Stress Knowledge Map
- Author(s)
- Carissa Bleker, Živa Ramšak, Andras Bittner, Vid Podpečan, Maja Zagorščak, Bernhard Wurzinger, Špela Baebler, Marko Petek, Maja Križnik, Annelotte van Dieren, Juliane Gruber, Leila Afjehi-Sadat, Wolfram Weckwerth, Anže Županič, Markus Teige, Ute C. Vothknecht, Kristina Gruden
- Abstract
Stress Knowledge Map (SKM; skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.
- Organisation(s)
- Functional and Evolutionary Ecology, Vienna University Library and Archive Services, Core Facility Shared Services UBB, Department of Biochemistry and Cell Biology
- External organisation(s)
- National Institute of Biology, Rheinische Friedrich-Wilhelms-Universität Bonn, Jožef Stefan Institute (IJS)
- Journal
- Plant Communications
- Volume
- 5
- DOI
- https://doi.org/10.1016/j.xplc.2024.100920
- Publication date
- 06-2024
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 106005 Bioinformatics
- Keywords
- ASJC Scopus subject areas
- Biotechnology, Biochemistry, Molecular Biology, Plant Science, Cell Biology
- Portal url
- https://ucrisportal.univie.ac.at/en/publications/stress-knowledge-map(0a8b7e1d-b9d8-4061-b664-0eeee911fe71).html