- New compounds, reactions, enzymes and pathways
- Addition of compound structures to existing compounds that previously lacked them
- Fixes to errors and other improvements to existing compound structures
- Updates to reaction equations to fix errors and so that they balance and are correctly protonated
- Updates to pathways to fix errors and incorporate new knowledge
- Updates and addition of EC Numbers, names, literature citations, links to other databases, and textual summaries.
Why should I use this tool?Aside from the obvious benefits of fixing errors in your PGDB, there are several reasons why it is a good idea to propagate MetaCyc updates with every new release.
- It will allow more of your reactions to balance, improving atom mapping and Route Search computations.
- It will greatly improve the process and results of building metabolic models via flux-balance analysis -- unbalanced reactions are automatically excluded from metabolic models by MetaFlux.
- It will facilitate apples-to-apples comparisons with other PGDBs built with (or updated to) the latest version of MetaCyc.
What does this tool do?Every compound, reaction and pathway in your PGDB is compared with the corresponding object in MetaCyc. Where there are differences between the two, the differences are classified according to type. The user is presented with a dialog that itemizes each difference by type and offers the opportunity to examine them and propagate the MetaCyc data either individually or en masse. If there is no corresponding object in MetaCyc, a search is conducted for a suitable object to merge it with, if any, and this option too is presented to the user.
|A dialog summarizing the differences between a PGDB and MetaCyc. In general, clicking on a Propagate All button applies all the MetaCyc updates for that category. Clicking on a Select for Update button opens a detail dialog, like the one shown below.|
|A detail dialog for compound structures, allowing the user to select a subset to be updated.|