Submitting Pathways for Incorporation into MetaCyc

We at MetaCyc would like to incorporate pathways created by other scientists into the database.

In addition, by submitting pathways to MetaCyc you increase the power of the PathoLogic metabolic-pathway prediction software. PathoLogic recognizes MetaCyc pathways in genome sequence data, and is now in use by more than 100 groups worldwide.  

If you would like to submit a pathway for inclusion in a future release of MetaCyc, please make sure that you curate the pathway following these guidelines:

• The pathway must be experimentally proven, and must be described in a published journal article

• Each pathway and enzyme must have summaries and literature citations

• Each pathway gene should have a link to a sequence database (e.g. Entrez); and a citation, if available

• Enzymes should have as much information as possible, such as optimal pH and temperature, Km values, inhibitor, activator and cofactor information, etc.

• Please include evidence codes for enzymes and pathways

• Please make sure to use the Author Crediting feature (found within the Pathway Info Editor) to add the names of the curators and their institution affiliations . This will insure that the appropriate credit for your pathway is published on the BioCyc web page.

For examples of pathways that have been curated based on these guidelines, please see

• formaldehyde oxidation VI

• ammonia oxidation I

• D-camphor degradation

How to Ensure that You and Your Organization Receive the Appropriate Credit

Pathway Tools includes an author crediting system that can attach author and organization credentials to individual pathways. We recommend that prior to creating new objects in the PGDB you should create an Organization frame for your institute and an Author frame for yourself. This way, items that you create afterwards will be associated with these frames, providing you with the credit that you deserve. This credit information would be retained upon exporting the pathways and importing them into MetaCyc. It is also possible to add credit information to older pathways that were created prior to the creation of your author frame, through the Pathway Info Editor.

Detailed instructions on how to create organization and author frames are found in the user manual, in the section "Creating author frames".

How to Send Pathways to MetaCyc

Pathways should be exported into a text file, which can be emailed to us at

The procedure for exporting a pathways is:

• Display the pathway in Pathway Tools; right click on its name and choose Edit -> Add pathway to file export list
• Repeat until you have added all pathways to be submitted
• From the file menu, choose Export  -> Selected pathways to file
• Email us the resulting text file

Please indicate if you would like your name and/or affiliation to appear on the pathway and enzyme pages.