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

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

doi:10.1016/j.xplc.2024.100920

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

Carissa Bleker (Corresponding author)
, 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 (Corresponding author)

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

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.

Original language	English
Article number	100920
Journal	Plant Communications
Volume	5
Issue number	6
DOIs	https://doi.org/10.1016/j.xplc.2024.100920
Publication status	Published - 10 Jun 2024

Funding

SKM was developed with funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement 862858 (ADAPT); the Slovenian Research Agency under grant agreements 1000-15-0105 , Z7-1888 , J4-1777 , P4-0165 , N4-0199 , and J4-3089 ; and ELIXIR , the research infrastructure for life science data through the ELIXIR Implementation Study \u201CIncreasing plant data findability for ELIXIR and beyond\u201D and ELIXIR-SI. We gratefully acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) to U.C.V. ( INST 217/939-1 FUGG ). SKM was developed with funding from the European Union's Horizon 2020 research and innovation programme under grant agreement 862858 (ADAPT); the Slovenian Research Agency under grant agreements 1000-15-0105, Z7-1888, J4-1777, P4-0165, N4-0199, Z4-50146, and J4-3089; and ELIXIR, the research infrastructure for life science data through the ELIXIR Implementation Study \u201CIncreasing plant data findability for ELIXIR and beyond\u201D and ELIXIR-SI. We gratefully acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) to U.C.V. (INST 217/939-1 FUGG).

Austrian Fields of Science 2012

106005 Bioinformatics

Keywords

knowledge graph
plant digital twin
plant signaling
plant stress responses
systems biology

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10.1016/j.xplc.2024.100920Licence: CC BY 4.0

https://phaidra.univie.ac.at/o:2069414Licence: CC BY 4.0

Cite this

Bleker, C., Ramšak, Ž., Bittner, A., Podpečan, V., Zagorščak, M., Wurzinger, B., Baebler, Š., Petek, M., Križnik, M., van Dieren, A., Gruber, J., Afjehi-Sadat, L., Weckwerth, W., Županič, A., Teige, M., Vothknecht, U. C., & Gruden, K. (2024). Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses. Plant Communications, 5(6), Article 100920. https://doi.org/10.1016/j.xplc.2024.100920

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

abstract = "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.",

keywords = "knowledge graph, plant digital twin, plant signaling, plant stress responses, systems biology",

author = "Carissa Bleker and {\v Z}iva Ram{\v s}ak and Andras Bittner and Vid Podpe{\v c}an and Maja Zagor{\v s}{\v c}ak and Bernhard Wurzinger and {\v S}pela Baebler and Marko Petek and Maja Kri{\v z}nik and \{van Dieren\}, Annelotte and Juliane Gruber and Leila Afjehi-Sadat and Wolfram Weckwerth and An{\v z}e {\v Z}upani{\v c} and Markus Teige and Vothknecht, \{Ute C.\} and Kristina Gruden",

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year = "2024",

month = jun,

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Bleker, C, Ramšak, Ž, Bittner, A, Podpečan, V, Zagorščak, M, Wurzinger, B, Baebler, Š, Petek, M, Križnik, M, van Dieren, A, Gruber, J, Afjehi-Sadat, L , Weckwerth, W, Županič, A, Teige, M, Vothknecht, UC & Gruden, K 2024, 'Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses', Plant Communications, vol. 5, no. 6, 100920. https://doi.org/10.1016/j.xplc.2024.100920

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AU - Bleker, Carissa

AU - Ramšak, Živa

AU - Bittner, Andras

AU - Podpečan, Vid

AU - Zagorščak, Maja

AU - Wurzinger, Bernhard

AU - Baebler, Špela

AU - Petek, Marko

AU - Križnik, Maja

AU - van Dieren, Annelotte

AU - Gruber, Juliane

AU - Afjehi-Sadat, Leila

AU - Weckwerth, Wolfram

AU - Županič, Anže

AU - Teige, Markus

AU - Vothknecht, Ute C.

AU - Gruden, Kristina

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AB - 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.

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ER -

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

Abstract

Funding

Austrian Fields of Science 2012

Keywords

Access to Document

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