1. Propagating Changed Annotation and Pathway Information

2. Revised Annotation Data
Revised annotations may contain
new genes
updated gene properties
updated functional descriptions
Curators don’t want to rebuild PGDB, don’t want to lose manual curation work
Curators may have spent a lot of time pruning out false positive pathway predictions – don’t want pathway prediction algorithm to reimport them
Curators want manual oversight over many kinds of changes

3. Incremental Pathologic Utility
Build->Update Build for Revised Annotation
reads revised annotation file (in .pf or .gbk format)
One per genetic element (required if creating new genes), OR
One file of updates for whole PGDB
compares w/ existing PGDB
presents summary of changes, GUI for applying updates
Curator can:
Apply a set of changes en masse (e.g. create all new genes)
Examine each change in a group and decide individually which to apply
Save progress and return later
Generate report of changes to import into spreadsheet

4. Updates Applied in Two Phases
Create new genes/monomers
Apply changes to slot values
Revise functional assignments
Phase 2
Rerun pathway prediction

5. Phase 1 Summary Dialog

7. Assign Selected Reactions Dialog

8. Phase 2 Rescoring Pathways
Rescore Pathways after desired annotation changes have been made
Software remembers which pathways were inferred last time
If a pathway has since been deleted, the software only considers it if there is now additional evidence for it
Summary lists:
Previously deleted pathways now w/ more evidence
Previously inferred pathways that should now be pruned
Newly inferred pathways
Pathways not in MetaCyc
For each list, curator can quickly check off pathways that should be deleted

11. Incorporating New MetaCyc Data
New version of MetaCyc
Revised pathways, reactions, compounds
New pathways
Tools->Propagate MetaCyc Data Updates
Shows differences in compounds, reactions, pathways
Curator can update all or selected for each class of difference
Does not create or delete pathways
PathoLogic->Refine->Rescore Pathways
Rescores Pathways and brings up Phase 2 dialog
May also want to re-run name matcher first

15. Notes/Caveats
Some updates only make sense in conjunction w/ others, e.g. pathway and its reactions.
If you can’t figure out what’s different, default action should be to propagate from MetaCyc.
Don’t intersperse edits from update tool w/ edits using standard editors.
Can choose to propagate from other reference PGDB instead.