This toolset enables interaction annotation, linking interactions through identifiers to online data sources for more information, visualizing data on interactions and importing metabolic models to visualize modelling results.

PathVisio is a popular pathway editing, analysis, and visualization tool. Here is a getting started guide for new users. Pathways can be drawn in PathVisio and genes and metabolites can be annotated as described in this online tutorial . Identifier mapping databases are available for genes and metabolites which enable data mapping and provide cross-references.

To enable the same for interactions the interaction identifier mapping database and FYI plugin were developed. A tutorial to annotate interactions and obtain more information from cross-references is available here.

Multi-omics data sets can be imported and visualized on the genes and metabolites of pathways as described in this tutorial. Data for interactions can be imported as described for the genes and metabolites. Visualization of data on interactions is described in this tutorial. Data can also be visualized on SBGN-PD representations of metabolic models encoded in SBML, which as be imported as described here.

Tools Developed

The Interaction Identifier Mapping database

The interaction database enables mapping data onto interactions and provides cross-references for annotated interactions present in the database. It is based on mappings obtained from the online interaction database Rhea (http://www.rhea-db.org/home). Which provides mappings between interaction identifiers from Enzyme classification: IntEnz, MetaCyc reactions, KEGG reactions, UniPathway enzymatic reactions and chemical reactions, MACiE (Mechanism, Annotation and Classification in Enzymes), Reactome, UniProt protein entries.

Bridge File
Source Code

PathVisio plugins

FYI plugin

The FYI (FindYourInteractions) plugin suggests suitable identifiers for the interactions by querying the Rhea database using its webservice. It queries Rhea using the webservice with the ChEBI/UniProt IDs or text labels of the two nodes that the selected interaction connects. Results are shown as a clickable table, selecting one of the results automatically annotates the interaction with the selected identifier.

Can be installed using the plugins manager.
Source Code

IntViz plugin

Enables visualization of single or multiple columns of data on the interactions in a pathway using colors and colour gradients. Dynamic visualization of time series data on interactions is possible using a slider. Multiple columns of data can be visualized as bar charts on interactions.

Can be installed using the plugins manager.
Source Code

PathSBML plugin

Imports SBML models as SBGN-PD diagrams in PathVisio. SBML models can be cheked for inconsistencies. The SBML components are shown in a hierarchical graph in the SBML side panel. Models can be imported directly from the Biomodels database. A force directed layout feature has been provided for the converted SBGN-PD diagrams.

Can be installed using the plugins manager.
Source Code

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