Stress Knowledge Map

Supported by the ADAPT project

Celebrating the publication of Stress Knowledge Map in Plant Communications

by Carissa on 2024-06-14

We are thrilled to announce the publication of our article in Plant Communications titled "Stress Knowledge Map: A Knowledge Graph Resource for Systems Biology Analysis of Plant Stress Responses." This comprehensive resource, developed by an international team of experts led by dr. Kristina Gruden, represents a significant advancement in our understanding of plant stress responses.

Introducing Stress Knowledge Map (SKM)

Stress Knowledge Map (SKM) is an innovative, publicly accessible resource designed to consolidate and contextualize the vast and complex data generated by modern "omics" technologies. This resource consists of two main components:

  • Plant Stress Signaling Model (PSS): A meticulously curated model of plant stress signaling that includes over 500 biochemical reactions.
  • Comprehensive Knowledge Network (CKN): An extensive network featuring over 480k molecular interactions, offering a broad overview of plant processes beyond just stress signaling.

SKM provides a single-entry point for researchers and crop breeders to investigate plant stress responses and growth trade-offs. The integration of knowledge from individual published articles and various resources, including KEGG, STRING, MetaCyc, and AraCyc, allows for interactive exploration and supports diverse systems biology analyses. By enabling both qualitative and quantitative modeling, SKM serves as a starting point for developing a digital twin of plants, facilitating hypothesis generation, experimental design, and deeper insights into experimental observations.

Adhering to the FAIR principles (Findable, Accessible, Interoperable, and Reusable), SKM is indexed in multiple repositories and databases, ensuring broad accessibility and usability. The SKM environment includes tools for content exploration, visualization, and export, as well as an interface for contributing updates based on novel discoveries.

Case studies and applications

The article showcases two case studies demonstrating how SKM can be utilized for complex analyses, systematic hypothesis generation, and the design of validation experiments. This versatile resource aids researchers in contextualizing new datasets within existing plant research, ultimately driving the development of stress-resilient crops and addressing global food security challenges.

A collaborative achievement

This publication of SKM was a collaborative effort involving researchers from the National Institute of Biology in Slovenia, the University of Bonn in Germany, the Jo┼żef Stefan Institute in Slovenia, and the University of Vienna in Austria. SKM marks a significant milestone in plant systems biology and underscores the importance of international collaboration in addressing pressing agricultural challenges.

For more details, read the full article in Plant Communications: https://doi.org/10.1016/j.xplc.2024.100920.

Please note that NEWT is a client-side application, and therefore relies on your local computer capabilities. Given the relatively large size of PSS, rendering the network may take a while.