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Stress Knowledge Map and beyond: ELIXIR community knowledge graph efforts in plant science and systems biology

Year: 2026
Type: article
Abstract: Understanding plant stress responses requires integrating complex, dispersed knowledge on molecular interactions into queryable, reusable resources. Stress Knowledge Map (SKM; skm.nib.si) addresses this by consolidating curated information on protein-protein interactions, transcriptional regulation, small RNA-transcript interactions, and enzymatic transformations in Arabidopsis thaliana. An additional workflow integrating multiple lines of evidence supports translation of this information to crop species including potato, tomato, and fruit trees. Together with associated analysis and modelling tools, SKM supports systematic contextualisation of multi-omic data and the development of dynamic systems biology models of stress signalling.ELIXIR community activities have been central to SKM's growth and dissemination. The implementation study "Increasing Plant data findability and reuse beyond ELIXIR" improved the accessibility and interoperability of plant knowledge resources across the plant sciences. At the de.NBI BioHackathon Germany 2023, SKM was indexed in FAIDARE, increasing its findability within the ELIXIR plant data infrastructure. An ELIXIR Plant Sciences Community staff exchange extended SKM further, enabling a BioChatter-based prototype for LLM-accessibility to lower barriers for experimental biologists.These developments revealed a broader need: standardised, reusable infrastructure for transforming systems biology models (in SBGN-ML and SBML formats) into human- and AI-accessible knowledge graphs. This motivated the ELIXIR Systems Biology Community's project at the 4th BioHackathon Germany (December 2025), which produced an initial common labelled property graph schema grounded in a standard ontology (SBO), SBGN and SBML BioCypher adapters, and initial support for SBML export - laying the groundwork for a community-wide framework and future AI integration across systems biology.
DOI: 10.5281/zenodo.22310083
Authors: Bleker, Carissa, Zagorščak, Maja, Juteršek, Mojca, Praček, Sergej, Zupanic, Anze, Gruden, Kristina, Sá, Bruno, Luna, Augustin, Doğay, Yağmur, Zrimec, Jan, Rougny, Adrien, Dogrusoz, Ugur, Ostaszewski, Marek, van Welzen, Matti, Lobentanzer, Sebastian
Institutions: National Institute of Biology, University of Minho, University of Luxembourg, University of Rostock, University Hospital Heidelberg, Helmholtz Munich, German Center for Diabetes Research
Language: English
Open Access status: green
OpenAlex ID: W7211875900
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