Stress Knowledge Map
A comprehensive knowledge graph resource for systems biology analysis of plant stress responses, containing mechanistic models and knowledge networks for plant stress signaling. It includes two knowledge graphs, the mechanistic Plant Stress Signalling model (PSS) and the Comprehensive Knowledge Network (CKN).
[{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "kristina.gruden@nib.si"}], "label": "Kristina Gruden"}, {"category": "Individual", "contact_details": [{"contact_type": "email", "value": "carissa.bleker@nib.si"}], "label": "Carissa Bleker"}, {"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.nib.si/"}], "label": "National Institute of Biology Slovenia"}]
[{"category": "GraphicalInterface", "description": "Interactive search and visualization tool for the mechanistic Plant Stress Signalling model", "id": "skm.pss.explorer", "name": "PSS Explorer", "original_source": ["skm"], "product_url": "https://skm.nib.si/pss"}, {"category": "GraphicalInterface", "description": "Interactive search and visualization tool for the Comprehensive Knowledge Network", "id": "skm.ckn.explorer", "name": "CKN Explorer", "original_source": ["skm"], "product_url": "https://skm.nib.si/ckn"}, {"category": "GraphProduct", "description": "Current PSS model in Systems Biology Graphical Notation XML format", "format": "sbgnml", "id": "skm.pss.live.sbgn", "name": "PSS Live Download (SBGN-ML)", "original_source": ["skm"], "product_file_size": 3204548, "product_url": "https://skm.nib.si/downloads/pss/public/sbgn"}, {"category": "GraphProduct", "description": "Current PSS model in Systems Biology Markup Language XML format", "format": "sbml", "id": "skm.pss.live.sbml", "name": "PSS Live Download (SBML)", "original_source": ["skm"], "product_file_size": 548527, "product_url": "https://skm.nib.si/downloads/pss/public/sbml"}, {"category": "GraphProduct", "description": "Current PSS model in DOT Language format compatible with Graphviz", "format": "dot", "id": "skm.pss.live.dot", "name": "PSS Live Download (DOT)", "original_source": ["skm"], "product_file_size": 595369, "product_url": "https://skm.nib.si/downloads/pss/public/graphviz"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are represented as nodes (as in PSS Explorer and database schema).", "format": "sif", "id": "skm.pss.live.sif.original.graph", "name": "PSS Live Download, original (SIF/LGL)", "original_source": ["skm"], "product_file_size": 161651, "product_url": "https://skm.nib.si/downloads/pss/public/sif-edges"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are represented as nodes (as in PSS Explorer and database schema). This file contains the node annotations.", "format": "sif", "id": "skm.pss.live.sif.original.annotations", "name": "PSS Live Download, original (SIF/LGL), node annotations", "original_source": ["skm"], "product_file_size": 401897, "product_url": "https://skm.nib.si/downloads/pss/public/sif-nodes"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges.", "format": "sif", "id": "skm.pss.live.sif.projection.graph", "name": "PSS Live Download, projection (SIF/LGL)", "original_source": ["skm"], "product_file_size": 253631, "product_url": "https://skm.nib.si/downloads/pss/public/rxn-edges"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges. This file contains the node annotations.", "format": "sif", "id": "skm.pss.live.sif.projection.annotations", "name": "PSS Live Download, projection (SIF/LGL), node annotations", "original_source": ["skm"], "product_file_size": 163587, "product_url": "https://skm.nib.si/downloads/pss/public/rxn-nodes"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges, FunctionalClusters are expanded to arabidopsis identifiers.", "format": "sif", "id": "skm.pss.live.sif.dinar.graph", "name": "PSS Live Download, DiNAR (SIF/LGL)", "original_source": ["skm"], "product_file_size": 361747, "product_url": "https://skm.nib.si/downloads/pss/public/dinar-edges"}, {"category": "GraphProduct", "description": "Current PSS model in Boolean network format compatible with BoolDog and BoolNet", "format": "boolnet", "id": "skm.pss.live.boolnet.graph", "name": "PSS Live Downloads (BoolNet)", "original_source": ["skm"], "product_file_size": 53198, "product_url": "https://skm.nib.si/downloads/pss/public/boolnet"}, {"category": "GraphProduct", "description": "Current PSS model in Boolean network format compatible with BoolDog and BoolNet. This file contains the node