New versions of Pathway Tools are released every six months, with
the current version being 18.5. Included in each new release is an
updated version of the MetaCyc database. The curators at SRI are
constantly working to improve MetaCyc, both adding new information,
and fixing errors in the existing data. Here are some of the kinds of
changes you can expect to see with each new release:
- 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.
Any new PGDB you create will have its reactions, pathways and metabolites imported from the most recent version of MetaCyc
and therefore benefit from all the latest changes. But what about your
old PGDBs? If they were created with an older version of MetaCyc,
then more and more of their information will become outdated over time. When you open an
old PGDB in a new version of Pathway Tools, you will be asked to
upgrade it. Upgrading applies schema changes that are
necessary in order for the PGDB to be able to operate with the new
software, but it will not incorporate the MetaCyc data updates. To
incorporate MetaCyc updates into your PGDB, you must invoke the
Tools →
Propagate MetaCyc Data Updates command for each of your PGDBs.
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.
