The eLignin Microbial Database v1.0.0

eLignin is a curated database of scientific knowledge on microbial degradation of lignin and lignin-derived aromatic compounds. It aims to bring the literature together in a searchable resource to support exploration of the organisms, substrates, pathways, reactions, enzymes, genes, transporters, and references that describe microbial lignin catabolism.

The original eLignin database was developed in a Lund University research project on lignin valorisation, funded by the Swedish Foundation for Strategic Research (2015–2020). The original closed-source LAMP application was deployed from 2016 until 2023.

In 2026, the project was refactored as a open-source single-container Django web app, designed for deployment on SciLifeLab Serve at elignin.serve.scilifelab.se. This v1.0.0 release is the first release of the refactored app.

Highlights

• Open science: The source code is released under the MIT License, and the curated dataset is released under CC BY 4.0. The database is rebuilt from version-controlled TSV files and pathway JSON-LD during container build-time.

• Portable deployment: eLignin is distributed as a single Docker container, enabling local use as well as deployment on SciLifeLab Serve.

• Interactive pathway maps: Pathway maps are rendered as interactive network visualisations using Cytoscape.js, replacing the static pathway images used by the legacy site.

• Structured pathway data: Pathways and reactions are represented as eLignin-specific JSON-LD based on the BioPAX Level 3 vocabulary. Pathway structures can be exported directly from the web interface.

• Clear evidence status: Empirically reported relationships are visibly separated from computationally inferred relationships. Predicted sections can be shown or hidden in the UI, and their inference basis is documented.

• Improved reuse and provenance: Curated data are available as version-controlled files, relationship tables can be downloaded as TSV, and reference pages include structured citation metadata and BibTeX.

• Modern quality controls: Automated checks validate the curated data, pathway membership, citation completeness, code quality, container builds, and dependency/security issues before a release image is published.

The initial v1.0.0 dataset contains 263 organisms, 138 substrates, 26 pathways, 75 reactions, 58 enzymes, 89 genes, 15 transporters, and 329 literature references. References currently extend through 2022.

The eLignin Microbial Database v1.0.0-rc.6

Pre-release for SciLifeLab Serve deployment testing.