Conference call 4/23/2008

Attendees : Ion, Harish, Jim, Anu.

Topic : MIRIAM/Parameter annotations, etc.

MIRIAM Annotations

• Presently, 'Add annotation' shows Creator, Date, Identifier options for all annotatable elements, it show only the required option for each element. For example, for species, reactions, the Creator or Date options are irrelevant and should be disabled or not displayed, etc.
• Harish to provide a list of all MIRIAM annotatable elements and the relevant options for each

Request for annotations/SBO terms in Parameters

• 2 additional fields (columns in Parameter table) in KineticParameters^? to accomodate Annotations and SBO terms
• Use SBO terms similar to existing 'ROLES' in KineticParameters^??
  • for Mass Action/Henri-Michaelas-Menten kinetics that have SBO terms, return the appropriate term, else return null?
• Should Annotations/SBO be exposed to user/editable?
  • example: SBO term for Mass Action kinetics/H-M-M Kinetics not editable, but others without known SBO term can be?

Error checking for GO terms?

Other miscellaneous (implementation) notes

• Change all 'Annotation' fields in VCell elements (objects) - biomodel, model, simulationContext, reactionStep, etc., etc. to 'Notes' and introduce an 'annotation' field for formal MIRIAM annotations (to be in sync with SBML).