Publicly available downloads
Note that these downloads are not static, and are updated in real-time. Static versions are available below.
Use one of the following drop-downs to optionally refine your download. Refinement is only available for downloads marked with a check ().
| Format | Link | Description | |
|---|---|---|---|
| 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. | ||
| SIF/LGL (Projection) | download | Simple interaction format. Reactions are collapsed to edges. Compatible with Cytoscape (cytoscape.org). |
|
| download | Accompanying node annotation file. | ||
| SBGN-ML | download | Systems Biology Graphical Notation XML format. As a limitation of the automated export, this SBGN does not have an ideal layout, the layout is automated using Graphviz and may be improved in the future. | |
| DOT Language | download | Based on generated SGBN. Compatible with Graphviz applications (graphviz.org). | |
| SBML | download | Systems Biology Markup Language XML format. As a limitation of the automated export, this SBML does not contain equations or kinetic parameters. For work on this, see Generating dynamic large-scale systems-biology data from a knowledge graph. | |
| 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, gene level) | 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). Node annotations: For genes, use the CKN node annotations file, for all other node types, use one of the other SIF node annotation files. |
|
| download | Accompanying node annotation file. | ||
| Datadiscovery JSON | download | Custom JSON format for FAIDARE data harvesting tool, used for indexing in the FAIDARE portal. Gene level. |
Note that these downloads are static, and are not updated in real-time.
PSS v1.0.0 (October 2023)
This is the latest version of PSS.
| 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 | Node annotation file | |
| SIF/LGL (Projection) | download | Simple interaction format. Reactions are collapsed to edges. Compatible with Cytoscape (cytoscape.org). |
| download | 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). Node annotations: For genes, use the CKN node annotations file, for all other node types, use use the above SIF 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 | Node annotation file |
PIS v2 (June 2018)
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 |
We provide orthologous genes between arabidopsis and select target species. For more detailed files and information on the translation pipeline, see the GitHub repository github.com/NIB-SI/skm-translate.
| Species | Common name | Reference genome/proteome | Link |
|---|---|---|---|
| Malus domestica (mdo) | apple | Golden Delicious GDDH13 v1.1 | download |
| Prunus amygdalus, Prunus dulcis (pdul) | almond | Texas v3.0, F1 | download |
| Prunus armeniaca (parm) | apricot | Marouch n14 v1.0 | download |
| Prunus avium (pavi) | wild cherry | Tieton v2.0 | download |
| Prunus cerasifera (pcer) | cherry plum | Montmorency v1.0.a2 | download |
| Prunus persica (ppe) | peach | Lovell v2.0.a1 | download |
| Prunus sibirica (psib) | siberian apricot | F106 v1.0 | download |
| Pyrus communis (pcox) | pear | d'Anjou v2.3.a1, hap 1 | download |
| Solanum lycopersicum (sly) | tomato | Heinz 1706 ITAG 4.0 | download |
| Solanum tuberosum (stu) | potato | UniTato | download |
| Vitis vinifera (vvi) | grapevine | T2T (v5) | download |