Background

WikiPathways allows you to add references to your pathway, either to individual nodes and interactions or to the pathway as a whole. PubMed references can easily be added via PathVisio, but references from other sources such as ISBN and DOI, must be added in a semi-manual way, described here. References must be added in a structured format, and the minimum amount of information needed is an identifier and the corresponding database, or id type. The following types of references are currently supported:

Database Identifier example
PubMed PMID: 22110403
ISBN 978-1-56619-909-4 (ISBN-13) or 1-56619-909-3 (ISBN-10)
DOI 10.1201/9780203503867
URL https://en.wikipedia.org/wiki/Pentose_phosphate_pathway

These instructions use a DOI reference as an example, but the general workflow would be the same for any of the above listed reference types.

Challenge

Add a DOI literature reference for Metabolism and Molecular Physiology of Saccharomyces Cerevisiae to a pathway.

  • Download the starter pathway and open the gpml in PathVisio.
  • Double-click on the textbox in the upper-left that includes title and organism (Pathway Information area).
  • Select the Literature tab and click the New reference button.
  • Enter the following information for the DOI reference:
    • Enter the DOI (10.1201/9780203503867) in the PubMed field. (Do NOT click Query PubMed).
    • Enter the title (Metabolism and Molecular Physiology of Saccharomyces Cerevisiae) in the Title field.
    • Enter the publication year (2004) in the Year field.
    • Enter the author names (J. Richard Dickinson, Michael Schweizer) in the Authors field, separated by semicolon.
    • We will leave the Source field empty.
  • Click Ok to exit out of the Literature reference properties interface, and save the gpml.
  • Next, open the gpml in a text editor. We are going to edit the reference we just added.
  • The literature reference we added earlier will be in the Biopax section of the GPML, which is usually at the end. The format of the reference should be as follows:


  • Update the contents of the bp:DB tag from PubMed to DOI.
  • When you are done, save your GPML file.
  • Drag-and-drop the GPML file below to check if it is correct.