Transcript Incremental PathoLogic

Propagating Changed Annotation and
Pathway Information
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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
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Incremental Pathologic Utility
 Build->Update
Build for Revised Annotation
 reads revised annotation file (in .pf or .gbk format)
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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
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Updates Applied in Two Phases
 Phase
1
 Create new genes/monomers
 Apply changes to slot values
 Revise functional assignments
 Phase 2
 Rerun pathway prediction
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Phase 1 Summary Dialog
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Assign Selected Reactions Dialog
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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
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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
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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.
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