Publicly available downloads
Note that these downloads are not static, and are updated in real-time. Static versions are available below.
| Format | Link | Description |
|---|---|---|
| SBGN-ML | download | Systems Biology Graphical Notation XML format |
| SBML | download | Systems Biology Markup Language XML format |
| DOT Language | download | Compatible with Graphviz applications (graphviz.org) |
| SIF/LGL (Original) | download | Simple interaction format. Reactions are represented as nodes (as in PSS Explorer and database schema). Compatible with Cytoscape (cytoscape.org), among others. |
| download | Accompanying node annotation file. | |
| SIF/LGL (Projection) | download | Simple interaction format. Reactions are collapsed to edges. Compatible with Cytoscape (cytoscape.org). |
| download | Accompanying node annotation file. | |
| SIF/LGL (DiNAR) | download | Simple interaction format. Reactions are collapsed to edges, FunctionalClusters are expanded to arabidopsis identifiers. Compatible with DiNAR (bio.tools/dinar) and Cytoscape (cytoscape.org). |
| download | Accompanying node annotation file. | |
| boolnet | download | Boolean network format compatible with BoolDog (nib-si.github.io/BoolDoG), pyboolnet (pyboolnet.readthedocs.io), and BoolNet (cran.r-project.org/package=BoolNet), among others. |
| download | Accompanying node annotation file. |
Note that these downloads are static, and are not updated in real-time.
October 2023 (PSS v1.0.0)
| Format | Link | Description |
|---|---|---|
| SBGN-ML | download | Systems Biology Graphical Notation XML format |
| SBML | download | Systems Biology Markup Language XML format |
| DOT Language | download | Compatible with Graphviz applications (graphviz.org) |
| SIF/LGL (Original) | download | Simple interaction format. Reactions are represented as nodes (as in PSS Explorer and database schema). Compatible with Cytoscape (cytoscape.org), among others. |
| download | Accompanying node annotation file. | |
| SIF/LGL (Projection) | download | Simple interaction format. Reactions are collapsed to edges. Compatible with Cytoscape (cytoscape.org). |
| download | Accompanying node annotation file. | |
| SIF/LGL (DiNAR) | download | Simple interaction format. Reactions are collapsed to edges, FunctionalClusters are expanded to arabidopsis identifiers. Compatible with DiNAR (bio.tools/dinar) and Cytoscape (cytoscape.org). |
| download | Accompanying node annotation file. | |
| boolnet | download | Boolean network format compatible with BoolDog (nib-si.github.io/BoolDoG), pyboolnet (pyboolnet.readthedocs.io), and BoolNet (cran.r-project.org/package=BoolNet), among others. |
| download | Accompanying node annotation file. |
June 2018 (PIS v2)
If you use this version, please additionally cite:
Download PIS-v2
Živa Ramšak, Anna Coll, Tjaša Stare, Oren Tzfadia, Špela Baebler, Yves Van de Peer, Kristina Gruden.
(2018). Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato.
Plant Physiology, Volume 178, Issue 1.
doi:10.1104/pp.18.00450
.
June 2023 (CKN v2)
| Format | Link | Description |
|---|---|---|
| SIF/LGL | download | Simple interaction format of reaction network compatible with DiNAR (bio.tools/dinar) and Cytoscape (cytoscape.org), among others. |
| download | Accompanying node annotation file |
June 2018 (CKN v1)
If you use this version, please additionally cite:
Živa Ramšak, Anna Coll, Tjaša Stare, Oren Tzfadia, Špela Baebler, Yves Van de Peer, Kristina Gruden.
(2018). Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato.
Plant Physiology, Volume 178, Issue 1.
doi:10.1104/pp.18.00450
.
| Format | Link | Description |
|---|---|---|
| SIF/LGL | download | Simple interaction format of reaction network compatible with DiNAR (bio.tools/dinar) and Cytoscape (cytoscape.org), among others. |
| download | Accompanying node annotation file |