cmem-plugin-reason 1.0.0__py3-none-any.whl

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Files changed (14) hide show
  1. cmem_plugin_reason/__init__.py +1 -0
  2. cmem_plugin_reason/doc/__init__.py +9 -0
  3. cmem_plugin_reason/doc/reason_doc.md +155 -0
  4. cmem_plugin_reason/doc/validate_doc.md +62 -0
  5. cmem_plugin_reason/file-icons--owl.svg +3 -0
  6. cmem_plugin_reason/fluent--brain-circuit-24-regular.svg +3 -0
  7. cmem_plugin_reason/plugin_reason.py +527 -0
  8. cmem_plugin_reason/plugin_validate.py +300 -0
  9. cmem_plugin_reason/robot.jar +0 -0
  10. cmem_plugin_reason/utils.py +245 -0
  11. cmem_plugin_reason-1.0.0.dist-info/LICENSE +201 -0
  12. cmem_plugin_reason-1.0.0.dist-info/METADATA +38 -0
  13. cmem_plugin_reason-1.0.0.dist-info/RECORD +14 -0
  14. cmem_plugin_reason-1.0.0.dist-info/WHEEL +4 -0
cmem_plugin_reason/__init__.py ADDED
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+ """reason - main package"""
cmem_plugin_reason/doc/__init__.py ADDED
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+ """doc"""
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+
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+ from pathlib import Path
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+
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+ with (Path(__path__[0]) / "reason_doc.md").open("r") as f:
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+ REASON_DOC = f.read()
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+
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+ with (Path(__path__[0]) / "validate_doc.md").open("r") as f:
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+ VALIDATE_DOC = f.read()
cmem_plugin_reason/doc/reason_doc.md ADDED
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+ A task performing OWL reasoning. With an OWL ontology and a data graph as input the reasoning result is written to a specified graph.
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+
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+ ## Options
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+
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+ ### Data graph IRI
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+
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+ The IRI of the input data graph. The graph IRI is selected from a list of graphs of types `di:Dataset`, `void:Dataset`
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+ and `owl:Ontology`.
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+
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+ ### Ontology graph IRI
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+
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+ The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
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+
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+ ### Output graph IRI
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+
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+ The IRI of the output graph for the reasoning result.
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+
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+ ⚠️ Existing graphs will be overwritten.
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+
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+ ### Reasoner
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+
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+ The following reasoner options are supported:
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+ - [ELK](https://code.google.com/p/elk-reasoner/) (elk)
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+ - [Expression Materializing Reasoner](http://static.javadoc.io/org.geneontology/expression-materializing-reasoner/0.1.3/org/geneontology/reasoner/ExpressionMaterializingReasoner.html) (emr)
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+ - [HermiT](http://www.hermit-reasoner.com/) (hermit)
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+ - [JFact](http://jfact.sourceforge.net/) (jfact)
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+ - [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural)
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+ - [Whelk](https://github.com/balhoff/whelk) (whelk)
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+
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+ ### Generated Axioms
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+
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+ The plugin provides the following parameters to include inferred axiom generators:
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+
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+ #### Class axiom generators
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+ - **Class inclusion (rdfs:subClassOf)**
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+ The reasoner will infer assertions about the hierarchy of classes, i.e.
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+ `SubClassOf:` statements.
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+ If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
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+ Student, Professor` holds, the reasoner will infer `Student SubClassOf: Person`.
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+
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+
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+ - **Class equivalence (owl:equivalentClass)**
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+ The reasoner will infer assertions about the equivalence of classes, i.e.
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+ `EquivalentTo:` statements.
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+ If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
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+ Student, Professor` holds, the reasoner will infer `Person EquivalentTo: Student and Professor`.
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+
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+
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+ - **Class disjointness (owl:disjointWith)**
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+ The reasoner will infer assertions about the disjointness of classes, i.e.
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+ `DisjointClasses:` statements.
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+ If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
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+ Student, Professor` holds, the reasoner will infer `DisjointClasses: Student, Professor`.
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+
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+
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+ - **Data property equivalence (owl:equivalentProperty)**
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+ The reasoner will infer axioms about the equivalence of data properties,
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+ i.e. `EquivalentProperties` statements.
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+ If there are data properties `identifier` and `enrollmentNumber`, such that `enrollmentNumber
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+ SubPropertyOf: identifier` and `identifier SubPropertyOf: enrollmentNumber` holds, the reasoner
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+ will infer `Student EquivalentProperties: identifier, enrollmentNumber`.
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+
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+
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+ - **Data property inclusion (rdfs:subPropertyOf)**
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+ The reasoner will infer axioms about the hierarchy of data properties,
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+ i.e. `SubPropertyOf:` statements.
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+ If there are data properties `identifier`, `studentIdentifier` and `enrollmentNumber`, such that
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+ `studentIdentifier SubPropertyOf: identifier` and `enrollmentNumber SubPropertyOf:
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+ studentIdentifier` holds, the reasoner will infer `enrollmentNumber SubPropertyOf: identifier`.
