Transcript Introduction - Bioinformatics Research Group at SRI International

Editing Pathway/Genome
Databases
Part II: Proteins, Genes, Transcription
Units
List of Editors
 Chemical
Compound Editor
 Reaction Editor
 Pathway Editor
 Protein Editor
 Gene Editor
 Intron Editor
 Transcription Unit Editor
 Publication Editor
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Invoking the Editors
 Right-Click
Edit
 Notes
 Show
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on an Object Handle
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Protein Editor
 Evidence
Codes
 Classification
 Synonyms
 Citations
 Protein Features
 Database Links
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Gene Editor
 Position
 Classification
 Synonyms
 Database
 Citations
Links
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Transcription Unit Editor
 Name
 List
of Genes
 Evidence Codes
 Name for Promoter (p1, p2,…)
 Position of Transcription Start Site
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Publication Editor
 Title
 Authors
 PubMed
ID
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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
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if the user does not have any unsaved updates in their wokspace
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