Propagating Changed Annotation and Pathway Information

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

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

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

Phase 1 Summary Dialog

Assign Selected Reactions Dialog

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

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

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.