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then more and more of their information will become outdated over time.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.
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. |
Why does this tool not run automatically when I upgrade my
PGDB?
There are two possible reasons why an object might be different
between your PGDB and MetaCyc: either the object has been updated in
MetaCyc, or it has been updated by you in your PGDB. There are two
possible reasons why an object might exist in your PGDB but not in
MetaCyc: either it has been created by you, or it has been deleted (or
merged with another object) in MetaCyc. The software
cannot distinguish between these cases, and we do not want to risk
overwriting any manual curation you might have done. Thus, even when
using this tool, changes are not propagated automatically -- the user
must approve them (although it is very easy to approve large classes
of changes with one click). Because of the manual oversight required,
we cannot include this process in the automated upgrade operation.
Will this tool bring in new compounds, reactions and pathways from
MetaCyc?
No new pathways will be imported into your PGDB from MetaCyc. If you
would like that to happen, invoke the Pathologic Refine → Rescore
Pathways command instead (or, preferably, as well). The only new
compounds and reactions that will be imported into your PGDB by this
tool will be those belonging to updated pathways and reactions.
How can I get more information?
Operation of this tool is described in more detail in the Pathway
Tools User Guide, Section 7.10 Updating a PGDB to Incorporate Updates
from MetaCyc.
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