1. Editing Pathway/Genome Databases
Part II: Proteins, Genes, Transcription Units

2. List of Editors Chemical Compound Editor Reaction Editor
Pathway Editor
Protein Editor
Gene Editor
Intron Editor
Transcription Unit Editor
Publication Editor

3. Invoking the Editors
Right-Click on an Object Handle
Edit
Notes
Show

4. Citations May be stored in Citations slot of objects:
As a single value (e.g., “[SMITH95]” or “[ ]” (Medline UID))
May be attached to specific slot values:
By putting citation in an annotation called CITATION
May be placed within the text in a COMMENT slot
Example text: “The subunit structure of this enzyme was determined by Jones et al. |CITS: [ ]|.”

5. Protein Editor Evidence Codes Classification Synonyms Citations
Protein Features
Database Links

6. Gene Editor
Position
Classification
Synonyms
Database Links
Citations

7. Transcription Unit Editor
Name
List of Genes
Evidence Codes
Name for Promoter (p1, p2,…)
Position of Transcription Start Site

8. Publication Editor
Title
Authors
PubMed ID

9. 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

10. 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 (*)

11. 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

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