Clinical Outcomes.Acta physiologica (Oxford, England) · 2025Review
- Multi-omics decodes host-specific and environmental microbiome interactions in sepsis.Frontiers in microbiology · 2025Review
- BioPAX in 2024: Where we are and where we are heading.Computational and structural biotechnology journal · 2024Review
- The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
22 authors.
Funding
Abstract
PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for the metabolomics community since 2010. Over the past 14 years, these pathway databases have grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in computing technology. This year's update, PathBank 2.0, brings a number of important improvements and upgrades that should make the database more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of primary or canonical pathways (from 1720 to 6951); (ii) a massive increase in the total number of pathways (from 110 234 to 605 359); (iii) significant improvements to the quality of pathway diagrams and pathway descriptions; (iv) a strong emphasis on drug metabolism and drug mechanism pathways; (v) making most pathway images more slide-compatible and manuscript-compatible; (vi) adding tools to support better pathway filtering and selecting through a more complete pathway taxonomy; (vii) adding pathway analysis tools for visualizing and calculating pathway enrichment. Many other minor improvements and updates to the content, the interface and general performance of the PathBank website have also been made. Overall, we believe these upgrades and updates should greatly enhance PathBank's ease of use and its potential applications for interpreting metabolomics data.
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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.