Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map (SKM; https://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 rea...

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Veröffentlicht in:Plant communications 2024-06, Vol.5 (6), p.100920, Article 100920
Hauptverfasser: Bleker, Carissa, Ramšak, Živa, Bittner, Andras, Podpečan, Vid, Zagorščak, Maja, Wurzinger, Bernhard, Baebler, Špela, Petek, Marko, Križnik, Maja, van Dieren, Annelotte, Gruber, Juliane, Afjehi-Sadat, Leila, Weckwerth, Wolfram, Županič, Anže, Teige, Markus, Vothknecht, Ute C., Gruden, Kristina
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Sprache:eng
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Zusammenfassung:Stress Knowledge Map (SKM; https://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. This study reports the assembly of Stress Knowledge Map (SKM), a publicly available resource containing two complementary knowledge graphs of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling and a large knowledge network. The paper also describes the additional features of SKM and shows how it can be used to generate hypotheses, design validation experiments, and gain new insights into experimental observations in plant biology.
ISSN:2590-3462
2590-3462
DOI:10.1016/j.xplc.2024.100920