Implementation of an open chemistry knowledge base with a Semantic Wiki.

Authors

Charlotte Neidiger, Tarek Saier, Kai Kühn, Victor Larignon, Michael Färber, Claudia Bizzarri, Helena Šimek Tosino, Laura Holzhauer, Michael Erdmann, An Nguyen, Dean Harvey, Pierre Tremouilhac, Claudia Kramer, Daniel Hansch, Fabian Schönle, Jana Alpin, Maximilian Hartmann, Jérome Wagner, Nicole Jung, Stefan Bräse

Published in

Journal of cheminformatics. Volume 17. Issue 1. Pages 99. Jul 06, 2025. Epub Jul 06, 2025.

Abstract

In this work, a concept for an open chemistry knowledge base was developed to integrate chemical research results into a collaboratively usable platform. To achieve this, we enhanced Semantic MediaWiki (SMW) to support the collection and structured summary of chemical data contained in publications. We implemented tools for capturing chemical structures in machine-readable formats and designed data forms along with a data model to ensure standardized input and organization of research results. These enhancements allow for effective data comparison and contextual analysis within an expandable Wiki environment. The use of the platform was specifically demonstrated by organizing and comparing research in the area of "CO₂ reduction in homogeneous photocatalytic systems," showcasing its potential to significantly enhance the collaborative collection of research outcomes.Scientific contributionThis work shows ways to collaboratively collect and manage subject-specific knowledge in the domain of chemistry via an open database. By integrating cheminformatic tools into Semantic Mediawiki, an established technology for building knowledge databases is made systematically usable for the chemical community. The integration of chemistry-specific workflows and forms allows the mapping of data from current research with links to the original sources. This work is intended to show how gaps in the information system of scientists can be closed without having to use commercial systems.

PMID:
40619391
Bibliographic data and abstract were imported from PubMed on 07 Jul 2025.

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