PathwayMap
Jump to navigation
Jump to search
A PathwayMap in ProMeTra is a SVG image designed using e.g. Inkscape which additionally contains some labeled rectangles. The labeling defines which experimental data associated to entities from functional genomics (transcripts, proteins, metabolites) can be represented inside the image.
File:PathwayMap$pathway.png
To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.
- Open a SVG Pathway image in Inkscape
File:PathwayMap$inkscape.png
- Select a rectangular image element (e.g. the Glycine rectangle as in the example)
File:PathwayMap$glycine.png
- Select XML Editor from the Edit Menu ...
File:PathwayMap$xmleditor.png
- Add the 'Metabolite' attribute and set the value to e.g. C00037
File:PathwayMap$attribute.png
Media:PathwayMap$sample.svg
File:PathwayMap$xml.png
You may also edit the SVG file (XML Format) with any text editor and add the Protein, Metabolite or Transcript identifiers to the rectangle elements manually. In the following example the Transcript element for the C.glutamicum gene identified by the locus_tag cg1337 is defined and another rectangle is connected to a Metabolite (KEGG Compound C00441).
File:PathwayMap$editor.png
