---
title: "HARMONY: Ontology-guided harmonization for unified discovery of public metabolomics studies"
id: "biorxiv-2-ontology-guided-harmonization-enables-unified-discovery-of-public-metabolomics"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-2-ontology-guided-harmonization-enables-unified-discovery-of-public-metabolomics"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1?rss=1"
published_at: "2026-07-27T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# HARMONY: Ontology-guided harmonization for unified discovery of public metabolomics studies
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-2-ontology-guided-harmonization-enables-unified-discovery-of-public-metabolomics
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1?rss=1)
- **Published At:** 2026-07-27T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- Public metabolomics repositories use heterogeneous metadata schemas and vocabularies, which constrain reliable search, comparison, and reuse of studies within and across databases. - The authors present **HARMONY**, an ontology-based framework and web platform that harmonizes study-level metadata and metabolite information across Metabolomics Workbench and MetaboLights. - HARMONY resolves eight biological and analytical metadata nodes: **species**, **sample source**, **disease**, **analytical technique**, **separation method**, **ion polarity**, **ionization source**, and **mass analyzer type**, while preserving original deposited terms as evidence. - A ninth node, **metabolite identity**, maps metabolite entities to **RefMet** across both repositories. - The system uses a two-step workflow: multi-source extraction to retrieve records missed by single-field lookups, followed by ontology mapping to convert repository-specific labels into shared query terms. - HARMONY substantially improves cross-repository retrieval compared with raw-text matching: reported corpus-wide retrievability increased from 75.5% to 89.6%. - The platform generated thousands of study-node retrievals and reconnected studies that raw-text search would have left unreachable within their own repositories. - Approximately 91% of Metabolomics Workbench and 85% of MetaboLights studies had at least six of the eight biological/analytical nodes harmonized. - The web platform (https://omicsinharmony.in) supports ontology-aware search, metadata filtering, within- and cross-repository study comparison, and metabolite-level querying. - Retrieval is backed by machine learning encoders that map study metadata into shared representations of biological and analytical context. - The manuscript is a preprint posted July 27, 2026; competing interests include equity holdings declared by two authors. - HARMONY provides a traceable, shared search interface intended to improve discoverability and comparison of metabolomics studies across public repositories.
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Shayantan Banerjee 1 Indian Institute of Technology Bombay; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Shayantan%2BBanerjee%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Banerjee%20S&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AShayantan%2BBanerjee%2B) Pratik Jalan 2 Indian Institite of Technology Bombay * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Pratik%2BJalan%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Jalan%20P&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3APratik%2BJalan%2B) Rudrapratap Chinhara 1 Indian Institute of Technology Bombay; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Rudrapratap%2BChinhara%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Chinhara%20R&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ARudrapratap%2BChinhara%2B) Chinmayee Kalle 2 Indian Institite of Technology Bombay * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Chinmayee%2BKalle%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kalle%20C&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AChinmayee%2BKalle%2B) Pramod Wangikar 1 Indian Institute of Technology Bombay; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Pramod%2BWangikar%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Wangikar%20P&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3APramod%2BWangikar%2B) * For correspondence: wangikar@iitb.ac.in Kshitij Jadhav 1 Indian Institute of Technology Bombay; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Kshitij%2BJadhav%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Jadhav%20K&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AKshitij%2BJadhav%2B) * [Abstract](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5658841/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5658841/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5658841/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5658841/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5658841/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Public metabolomics repositories contain thousands of studies, but differences in metadata structure, vocabulary, and repository-specific terms still limit reliable search, comparison, and reuse within and across databases. Here we present HARMONY, an ontology-based framework and web platform that harmonizes study-level metadata and metabolite information across Metabolomics Workbench and MetaboLights studies. HARMONY resolves eight biological and analytical metadata nodes, including species, sample source, disease, analytical technique, separation method, ion polarity, ionization source, and mass analyzer type, while preserving the original deposited terms as evidence. A ninth node, metabolite identity, maps metabolite entities to RefMet across both repositories. HARMONY uses a two-step workflow: Multi-source extraction retrieves records missed by single-field lookups, and ontology mapping then converts repository-specific labels into shared query terms, substantially closing the cross-repository retrieval gap relative to raw matching. Across the full corpus, HARMONY increased cross-repository retrievability from 75.5% to 89.6%, yielding thousands of study-node retrievals and reconnecting studies that raw-text search would have left unreachable within their own repositories. Approximately 91% of Metabolomics Workbench and 85% of MetaboLights studies had at least six of the eight nodes harmonized. The resulting platform, available at https://omicsinharmony.in, supports ontology-aware search, metadata filtering, within- and cross-repository study comparison, and metabolite-level querying, with retrieval backed by machine learning encoders that map study metadata into shared representations of biological and analytical context. HARMONY provides the metabolomics community with a shared, traceable search interface for study discovery and comparison within and across public repositories. ### Competing Interest Statement PW holds equity in Clarity Bio Systems India Pvt. Ltd., Pune 411016, India KJ holds equity in RadAI Pvt. Ltd, India Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC 4.0 International license](http://creativecommons.org/licenses/by-nc/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/07/27/2026.07.23.740366.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.07.23.740366v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) Ontology-guided harmonization enables unified discovery of public metabolomics studies within and across repositories Shayantan Banerjee, Pratik Jalan, Rudrapratap Chinhara, Chinmayee Kalle, Pramod Wangikar, Kshitij Jadhav bioRxiv 2026.07.23.740366; doi: https://doi.org/10.64898/2026.07.23.740366 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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