Implementation of an open chemistry knowledge base with a Semantic Wiki

TL;DR

This paper introduces a collaborative platform for chemists to collect and organize research data using a Semantic Wiki, enhancing data sharing and analysis.

Contribution

The paper introduces a cheminformatics-enabled Semantic MediaWiki for collaborative chemical knowledge management, integrating chemical structures and research data.

Findings

A Semantic MediaWiki was enhanced to support chemical data collection and structured summaries.

Tools for capturing chemical structures in machine-readable formats were implemented.

The platform's effectiveness was demonstrated in organizing research on CO2 reduction in photocatalytic systems.

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 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.

The online version contains supplementary material available at 10.1186/s13321-025-01037-w.

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