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Editing Pathway/Genome Databases

Editing Pathway/Genome Databases. Pathway 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

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Editing Pathway/Genome Databases

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  1. Editing Pathway/Genome Databases

  2. Pathway 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

  3. List of Editors • Gene Editor • Transcription Unit Editor • Protein Editor • Reaction Editor • Chemical Compound Editor • Pathway Editor • Publication Editor • Metabolic Overview Editor

  4. Invoking the Editors • Right-Click on an Object Handle • Edit • Show

  5. Saving Changes • The user must save changes explicitly with Save KB • To discard changes made since last save • Special -> KB -> Revert KB

  6. Creating Links with External Databases • Object Correspondence • Creating links to a pathway/genome db • Creating links from a pathway/genome db

  7. Ocelot Concurrency Control I • Simultaneous updates • Optimistic concurrency control • optimistic: assumes conflicts will be infrequent • allows users to make changes at will • checks for conflicts at times of saving

  8. Ocelot 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 KB • Unsaved KB indicator (*)

  9. Ocelot Concurrency Control III • Revert KB operation • Refresh KB operation • automatically at 2:00 am • if the user does not have any unsaved updates in their wokspace

  10. Editing 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

  11. The Special Menu: KB • Show KB Modifications • Revert KB • Refresh KB • Reconnect to Oracle • Checkpoint KB • Restore Checkpoint • Delete KB

  12. Constraint 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

  13. Consistency 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

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