BioPAX Plug-In

The BioPAX Import Plug-In allows to open files in the BioPAX file format which is an open standard to exchange biological pathway data. Currently, only the import of BioPAX files is supported. File export may be subject to future developments.

After installation, the Open File Dialog allows to select BioPAX files (file name suffix *.rdf, *.biopax, *.owl or *.xml). The BioPAX standard was developed in different layers. Only BioPAX layer 3 can be imported by Omix.
A BioPAX file can describe different biological entities and processes. The BioPAX plug-in does only import small molecules and biochemical reactions in combination with compartmentalization and metabolic pathways. All other possible content like proteins, RNA, genes, database and literature references etc. is omitted.

After loading the network from BioPAX file all reactions and metabolites are not drawn on the drawing area but listed in the component view (highlighted red) because, no positioning information is available for the components. You can place the individual items on the drawing area by drag and drop, you can use the layout pattern and motif stamp feature of Omix (see User Manual) and/or you can use the AutoLayout Plug-In in order to arrange the network on the drawing area.

Non-positioned network nodes available in the component view
Non-positioned network nodes available in the component view

The BioPAX Plug-In is in early development state and thus, to be considered non-stable.