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

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

Citations May be stored in Citations slot of objects: As a single value (e.g., “[SMITH95]” or “[85224678]” (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: [88345698]|.”

Protein Editor Evidence Codes Classification Synonyms Citations Protein Features Database Links

Gene Editor Position Classification Synonyms Database Links Citations

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

Publication Editor Title Authors PubMed ID

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

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 (*)

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

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

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