Download Introduction - Bioinformatics Research Group at SRI International

Editing Pathway/Genome
Databases
Pathway Tools Paradigm
 Separate
database from user interface
 Navigator
 Editors
 Reuse
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provides one view of the DB
provide an alternative view of the DB
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
List of Editors
 Gene
Editor
 Transcription Unit Editor
 Protein Editor
 Reaction Editor
 Chemical Compound Editor
 Pathway Editor
 Publication Editor
 Metabolic Overview Editor
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Invoking the Editors
 Right-Click
Edit
 Show

on an Object Handle
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Saving Changes
 The
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user must save changes explicitly with Save
KB
 To
discard changes made since last save
 Special -> KB -> Revert KB
Creating Links with External
Databases
 Object
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Correspondence
 Creating links to a pathway/genome db
 Creating links from a pathway/genome db
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
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Ocelot Concurrency Control II
 Save
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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 (*)
Ocelot Concurrency Control III
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 Revert
KB operation
 Refresh KB operation
 automatically at 2:00 am

if the user does not have any unsaved updates in their wokspace
Editing rules: Support Policy
 Do
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not alter KB schema
 e.g. do not add or remove classes or slots
 Do not modify the E. coli or MetaCyc datasets
The Special Menu: KB
 Show
KB Modifications
 Revert KB
 Refresh KB
 Reconnect to Oracle
 Checkpoint KB
 Restore Checkpoint
 Delete KB
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Constraint Checking
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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 :
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
value type
value cardinality
Inverse
Cardinality
Lisp-predicate
Consistency Checking
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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