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Validation Topics

  • List of current rules: [[ValidationRules]]
  • Currently, libSBGN rules are written in Schematron. See [[SchematronHowto]]

Syntax for @see Entries

Validation rules in libSBGN should be tagged with a "see" attribute that refers to an SBGN specification that points to a validation rule.

sbgn-(SBGN_LANG_ABBREV)-L(LEVEL_NUM)V(VERSION_NUM)-(SPEC_ENTRY)#(BULLET_NUM)

  • SBGN_LANG_ABBREV - pd, er, af
  • LEVEL_NUM - Digit
  • VERSION_NUM - Digit or number with decimal
  • SPEC_ENTRY - Digits separated by periods indicating the section where the rule is described.
  • BULLET_NUM - Digit indicating the bulleted item describing a rule.

Example: sbgn-pd-L1V1.3-3.5.2.2#1

Rule Categories (Roles)

Rules are tagged using the following categories to denote severity and status.

  • error - Failure to pass this rule type results in invalidation
  • warning - Point to recommendations; failure to meet these recommendations does not result in invalidation.
  • unimplemented - Represent "stubs" for rules that remain to be implemented.
  • untestable - Rules that are that are untestable. Such rules may result from the need to have expert knowledge of a biological system to carry out the validation.
    • Example: If more than one set of stoichiometries can be applied to the flux arcs of the process then the stoichiometry of the flux arcs must be displayed. (sbgn-pd-L1V1.3-3.5.2.1#8)

Error Test Files

Creators of error test files should create both the correct and incorrect cases.

Naming Convention

Test files containing errors are named using the following components:

ruleId-assertionId_pass/fail-errorCount_testCount (

  • Error code for rule
  • If multiple assertions are made then which one is being tested (in the order they appear in the ruleset).
  • pass/fail, whether the file passes or fail the rule followed by an error count of any existing errors.
  • Use testCount if multiple files test the same rule.
  • If multiple rules are broken, the name should take the ruleId of the first rule broken.

Example: pd10102-3_fail-1_1.sbgn

The file failed rule pd10102 assertion 3 with 1 error. If more than one file tested this rule, then the final 1 would uniquely identify this file.