ArticlePLoS computational biology2024
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Assessing the metabolomics "dark matter" by a detectable khipu model.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Article
- Distinct biochemical phenotypes of HIV exposed infants driven by antiviral medication.medRxiv : the preprint server for health sciences · 2026Article
- Mass Spectrometry-Based Metabolomics in Pediatric Health and Disease.Metabolites · 2026Review
- Practicing Data Science in Interactive Notebooks.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Metabolomics Data Processing Using the Asari Toolkit.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Constructing a consensus serum metabolome.bioRxiv : the preprint server for biology · 2025Article
- Introducing "Identification Probability" for Automated and Transferable Assessment of Metabolite Identification Confidence in Metabolomics and Related Studies.Analytical chemistry · 2025Review
- Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web.Journal of the American Society for Mass Spectrometry · 2024Article
- Introducing 'identification probability' for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
- Update of
Authors and funding
6 authors.
Funding
Abstract
To standardize metabolomics data analysis and facilitate future computational developments, it is essential to have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We demonstrate the performance of the pipeline, and the details in annotation and quality control using large-scale LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously published datasets are also reanalyzed to showcase its utility in biological data analysis. This pipeline allows users to streamline data processing, quality control, annotation, and standardization in an efficient and transparent manner. This work fills a major gap in the Python ecosystem for computational metabolomics.
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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 Socratic graph.