Araport (Arabidopsis Information Portal)
Araport (the Arabidopsis Information Portal) was a J. Craig Venter Institute (JCVI) project that provided an integrated data warehouse, genome browser, and analysis apps for Arabidopsis thaliana research. Its central product, Araport11, is the complete 2016/2017 reannotation of the A. thaliana Col-0 reference genome, refining gene models and adding non-coding RNAs based on extensive RNA-seq evidence. The Araport web portal was retired around 2018 after funding ended, with its data and services migrated to TAIR, NCGR, and the Bio-Analytic Resource (BAR/ThaleMine). The Araport11 gene/locus annotation remains a standard reference annotation, distributed via TAIR and Phytozome, and is used by downstream resources such as the Stress Knowledge Map.
[{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.arabidopsis.org/"}], "label": "The Arabidopsis Information Resource (TAIR), Phoenix Bioinformatics"}]
[{"category": "DataSource", "description": "The Araport11 reannotation of the Arabidopsis thaliana Col-0 reference genome (gene models, transcripts, and non-coding RNAs), distributed through the JGI Phytozome plant genomics portal.", "format": "gff", "id": "araport.araport11", "name": "Araport11 Genome Annotation (Phytozome)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "araport"}], "product_url": "https://phytozome-next.jgi.doe.gov/info/Athaliana_Araport11"}, {"category": "GraphicalInterface", "description": "ThaleMine, the InterMine-based data warehouse originally developed for Araport, now hosted at the Bio-Analytic Resource for Plant Biology (BAR), serving Araport11-based gene and functional data.", "format": "http", "id": "araport.thalemine", "name": "ThaleMine (BAR)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "araport"}], "product_url": "https://bar.utoronto.ca/thalemine/"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 548527, "product_url": "https://skm.nib.si/downloads/pss/public/sbml"}, {"category": "GraphProduct", "description": "PSS model (v1.0.0, October 2023) in DOT Language format compatible with Graphviz. The live/current DOT export endpoint was retired upstream; this points to the latest published versioned DOT export.", "format": "dot", "id": "skm.pss.live.dot", "name": "PSS Download (DOT, v1.0.0)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 405988, "product_url": "https://skm.nib.si/downloads/pss-version/v1.0.0/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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 2732107, "product_url": "https://skm.nib.si/downloads/ckn/v2-2023.06/edges"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 885747, "product_url": "https://skm.nib.si/downloads/ckn/v2-2023.06/nodes"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 318666, "product_url": "https://skm.nib.si/downloads/ckn/v1-2018.06/edges"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 702407, "product_url": "https://skm.nib.si/downloads/ckn/v1-2018.06/nodes"}]
{"activity_status": "inactive", "category": "DataSource", "collection": ["ber"], "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://www.arabidopsis.org/"}], "label": "The Arabidopsis Information Resource (TAIR), Phoenix Bioinformatics"}], "creation_date": "2026-06-18T00:00:00Z", "description": "Araport (the Arabidopsis Information Portal) was a J. Craig Venter Institute (JCVI) project that provided an integrated data warehouse, genome browser, and analysis apps for Arabidopsis thaliana research. Its central product, Araport11, is the complete 2016/2017 reannotation of the A. thaliana Col-0 reference genome, refining gene models and adding non-coding RNAs based on extensive RNA-seq evidence. The Araport web portal was retired around 2018 after funding ended, with its data and services migrated to TAIR, NCGR, and the Bio-Analytic Resource (BAR/ThaleMine). The Araport11 gene/locus annotation remains a standard reference annotation, distributed via TAIR and Phytozome, and is used by downstream resources such as the Stress Knowledge Map.", "domains": ["genomics", "organisms", "agriculture"], "homepage_url": "https://www.araport.org/", "id": "araport", "last_modified_date": "2026-06-18T00:00:00Z", "layout": "resource_detail", "license": {"id": "", "label": "Not specified"}, "name": "Araport (Arabidopsis Information Portal)", "products": [{"category": "DataSource", "description": "The Araport11 reannotation of the Arabidopsis thaliana Col-0 reference genome (gene models, transcripts, and non-coding RNAs), distributed through the JGI Phytozome plant genomics portal.", "format": "gff", "id": "araport.araport11", "name": "Araport11 Genome Annotation (Phytozome)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "araport"}], "product_url": "https://phytozome-next.jgi.doe.gov/info/Athaliana_Araport11"}, {"category": "GraphicalInterface", "description": "ThaleMine, the InterMine-based data warehouse originally developed for Araport, now hosted at the Bio-Analytic Resource for Plant Biology (BAR), serving Araport11-based gene and functional data.", "format": "http", "id": "araport.thalemine", "name": "ThaleMine (BAR)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "araport"}], "product_url": "https://bar.utoronto.ca/thalemine/"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 548527, "product_url": "https://skm.nib.si/downloads/pss/public/sbml"}, {"category": "GraphProduct", "description": "PSS model (v1.0.0, October 2023) in DOT Language format compatible with Graphviz. The live/current DOT export endpoint was retired upstream; this points to the latest published versioned DOT export.", "format": "dot", "id": "skm.pss.live.dot", "name": "PSS Download (DOT, v1.0.0)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 405988, "product_url": "https://skm.nib.si/downloads/pss-version/v1.0.0/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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 2732107, "product_url": "https://skm.nib.si/downloads/ckn/v2-2023.06/edges"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 885747, "product_url": "https://skm.nib.si/downloads/ckn/v2-2023.06/nodes"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 318666, "product_url": "https://skm.nib.si/downloads/ckn/v1-2018.06/edges"}, {"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": [{"relation_type": "prov:hadPrimarySource", "source": "skm"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "kegg"}, {"relation_type": "prov:hadPrimarySource", "source": "biocyc"}, {"relation_type": "prov:hadPrimarySource", "source": "metacyc"}, {"relation_type": "prov:hadPrimarySource", "source": "tair"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "po"}, {"relation_type": "prov:hadPrimarySource", "source": "araport"}, {"relation_type": "prov:hadPrimarySource", "source": "gomapman"}], "product_file_size": 702407, "product_url": "https://skm.nib.si/downloads/ckn/v1-2018.06/nodes"}], "publications": [{"authors": ["Cheng CY", "Krishnakumar V", "Chan AP", "Thibaud-Nissen F", "Schobel S", "Town CD"], "doi": "10.1111/tpj.13415", "id": "https://www.ncbi.nlm.nih.gov/pubmed/27862469", "journal": "Plant J", "preferred": true, "title": "Araport11: a complete reannotation of the Arabidopsis thaliana reference genome", "year": "2017"}]}