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 designed for natural product literature curation that integrates COCONUT-aware schema mapping, CIP-based stereochemical validation, and human-in-the-loop structure refinement. 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 a Human-in-the-loop 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.

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Author:Kohulan RajanORCiD, Viktor Weißenborn, Laurin Lederer, Christoph SteinbeckORCiD, Achim ZielesnyORCiD
URN:urn:nbn:de:hbz:1010-opus4-49019
DOI:https://doi.org/10.1039/D5DD00313J
Parent Title (English):Digital Discovery
Publisher:Royal Society of Chemistry
Document Type:Article
Language:English
Date of Publication (online):2025/12/18
Date of first Publication:2025/09/21
Publishing Institution:Westfälische Hochschule Gelsenkirchen Bocholt Recklinghausen
Release Date:2026/01/05
Volume:2025
Issue:4
Page Number:12
First Page:3137
Last Page:3148
Institutes:Institute / Institut für biologische und chemische Informatik
Licence (German):Creative Commons - Namensnennung
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