annotations.", "format": "boolnet", "id": "skm.pss.live.boolnet.annotations", "name": "PSS Live Downloads (BoolNet), node annotations", "original_source": ["skm"], "product_file_size": 70946, "product_url": "https://skm.nib.si/downloads/pss/public/boolnet-annot"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v2 in SIF/LGL format with 26,234 entities and ~500,000 interactions", "edge_count": 500000, "format": "sif", "id": "skm.ckn.v2.graph", "name": "CKN v2 (June 2023)", "node_count": 26234, "original_source": ["skm"], "product_file_size": 2732107, "product_url": "https://skm.nib.si/downloads/ckn/v2-2023.06"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v2 in SIF/LGL format with 26,234 entities and ~500,000 interactions. This file contains the node annotations.", "format": "sif", "id": "skm.ckn.v2.annotations", "name": "CKN v2 (June 2023), node annotations", "original_source": ["skm"], "product_file_size": 885747, "product_url": "https://skm.nib.si/downloads/ckn-annot/v2-2023.06"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v1 in SIF/LGL format", "format": "sif", "id": "skm.ckn.v1.graph", "name": "CKN v1 (June 2018)", "original_source": ["skm"], "product_file_size": 318666, "product_url": "https://skm.nib.si/downloads/ckn/v1-2018.06"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v1 in SIF/LGL format. This file contains the node annotations.", "format": "sif", "id": "skm.ckn.v1.annotations", "name": "CKN v1 (June 2018), node annotations", "original_source": ["skm"], "product_file_size": 702407, "product_url": "https://skm.nib.si/downloads/ckn-annot/v1-2018.06"}]
{"activity_status": "active", "category": "KnowledgeGraph", "collection": ["ber"], "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "kristina.gruden@nib.si"}], "label": "Kristina Gruden"}, {"category": "Individual", "contact_details": [{"contact_type": "email", "value": "carissa.bleker@nib.si"}], "label": "Carissa Bleker"}, {"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.nib.si/"}], "label": "National Institute of Biology Slovenia"}], "creation_date": "2025-06-17T00:00:00Z", "description": "A comprehensive knowledge graph resource for systems biology analysis of plant stress responses, containing mechanistic models and knowledge networks for plant stress signaling. It includes two knowledge graphs, the mechanistic Plant Stress Signalling model (PSS) and the Comprehensive Knowledge Network (CKN).", "domains": ["plant science", "organisms", "systems biology", "pathways"], "evaluation_page": "resource/skm/skm_eval_automated.html", "homepage_url": "https://skm.nib.si/", "id": "skm", "language": "en", "last_modified_date": "2026-01-06T00:00:00Z", "layout": "resource_detail", "license": {"id": "http://creativecommons.org/licenses/by-nc-sa/3.0/", "label": "CC-BY-NC-SA-3.0"}, "name": "Stress Knowledge Map", "products": [{"category": "GraphicalInterface", "description": "Interactive search and visualization tool for the mechanistic Plant Stress Signalling model", "id": "skm.pss.explorer", "name": "PSS Explorer", "original_source": ["skm"], "product_url": "https://skm.nib.si/pss"}, {"category": "GraphicalInterface", "description": "Interactive search and visualization tool for the Comprehensive Knowledge Network", "id": "skm.ckn.explorer", "name": "CKN Explorer", "original_source": ["skm"], "product_url": "https://skm.nib.si/ckn"}, {"category": "GraphProduct", "description": "Current PSS model in Systems Biology Graphical Notation XML format", "format": "sbgnml", "id": "skm.pss.live.sbgn", "name": "PSS Live Download (SBGN-ML)", "original_source": ["skm"], "product_file_size": 3204548, "product_url": "https://skm.nib.si/downloads/pss/public/sbgn"}, {"category": "GraphProduct", "description": "Current PSS model in Systems Biology Markup Language XML format", "format": "sbml", "id": "skm.pss.live.sbml", "name": "PSS Live Download (SBML)", "original_source": ["skm"], "product_file_size": 548527, "product_url": "https://skm.nib.si/downloads/pss/public/sbml"}, {"category": "GraphProduct", "description": "Current PSS model in DOT Language format compatible with Graphviz", "format": "dot", "id": "skm.pss.live.dot", "name": "PSS Live Download (DOT)", "original_source": ["skm"], "product_file_size": 595369, "product_url": "https://skm.nib.si/downloads/pss/public/graphviz"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are represented as nodes (as in PSS Explorer and database schema).", "format": "sif", "id": "skm.pss.live.sif.original.graph", "name": "PSS