Skip to content
This repository has been archived by the owner on Jan 20, 2023. It is now read-only.

schematron_rules_pd

Jump to bottom
Travis CI User edited this page Mar 26, 2019 · 1 revision

Systems Biology Graphical Notation

###Home

###Events

###Editor Meeting Notes

###LibSBGN

###Specification Development

Clone this wiki locally

00000: sanity-check

  • Role:
  • See:
  • Diagnostics: This assertion should always fail. Timestamp: Namespace:

00001: check-id

  • Role: error
  • See:
  • Diagnostics: ID needs to be unique.

00002: check-idref

  • Role: error
  • See:
  • Diagnostics: An arc target should be a glyph defined in the diagram.

pd10101:

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class consumption must have source reference to glyph of EPN classes

pd10102: check-consumption-target-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class consumption must have target reference to port on glyph with PN classes

pd10103: check-consumption-source_and_sink-source-count-equals-1

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: The 'source and sink' glyph can be connected to at most one consumption glyph.

pd10104: check-consumption-dissociation-target-count-equals-1

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: The 'dissociation' glyph can only be connected to one consumption glyph.

pd10105: check-production-source-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class production must have source reference to port on glyph with PN classes and target reference to glyph of EPN classes

pd10106: check-production-target-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class production must have target reference to glyph of EPN classes

pd10107: check-production-source_and_sink-target-count-equals-1

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: The 'source and sink' glyph can be connected to at most one production glyph.

pd10108: check-production-association-source-count-equals-1

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: The association glyph can only be connected to one production glyph.

pd10109: check-modulation-source-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Modulation arc must have source reference to glyph of EPN classes or a logical operator

pd10110: check-modulation-target-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Modulation arc must have target reference to PN classes

pd10111: check-and_or_not-source-count-equals-1

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: 'and', 'or', and 'not' glyphs must be the source for exactly one arc.

pd10112: check-compartment-ref

  • Role: error
  • See:
  • Diagnostics: If there are compartments defined, top-level glyphs must have a compartmentRef."

pd10124: check-logic-arc-source-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class logic arc must have source reference to glyph of EPN classes, or logic gates

pd10125: check-logic-arc-target-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class logic arc must have target reference to a logical operator

pd10126: check-logic_arc-not-target-count-equals-1

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: The 'not' glyph can only be the target of one logic arc glyph.

pd10127: check-equivalence-arc-source-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class equivalence arc must have source reference to glyph of EPN classes

pd10128: check-equivalence-arc-target-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: Arc with class equivalence arc must have target reference to glyph of classes 'tag', 'submap' or 'terminal'

pd10129: state-var-unique

  • Role: error
  • See: sbgn-pd-L1V1.3-3.5.1-1
  • Diagnostics: All state variables associated with a Stateful Entity Pool Node should be unique and note duplicated within that node.

pd10130: subunit-mod-arc-source

  • Role: error
  • See:
  • Diagnostics: [NOT SURE]

pd10131: epns-must-connect

  • Role: error
  • See: sbgn-pd-L1V1.3-3.5.1-3
  • Diagnostics: EPNs should not be orphaned (i.e. they must be associated with at least one arc.)

pd10132: pns-port-count-eq-2

  • Role: error
  • See: sbgn-pd-L1V1.3-3.5.2.1-1
  • Diagnostics: All process nodes (with the exception of phenotype) must have a LHS and RHS.

pd10133: pns-arc-count-eq-2

  • Role: error
  • See: sbgn-pd-L1V1.3-3.5.2.1-2,3
  • Diagnostics: All EPNs on the LHS of a process must be unique.

pd10134: multiple-stoichiometries

  • Role: untestable
  • See: sbgn-pd-L1V1.3-3.5.2.1-8
  • Diagnostics: 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.

pd10135: undefined-unknown-stochiometry

  • Role: unimplemented
  • See: sbgn-pd-L1V1.3-3.5.2.1-7
  • Diagnostics: If the stoichiometry is undefined or unknown this should be indicated by the use of a question mark ("?").

pd10140: check-glyph-class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.5.2.1-2,3
  • Diagnostics: This 'glyph class' is not allowed in Process Description

pd10141: pns-port-count-eq-2

  • Role: error
  • See: sbgn-pd-L1V1.3-3.5.2.1-1
  • Diagnostics: All process nodes should have at least one input and at least one ouput pointing to the arcs

pd10142: check-logic-arc--class

  • Role: error
  • See: sbgn-pd-L1V1.3-3.4.1
  • Diagnostics: logic Arc must be connected to either 'OR', 'AND' or 'NOT'