Molecular biology domain

The Molecular biology domain specifies ontology in the molecular biology domain. There are two versions.

The Molecular biology domain version 1

Detection: The FiniteSatUSE tool detects a finite satisfiability problem.

Identification: The identification component identifies three cycles: cycle 1, cycle 2 and cycle 3.

Pattern: The problem corresponds to the  Multiplicity Hierarchy Cycle Pattern.

The Molecular biology domain version 2 repairs the identified cycles 12 and 3 by relaxation of the cardinality constraint on  the Reaction side of the substrate association from 1..* to 0..*.

Detection: The FiniteSatUSE tool still detects a finite satisfiability problem

Identification: The identification component fails.

Explanation: The finite satisfiability problem is caused by a critical set of GS paths, which is marked in the class diagram here. The identification component fails because the finite satisfiability problem is caused by GS constraints. The paper Finite Satisfiability of UML Class Diagrams with Constrained Class Hierarchy introduces critical sets of GS paths as an identification structure for finite satisfiability problems that are caused by GS constraints. Implementation  Is Underway.

Pattern: The problem is explained in to the disjoint pattern.

Running the FiniteSatUSE tool on the Molecular biology domain version 1

USE fileGenom Domain
Detection resultDetection:
Problem creation time: 26 ms.
Problem solving time: 23 ms.

The model is not finitly satisfiable

Detection execution time: 48 ms.

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Overall execution time: 67 ms.
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Identification resultCritical cycle alert!
assoc_catafunctional -> CatalyzedReaction -> Reaction -> assoc_reactionchem -> Chemical -> Molecule -> MacroMolecule -> Protein -> FunctionalProtein -> Enzyme -> assoc_catafunctional

The involved constraints in the cycle are:
Association reactionchem
Minimum multiplicity constraint 1.0 next to Reaction and maximum multiplicity constraint 1.0 next to Chemical
Association catafunctional
Minimum multiplicity constraint 2.0 next to Enzyme and maximum multiplicity constraint 1.0 next to CatalyzedReaction

Class Hierarchies:
Super: CatalyzedReaction, Sub: Reaction

Class Hierarchies:
Super: Chemical, Sub: Molecule

Class Hierarchies:
Super: Molecule, Sub: MacroMolecule

Class Hierarchies:
Super: MacroMolecule, Sub: Protein

Class Hierarchies:
Super: Protein, Sub: FunctionalProtein

Class Hierarchies:
Super: FunctionalProtein, Sub: Enzyme

Continue looking for more cycles? (yes/no/all)
all

Critical cycle alert!
assoc_catafunctional -> CatalyzedReaction -> Reaction -> assoc_reactionchem -> Chemical -> Compound -> MacroMolecule -> Protein -> FunctionalProtein -> Enzyme -> assoc_catafunctional

The involved constraints in the cycle are:
Association reactionchem
Minimum multiplicity constraint 1.0 next to Reaction and maximum multiplicity constraint 1.0 next to Chemical
Association catafunctional
Minimum multiplicity constraint 2.0 next to Enzyme and maximum multiplicity constraint 1.0 next to CatalyzedReaction

Class Hierarchies:
Super: CatalyzedReaction, Sub: Reaction

Class Hierarchies:
Super: Chemical, Sub: Compound

Class Hierarchies:
Super: Compound, Sub: MacroMolecule

Class Hierarchies:
Super: MacroMolecule, Sub: Protein

Class Hierarchies:
Super: Protein, Sub: FunctionalProtein

Class Hierarchies:
Super: FunctionalProtein, Sub: Enzyme


Critical cycle alert!
assoc_catafunctional -> CatalyzedReaction -> Reaction -> assoc_reactionchem -> Chemical -> Molecule -> assoc_containsmacro -> MacroMolecule -> Protein -> FunctionalProtein -> Enzyme -> assoc_catafunctional

The involved constraints in the cycle are:
Association reactionchem
Minimum multiplicity constraint 1.0 next to Reaction and maximum multiplicity constraint 1.0 next to Chemical
Association containsmacro
Minimum multiplicity constraint 1.0 next to Molecule and maximum multiplicity constraint 1.0 next to MacroMolecule
Association catafunctional
Minimum multiplicity constraint 2.0 next to Enzyme and maximum multiplicity constraint 1.0 next to CatalyzedReaction

Class Hierarchies:
Super: CatalyzedReaction, Sub: Reaction

Class Hierarchies:
Super: Chemical, Sub: Molecule

Class Hierarchies:
Super: MacroMolecule, Sub: Protein

Class Hierarchies:
Super: Protein, Sub: FunctionalProtein

Class Hierarchies:
Super: FunctionalProtein, Sub: Enzyme


Identification Complete

Total identification time:3050 ms.

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Overall execution time: 3055 ms.
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Running the FiniteSatUSE tool on the Molecular biology domain version 2

USE file
Detection resultDetection:
Problem creation time:3 ms.
Problem solving time:3 ms.

The model is not finitly satisfiable

Detection execution time: 6 ms.

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Overall execution time: 10 ms.
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Identification result****************************************************************************
Identification:
Problem creation time:29 ms.
Problem solving time:23 ms.
Identification Failed: The class diagram includes elements that currently are not handled by the FiniteSatUSE’s identification method!

Total identification time:120 ms.

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Overall execution time: 10 ms.
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