Stress Knowledge Map

Supported by the ADAPT project

About PSS

The Plant Stress Signalling model (PSS) is a detailed mechanistic model of plant stress signalling, resulting from bottom-up manual curation. The majority of information in PSS originated from the model species Arabidopsis thaliana. PSS represents a basis for network and dynamical modelling of stress responses.

PSS covers the complete stress response cascade within the plant cell, including perception of abiotic stress factors (heat, drought, waterlogging), biotic stress factors (extra- and intracellular pathogens, herbivores), the signalling cascades (Ca2+, ROS, MAPKs), phytohormone synthesis and signalling, and relevant transcriptional and posttranscriptional regulation known to participate in stress signalling, and concludes in the synthesis of molecules providing tangible protection against stress. To capture the trade-offs between stress response and growth, PSS also includes main known regulators of growth (TOR) and major processes leading to growth. To evaluate potential impact on crop yields PSS contains tuberisation signalling from potato, as an example.

PSS layers

PSS is hosted as a neo4j graph database, with a dedicated schema (PSS schema) that defines the types of entities and interactions (reaction) present. To see details about the reaction types in PSS, go to Contribution guidelines | Selecting reaction type.

PSS explore options

Newt interface

Available at: Newt interface

In order to display PSS from a systems biology perspective, SKM utilizes Newt, an open source, browser based Systems Biological Graphical Notation (SBGN) editor and viewer. For more information on Newt, and for tutorial and user instructions, please see: Newt Pathway Viewer & Editor.

Within the Newt representation, the reactions grouped by biologically relevant pathways. Nodes are coloured by molecular type, and to be able to also discern the cellular compartment, node borders are coloured by compartment.

The colour legend is as below:
NEWT glyph colur legend
The glyph legend (simplified from SBGN reference guide):
SBGN glyph legend

Search result nodes are highlighted by a thick red border:

Newt highlight

Note: on entry of a new reaction, the page needs to be fully refreshed for the new reaction to appear.

PSS Explorer

Available at: PSS Explorer

The biomine-like exploration interface allows for interactive search queries of PSS, shortest path, and neighbourhood extraction.

Right clicking on a node brings up a sub-menu, including expanding node neighbours. Right clicking on the canvas brings up the option to freeze all node positions. More information on the interface is available in the side panel.

When applicable, the sub-menu of the node also contains a link to query the Arabidopsis identifiers associated with the node in KnetMiner.

Using the "Export" menu, the results of a search can be saved as a edge table, node table, or PNG.

Note: on entry of a new reaction, the page needs to be fully refreshed for the new reaction to appear.

Searching by property

Available at: Search

In the "Search" interface, users can find reactions and FunctionalClusters entered into PSS via a number of properties (such as DOI, PMID , or node identifiers).

Please note that NEWT is a client-side application, and therefore relies on your local computer capabilities. Given the relatively large size of PSS, rendering the network may take a while.