ArticleMetabolites2023
md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases.
Article in Metabolites, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- High-Quality Predicted Metabolite-Pathway Annotations Expand Pathway Coverage and Increase Enriched Pathway Detection Across Metabolomics Datasets.Metabolites · 2026Article
- Article
- Article
- Predicting the pathway involvement of metabolites annotated in the MetaCyc knowledgebase.BMC bioinformatics · 2026Article
- High-Quality Predicted Pathway Annotations Greatly Improve Pathway Enrichment Analysis of Metabolomics Datasets.bioRxiv : the preprint server for biology · 2025Article
- Chemical representation standardization needed to generalize metabolic pathway involvement prediction across the Kyoto Encyclopedia of Genes and Genomes, Reactome, and MetaCyc knowledgebases.bioRxiv : the preprint server for biology · 2025Article
- Predicting the Pathway Involvement of Compounds Annotated in the Reactome Knowledgebase.Metabolites · 2025Article
- Predicting the Pathway Involvement of All Pathway and Associated Compound Entries Defined in the Kyoto Encyclopedia of Genes and Genomes.Metabolites · 2024Article
- Predicting the Association of Metabolites with Both Pathway Categories and Individual Pathways.Metabolites · 2024Article
- Predicting the Pathway Involvement of Metabolites in Both Pathway Categories and Individual Pathways.bioRxiv : the preprint server for biology · 2024Article
- Predicting the Pathway Involvement of Metabolites Based on Combined Metabolite and Pathway Features.Metabolites · 2024Article
- Predicting The Pathway Involvement Of Metabolites Based on Combined Metabolite and Pathway Features.bioRxiv : the preprint server for biology · 2024Article
- Benchmark Dataset for Training Machine Learning Models to Predict the Pathway Involvement of Metabolites.Metabolites · 2023Article
- Benchmark dataset for training machine learning models to predict the pathway involvement of metabolites.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
A major challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents md_harmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. The md_harmonize package utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on a compound's chemical structure. The resulting harmonized compounds and reactions can be used for various downstream analyses, including the construction of atom-resolved metabolic networks and models for metabolic flux analysis. Parts of the md_harmonize package have been optimized using a variety of computational techniques to allow certain NP-complete problems handled by the software to be tractable for these specific use-cases. The software is available on GitHub and through the Python Package Index, with end-user documentation hosted on GitHub Pages.
Indexed as
Identifiers
What OpenQuestion holds
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.