propagating changed annotation and pathway information

SRI International Bioinformatics1

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

Phase 1 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 itSummary 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.

propagating changed annotation and pathway information

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