Live Download, original (SIF/LGL)", "original_source": ["skm"], "product_file_size": 161651, "product_url": "https://skm.nib.si/downloads/pss/public/sif-edges"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are represented as nodes (as in PSS Explorer and database schema). This file contains the node annotations.", "format": "sif", "id": "skm.pss.live.sif.original.annotations", "name": "PSS Live Download, original (SIF/LGL), node annotations", "original_source": ["skm"], "product_file_size": 401897, "product_url": "https://skm.nib.si/downloads/pss/public/sif-nodes"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges.", "format": "sif", "id": "skm.pss.live.sif.projection.graph", "name": "PSS Live Download, projection (SIF/LGL)", "original_source": ["skm"], "product_file_size": 253631, "product_url": "https://skm.nib.si/downloads/pss/public/rxn-edges"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges. This file contains the node annotations.", "format": "sif", "id": "skm.pss.live.sif.projection.annotations", "name": "PSS Live Download, projection (SIF/LGL), node annotations", "original_source": ["skm"], "product_file_size": 163587, "product_url": "https://skm.nib.si/downloads/pss/public/rxn-nodes"}, {"category": "GraphProduct", "description": "Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges, FunctionalClusters are expanded to arabidopsis identifiers.", "format": "sif", "id": "skm.pss.live.sif.dinar.graph", "name": "PSS Live Download, DiNAR (SIF/LGL)", "original_source": ["skm"], "product_file_size": 361747, "product_url": "https://skm.nib.si/downloads/pss/public/dinar-edges"}, {"category": "GraphProduct", "description": "Current PSS model in Boolean network format compatible with BoolDog and BoolNet", "format": "boolnet", "id": "skm.pss.live.boolnet.graph", "name": "PSS Live Downloads (BoolNet)", "original_source": ["skm"], "product_file_size": 53198, "product_url": "https://skm.nib.si/downloads/pss/public/boolnet"}, {"category": "GraphProduct", "description": "Current PSS model in Boolean network format compatible with BoolDog and BoolNet. This file contains the node annotations.", "format": "boolnet", "id": "skm.pss.live.boolnet.annotations", "name": "PSS Live Downloads (BoolNet), node annotations", "original_source": ["skm"], "product_file_size": 70946, "product_url": "https://skm.nib.si/downloads/pss/public/boolnet-annot"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v2 in SIF/LGL format with 26,234 entities and ~500,000 interactions", "edge_count": 500000, "format": "sif", "id": "skm.ckn.v2.graph", "name": "CKN v2 (June 2023)", "node_count": 26234, "original_source": ["skm"], "product_file_size": 2732107, "product_url": "https://skm.nib.si/downloads/ckn/v2-2023.06"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v2 in SIF/LGL format with 26,234 entities and ~500,000 interactions. This file contains the node annotations.", "format": "sif", "id": "skm.ckn.v2.annotations", "name": "CKN v2 (June 2023), node annotations", "original_source": ["skm"], "product_file_size": 885747, "product_url": "https://skm.nib.si/downloads/ckn-annot/v2-2023.06"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v1 in SIF/LGL format", "format": "sif", "id": "skm.ckn.v1.graph", "name": "CKN v1 (June 2018)", "original_source": ["skm"], "product_file_size": 318666, "product_url": "https://skm.nib.si/downloads/ckn/v1-2018.06"}, {"category": "GraphProduct", "description": "Comprehensive Knowledge Network v1 in SIF/LGL format. This file contains the node annotations.", "format": "sif", "id": "skm.ckn.v1.annotations", "name": "CKN v1 (June 2018), node annotations", "original_source": ["skm"], "product_file_size": 702407, "product_url": "https://skm.nib.si/downloads/ckn-annot/v1-2018.06"}], "publications": [{"authors": ["Carissa Bleker", "\u017diva Ram\u0161ak", "Andras Bittner", "Vid Podpe\u010dan", "Maja Zagor\u0161\u010dak", "Bernhard Wurzinger", "\u0160pela Baebler", "Marko Petek", "Maja Kri\u017enik", "Annelotte van Dieren", "Juliane Gruber", "Leila Afjehi-Sadat", "Wolfram Weckwert", "An\u017ee \u017dupani\u010d", "Markus Teige", "Ute C. Vothknecht", "Kristina Gruden"], "doi": "doi:10.1016/j.xplc.2024.100920", "id": "https://doi.org/10.1016/j.xplc.2024.100920", "journal": "Plant Communications", "title": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "year": "2024"}], "repository": "https://github.com/NIB-SI/skm-tools", "taxon": ["NCBITaxon:33090"], "version": "1.0"}