Editing Pathway/Genome Databases

SRI InternationalBioinformaticsPathway Tools Paradigm

Separate database from user interface

Navigator provides one view of the DB

Editors provide an alternative view of the DB

Reuse information whenever possible! Compounds are the building blocks of reactions Reactions are the building blocks of compounds A PGDB should not describe the same biological entity more

than once

SRI InternationalBioinformaticsList of Editors

Gene EditorTranscription Unit EditorProtein EditorReaction EditorChemical Compound EditorPathway EditorPublication EditorMetabolic Overview Editor

SRI InternationalBioinformaticsInvoking the Editors

Right-Click on an Object Handle Edit Show

SRI InternationalBioinformaticsSaving Changes

The user must save changes explicitly with Save KB

To discard changes made since last save Special -> KB -> Revert KB

SRI InternationalBioinformaticsCreating Links with External

Databases

Object CorrespondenceCreating links to a pathway/genome dbCreating links from a pathway/genome db

SRI InternationalBioinformaticsOcelot Concurrency Control I

Simultaneous updatesOptimistic concurrency control

optimistic: assumes conflicts will be infrequent allows users to make changes at will checks for conflicts at times of saving

SRI InternationalBioinformaticsOcelot Concurrency Control II

Save KB operation 1. Ocelot checks whether any changes made by user conflict

with changes that may have been saved recently by others 2. No conflicts found => save to Oracle

Saves to current organism KBUnsaved KB indicator (*)

SRI InternationalBioinformaticsOcelot Concurrency Control III

Revert KB operationRefresh KB operation

automatically at 2:00 am if the user does not have any unsaved updates in their wokspace

SRI InternationalBioinformaticsEditing rules: Support Policy

Do not alter KB schema e.g. do not add or remove classes or slots

Do not modify the E. coli or MetaCyc datasets

SRI InternationalBioinformaticsThe Special Menu: KB

Show KB ModificationsRevert KBRefresh KBReconnect to OracleCheckpoint KBRestore CheckpointDelete KB

SRI InternationalBioinformaticsConstraint Checking

General rules that constrain the valid relationships among instances

Constraints are checked when new facts are asserted to assure that the KB remains logically consistent

Constraints on slots: Domain violation checks to make sure they should be in instances of that

class Range violation :

value type value cardinality

Inverse Cardinality Lisp-predicate

SRI InternationalBioinformaticsConsistency Checking

Removes newlines from names Converts < to | in string citations Check isozyme sequence similarity Fix references from polypeptides to genes Changes compound names to ids in a variety of slots Matches physiological regulators to other regulators Cross-references compounds to reactions Checks pathways predecessors/reactions/subs Check reactions Check compound structures Calculates sub- and super-pathways Finds missing sub-pathways links Verifies chromosome components and positions