# MetaboT: AI-based agent for interaction with metabolomics knowledge graphs

Madina Bekbergenova, Lucas Pradi, Benjamin Navet, Yousouf Taghzouti, Emma Tysinger, Jean-Luc Wolfender, Wout Bittremieux, Fabien Gandon, Louis-Félix Nothias

► To cite this version:

Madina Bekbergenova, Lucas Pradi, Benjamin Navet, Yousouf Taghzouti, Emma Tysinger, et al. MetaboT: AI-based agent for interaction with metabolomics knowledge graphs. EDSFA 2nd year

PhD Workshop, May 2025, Sophia -Antipolis, France. hal-05235422

HAL Id: hal-05235422

https://hal.science/hal-05235422v1

Submitted on 1 Oct 2025

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# MetaboT: A Conversational AI-Agent for Accessible Mass Spectrometry Metabolomics Data Mining

Madina Bekbergenova¹, ²; Lucas Pradi¹, ²; Emma Tysinger¹, ³; Benjamin Navet²; Olivier Kirchhoffer⁴; Jean-Luc Wolfender⁴; Florence Mehl⁵; Marco Pagni⁵; Wout Bittremieux⁶, *; Fabien Gandon⁷; Louis Felix Nothias¹, ²,*

¹Université Côte d'Azur, CNRS, ICN, Nice, France; ²Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur, Sophia-Antipolis, France; ³MIT, Cambridge, MA; ⁴School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland; ⁵Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; ⁶University of Antwerp, Department of Computer Science, Antwerp, Belgium; ⁷INRIA, Université Côte d'Azur, CNRS, I3S, Sophia-Antipolis, France

<figure><img src="image_2.png" /><figcaption>## From raw LC-MS data to Knowledge Graph</figcaption></figure>

<figure><img src="image_3.png" /></figure>

## SPARQL query

Question: How many features have the same SIRIUS and ISDB annotation?

PREFIX enpkg: <https://enpkg.commons-lab.org/kg/> 
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT (COUNT(?feature) AS ?count)
WHERE

{ ?feature rdf:type enpkg:LCMSFeature .
?feature enpkg:has_sirius annotation ?sirius annotation .
?sirius annotation rdf:type enpkg:Sirius StructureAnnotation .
?sirius annotation enpkg:has InChIkey2D ?sirius ik2d .
?feature enpkg:has isdb annotation ?isdb annotation .
?isdb annotation rdf:type enpkg:IsdbAnnotation .
?isdb annotation enpkg:has InChIkey2D ?isdb ik2d .
FILTER(?isdb ik2d = ?sirius ik2d) . }

RDF

<figure><img src="image_4.png" /></figure>

## Background

Knowledge graphs (KGs) provide a powerful way to represent complex information through **semantic structures**. Mining KGs can be efficiently performed using a **specialized query language** like SPARQL. With KGs being inherently aligned with natural language, the emerging capabilities of **large language models (LLMs)** present new opportunities for facilitating the querying of these graphs. We propose an **AI-framework** that integrates **KGs and LLMs** to effectively interrogate **complex metabolomics data** encapsulated within KGs.

<figure><img src="image_5.png" /></figure>

## Methods

We developed **MetaboT**, an AI system that uses LLM agents to translate user questions into SPARQL queries for data mining. MetaboT executes these queries on a KG and provides answers, simplifying interactions with complex metabolomics data. As a **proof of concept**, it currently accesses a mass spectrometry dataset of 1,600 plant extracts [1]. Preliminary results show that **MetaboT** effectively answers various queries, though some limitations remain. To address these, we introduced a self-correcting process that guides users on how to reformulate their queries or adjust expectations based on the scope of MetaboT and the KG.

<figure><img src="image_6.png" /><figcaption>## MetaboT AI agent and chatbot interface</figcaption></figure>

<figure><img src="image_7.png" /></figure>

Which samples contain the largest number of metabolites annotated as diterpene esters ?

Here is the list of samples. [...].
Do you want to see detailed annotations?

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

Can you generate a distribution plot for the number of metabolite annotations per *Euphorbia* species in the three datasets ?

<figure><img src="image_10.png" /></figure>

Here is the distribution for
these datasets:

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

For metabolites previously reported in the *Euphorbia* genus, which one can be annotated similarly in both positive and negative ionisation modes ?

<figure><img src="image_13.png" /></figure>

Here is the list of features that could be annotated
with SIRIUS ionisation modes [...]. Do you want to
visualize them as a structural similarity graph ?

metabot.holobiomicslab.eu

References
[1] Allard, PM, et al., *GigaScience*, Volume 12, 2023, giac124, https://doi.org/10.1093/gigascience/giac124
[2] Gaudry, A. et al., *ACS Cent. Sci.*, 2024, 10, 3, 494–510. https://doi.org/10.1093/gigascience/giac124

Funding

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UNIVERSITÉ
CÔTE D'AZUR

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Holobiomics Lab