ProMeTraWiki/PathwayMap

ProMeTra PathwayMaps

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. Users can add other graphical elements such as lines, shapes, and text to SVG PathwayMaps, only the specially labeled elements will be modified by ProMeTra.

File:ProMeTraWiki$$PathwayMap$pathway.png

Annotate SVG elements using Inkscape

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:ProMeTraWiki$$PathwayMap$inkscape.png

• Select a rectangular image element (e.g. the Glycine rectangle as in the example)

 File:ProMeTraWiki$$PathwayMap$glycine.png

• Select XML Editor from the Edit Menu ...

 File:ProMeTraWiki$$PathwayMap$xmleditor.png

• Add the Metabolite attribute and set the value to e.g. C00037

 File:ProMeTraWiki$$PathwayMap$xml.png

Annotate SVG elements using a text Editor

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:ProMeTraWiki$$PathwayMap$editor.png

Data connection

ProMeTra will be able to identify the attributes Protein, Metabolite or Transcript in your rectangular SVG elements and use the associated identifiers (e.g. C00037) to connect to experimental datasets that users upload or obtain from MeltDB, ProSE or Emma2 via WebServices.