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MARCUS: Molecular Annotation and Recognition for Curating Unravelled Structures

  • The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions operate in isolation, which limits their scalability for comprehensive literature curation. Here we present MARCUS (Molecular Annotation and Recognition for Curating Unravelled Structures), a tool to aid curators in performing literature curation in the field of natural products. This integrated web-based platform combines automated text annotation, multi-engine OCSR, and direct submission capabilities to the COCONUT database. MARCUS employs a fine-tuned GPT-4 model to extract chemical entities and utilises an ensemble approach integrating DECIMER, MolNexTR, and MolScribe for structure recognition. The platform aims to streamline the data extraction workflow from PDF upload to database submission, significantly reducing curation time. MARCUS bridges the gap between unstructured chemical literature and machine-actionable databases, enabling FAIR data principles and facilitating AI-driven chemical discovery. Through open-source code, accessible models, and comprehensive documentation, the web application enhances accessibility and promotes community-driven development. This approach facilitates unrestricted use and encourages the collaborative advancement of automated chemical literature curation tools. We dedicate MARCUS to Dr Marcus Ennis, the longest-serving curator of the ChEBI database, on the occasion of his 75th birthday.

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Author:Achim Zielesny, Viktor Weißenborn, Laurin Lederer, Christoph Steinbeck, Kohulan Rajan
URN:urn:nbn:de:hbz:1010-opus4-48310
DOI:https://doi.org/10.26434/chemrxiv-2025-9p1q1
Parent Title (German):ChemRxiv
Document Type:Preprint
Language:English
Date of Publication (online):2025/07/09
Date of first Publication:2025/07/09
Publishing Institution:Westfälische Hochschule Gelsenkirchen Bocholt Recklinghausen
Release Date:2025/10/09
Institutes:Institute / Institut für biologische und chemische Informatik
Licence (German):Es gilt das Urheberrechtsgesetz
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