is a Data Source.
It is part of the BER collection.
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.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| araport.araport11 | Araport11 Genome Annotation (Phytozome) | Athaliana_Araport11 | DataSource | gff | The Araport11 reannotation of the Ara... |
| araport.thalemine | ThaleMine (BAR) | thalemine | GraphicalInterface | http | ThaleMine, the InterMine-based data w... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| skm.pss.live.sbgn | PSS Live Download (SBGN-ML) | sbgn (3.1 MB) | GraphProduct | sbgnml | had primary source | Current PSS model in Systems Biology ... |
| skm.pss.live.sbml | PSS Live Download (SBML) | sbml (535.7 KB) | GraphProduct | sbml | had primary source | Current PSS model in Systems Biology ... |
| skm.pss.live.dot | PSS Download (DOT, v1.0.0) | graphviz (396.5 KB) | GraphProduct | dot | had primary source | PSS model (v1.0.0, October 2023) in D... |
| skm.pss.live.sif.original.graph | PSS Live Download, original (SIF/LGL) | sif-edges (157.9 KB) | GraphProduct | sif | had primary source | Current PSS model in Simple Interacti... |
| skm.pss.live.sif.original.annotations | PSS Live Download, original (SIF/LGL), node annotations | sif-nodes (392.5 KB) | GraphProduct | sif | had primary source | Current PSS model in Simple Interacti... |
| skm.pss.live.sif.projection.graph | PSS Live Download, projection (SIF/LGL) | rxn-edges (247.7 KB) | GraphProduct | sif | had primary source | Current PSS model in Simple Interacti... |
| skm.pss.live.sif.projection.annotations | PSS Live Download, projection (SIF/LGL), node annotations | rxn-nodes (159.8 KB) | GraphProduct | sif | had primary source | Current PSS model in Simple Interacti... |
| skm.pss.live.sif.dinar.graph | PSS Live Download, DiNAR (SIF/LGL) | dinar-edges (353.3 KB) | GraphProduct | sif | had primary source | Current PSS model in Simple Interacti... |
| skm.pss.live.boolnet.graph | PSS Live Downloads (BoolNet) | boolnet (52.0 KB) | GraphProduct | boolnet | had primary source | Current PSS model in Boolean network ... |
| skm.pss.live.boolnet.annotations | PSS Live Downloads (BoolNet), node annotations | boolnet-annot (69.3 KB) | GraphProduct | boolnet | had primary source | Current PSS model in Boolean network ... |
| skm.ckn.v2.graph | CKN v2 (June 2023) | edges (2.6 MB) | GraphProduct | sif | had primary source | Comprehensive Knowledge Network v2 in... |
| skm.ckn.v2.annotations | CKN v2 (June 2023), node annotations | nodes (865.0 KB) | GraphProduct | sif | had primary source | Comprehensive Knowledge Network v2 in... |
| skm.ckn.v1.graph | CKN v1 (June 2018) | edges (311.2 KB) | GraphProduct | sif | had primary source | Comprehensive Knowledge Network v1 in... |
| skm.ckn.v1.annotations | CKN v1 (June 2018), node annotations | nodes (685.9 KB) | GraphProduct | sif | had primary source | Comprehensive Knowledge Network v1 in... |
Araport, the Arabidopsis Information Portal, was a J. Craig Venter Institute (JCVI) project that delivered an integrated, community-facing data warehouse and set of web applications for Arabidopsis thaliana genomics. Its flagship output was Araport11, a complete reannotation of the A. thaliana Col-0 reference genome published in 2016/2017, which updated gene models and incorporated newly characterized non-coding RNAs using deep RNA-seq evidence.
After project funding ended, the Araport web portal was sunset around 2018, and its functionality was distributed across The Arabidopsis Information Resource (TAIR, arabidopsis.org), the National Center for Genome Resources (NCGR), and the Bio-Analytic Resource for Plant Biology (BAR). Although the portal itself is inactive, the Araport11 annotation lives on as a standard reference annotation served through TAIR and JGI Phytozome, and it is the gene/locus annotation used by the Stress Knowledge Map (SKM).
Created: June 18, 2026 | Last modified: June 18, 2026