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Incremental PathoLogic

Incremental PathoLogic. Motivation. 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

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Incremental PathoLogic

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  1. Incremental PathoLogic

  2. Motivation • 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 • Phase 1 • Create new genes/monomers • Apply changes to slot values • Revise functional assignments • Phase 2 • Rerun pathway prediction

  5. Phase 1 Summary Dialog

  6. Assign Selected Reactions Dialog

  7. 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

  8. Other Kinds of Incremental Updating • 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

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