Ask Pathway Tools logo   Pathway Tools Question & Answer forum for SRI's Pathway Tools

Ask Your Question

How to propagate MetaCyc data updates in Patway Tools 19.5

asked 2016-02-11 08:13:05 -0600

rpelicae gravatar image


I include the link ( to the previous question/answer which was made with an anonymous account.

I have downloaded a BioCyc Tier 3 PGDB in Pathway Tools from the PGDB Registry. This PGDB was originally made with Pathologic using Pathway Tools 18.5 and MetaCyc 18.5.

I would like to use this PGDB for metabolic modeling purposes using MetaFlux, however to allow proper manual curation and according to this blog ( I'd need to propagate updates in MetaCyc to my PGDB. I have already upgraded the PGDB schema to the new Pathway Tools 19.5, however according to the manual this does not include the propagation of MetaCyc updates.

I have already done some manual curation (e.g. pruning false-positive pathways, ...) which I would like to keep, but no major Reaction or Pathway edits (although I may want to do this in the future).

How could I make the 'Propagate MetaCyc Data Updates' available in my version of Pathway Tools?

edit retag flag offensive close merge delete

2 Answers

Sort by ยป oldest newest most voted

answered 2016-02-12 04:53:24 -0600

rpelicae gravatar image

This is actually what I do, when I open Pathway Tools I select my PGDB in the Organism Summary Page. This opens me the Single Database Page of the PGDB I selected. Then I invoke the Tools menu in the Navigator and I don't see the 'Propagate MetaCyc Data Updates' in the menu. It doesn't seem disabled, it's just not there.

I'm on Pathway Tools version 19.5 on Mac OSX 10.9.5

Any ideas? Is there a way to run this tool on the command-line?

edit flag offensive delete link more


There maybe a bug in the Mac runtime. I will investigate why that menu option is not appearing on the Mac.

ptools-admin gravatar imageptools-admin ( 2016-02-12 15:11:57 -0600 )edit

I installed Pathway Tools 19.5 on a Ubuntu VM and the 'Propagate MetaCyc Data Updates' is also not available in the Linux distribution. However, installing the 19.0 version on Ubuntu did lead to a Tools menu where I could find this option and succesfully propagate MetaCyc updates to a PGDB.

rpelicae gravatar imagerpelicae ( 2016-02-15 07:19:25 -0600 )edit

Any work around for this problem on the 19.5 version for Mac? Possibly running the tool on the command line?

rpelicae gravatar imagerpelicae ( 2016-02-15 07:20:47 -0600 )edit

Would it be possible to install MetaCyc version 19.5 in Pathway Tools 19.0? So as to only propagate MetaCyc changes to current PGDB's in ptools-local/pgdbs but keep the current 19.0 tools, while waiting for a fix.

rpelicae gravatar imagerpelicae ( 2016-02-15 07:45:59 -0600 )edit

We've just released a patch to re-enable the Propagate menu option. Restart Pathway Tools and it should download the patch.

ptools-admin gravatar imageptools-admin ( 2016-02-16 12:39:28 -0600 )edit

answered 2016-02-11 11:40:09 -0600

ptools-admin gravatar image

Most commands apply to a specific PGDB. This command in particular propagates from MetaCyc to your target (selected) organism. So you must have your target organism selected before running this command. If you have MetaCyc as your selected organism, the menu item will be disabled. Try selecting your organism, then selecting the menu command.

edit flag offensive delete link more

Your Answer

Please start posting anonymously - your entry will be published after you log in or create a new account.

Add Answer

Question Tools

1 follower


Asked: 2016-02-11 08:13:05 -0600

Seen: 6,400 times

Last updated: Feb 12 '16