Implementation of an open chemistry knowledge base with a Semantic Wiki

• Published in: Journal of cheminformatics Vol. 17; no. 1; pp. 99 - 10
• Main Authors: Neidiger, Charlotte, Saier, Tarek, Kühn, Kai, Larignon, Victor, Färber, Michael, Bizzarri, Claudia, Šimek Tosino, Helena, Holzhauer, Laura, Erdmann, Michael, Nguyen, An, Harvey, Dean, Tremouilhac, Pierre, Kramer, Claudia, Hansch, Daniel, Schönle, Fabian, Alpin, Jana, Hartmann, Maximilian, Wagner, Jérome, Jung, Nicole, Bräse, Stefan
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 06.07.2025; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Carbon dioxide; Chemical research; Chemistry; Chemistry and Materials Science; Collaboration; Computational Biology/Bioinformatics; Computer Applications in Chemistry; Documentation and Information in Chemistry; FAIR data; Knowledge; Knowledge bases (artificial intelligence); Large language models; MediaWiki; Open science; Pilot projects; Scientists; Semantic web; Semantics; Software; Theoretical and Computational Chemistry; Semantic web; Databases; Open science; MediaWiki; FAIR data
• ISSN: 1758-2946; 1758-2946
• DOI: 10.1186/s13321-025-01037-w

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 “CO 2 reduction in homogeneous photocatalytic systems,” showcasing its potential to significantly enhance the collaborative collection of research outcomes. Scientific contribution This 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.