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+
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+
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+ #### Individual axiom generators
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+ - **Individual class assertions (rdf:type)**
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+ The reasoner will infer assertions about the classes of individuals, i.e.
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+ `Types:` statements.
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+ Assume, there are classes `Person`, `Student` and `University` as well as the property
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+ `enrolledIn`, such that `Student EquivalentTo: Person and enrolledIn some University` holds. For
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+ the individual `John` with the assertions `John Types: Person; Facts: enrolledIn
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+ LeipzigUniversity`, the reasoner will infer `John Types: Student`.
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+
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+
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+ - **Individual property assertions**
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+ The reasoner will infer assertions about the properties of individuals,
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+ i.e. `Facts:` statements.
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+ Assume, there are properties `enrolledIn` and `offers`, such that `enrolled SubPropertyChain:
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+ enrolledIn o inverse (offers)` holds. For the individuals `John`and `LeipzigUniversity` with the
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+ assertions `John Facts: enrolledIn KnowledgeRepresentation` and `LeipzigUniversity Facts: offers
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+ KnowledgeRepresentation`, the reasoner will infer `John Facts: enrolledIn LeipzigUniversity`.
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+
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+
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+ #### Object property axiom generators
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+ - **Object property equivalence (owl:equivalentProperty)**
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+ The reasoner will infer assertions about the equivalence of object
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+ properties, i.e. `EquivalentTo:` statements.
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+ If there are object properties `hasAlternativeLecture` and `hasSameTopicAs`, such that
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+ `hasAlternativeLecture Characteristics: Symmetric` and `hasSameTopicAs InverseOf:
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+ hasAlternativeLecture` holds, the reasoner will infer `EquivalentProperties: hasAlternativeLecture,
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+ hasSameTopicAs`.
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+
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+
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+ - **Object property inversion (owl:inverseOf)**
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+ The reasoner will infer axioms about the inversion about object
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+ properties, i.e. `InverseOf:` statements.
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+ If there is a object property `hasAlternativeLecture`, such that `hasAlternativeLecture
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+ Characteristics: Symmetric` holds, the reasoner will infer `hasAlternativeLecture InverseOf:
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+ hasAlternativeLecture`.
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+
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+
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+ - **Object property inclusion (rdfs:subPropertyOf)**
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+ The reasoner will infer axioms about the inclusion of object properties,
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+ i.e. `SubPropertyOf:` statements.
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+ If there are object properties `enrolledIn`, `studentOf` and `hasStudent`, such that `enrolledIn
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+ SubPropertyOf: studentOf` and `enrolledIn InverseOf: hasStudent` holds, the reasoner will infer
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+ `hasStudent SubPropertyOf: inverse (studentOf)`.
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+
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+
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+ - **Object property ranges (rdfs:range)**
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+ The reasoner will infer axioms about the ranges of object properties,
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+ i.e. `Range:` statements.
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+ If there are classes `Student` and `Lecture` as wells as object properties `hasStudent` and
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+ `enrolledIn`, such that `hasStudent Range: Student and enrolledIn some Lecture` holds, the
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+ reasoner will infer `hasStudent Range: Student`.
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+
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+
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+ - **Object property domains (rdfs:domain)**
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+ The reasoner will infer axioms about the domains of object
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+ properties, i.e. `Domain:` statements.
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+ If there are classes `Person`, `Student` and `Professor` as wells as the object property
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+ `hasRoleIn`, such that `Professor SubClassOf: Person`, `Student SubClassOf: Person` and
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+ `hasRoleIn Domain: Professor or Student` holds, the reasoner will infer `hasRoleIn Domain: Person`.
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+
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+
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+ ### Validate OWL2 profiles
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+ Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph.
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+
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+ ### Process valid OWL profiles from input
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+
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+ If enabled along with the "Validate OWL2 profiles" parameter, the valid profiles, ontology IRI and reasoner option is
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+ taken from the config port input (parameters "valid_profiles", "ontology_graph_iri" and "reasoner") and the OWL2
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+ profiles validation is not done in the plugin. The valid profiles input is a comma-separated string (e.g. "Full,DL").
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+
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+ ### Add ontology graph import to result graph
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+
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+ Add the triple `<output_graph_iri> owl:imports <ontology_graph_iri>` to the output graph.
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+
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+ ### Add result graph import to ontology graph
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+ Add the triple `<ontology_graph_iri> owl:imports <output_graph_iri>` to the ontology graph
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+
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+ ### Maximum RAM Percentage
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+
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+ Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
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+
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+ ⚠️ Setting the percentage too high may result in an out of memory error.
cmem_plugin_reason/doc/validate_doc.md ADDED
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+ A task validating the consistency of an OWL ontology and generating an explanation if inconsistencies are found.
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+ The plugin outputs the explanation as text in Markdown format on the path "markdown", the ontology IRI on the path
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+ "ontology_graph_iri", and, if enabled, the valid OWL2 profiles on the path "valid_profiles" as a comma-separated string.
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+
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+ ## Options
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+
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+ ### Ontology graph IRI
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+
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+ The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
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+
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+ ### Reasoner
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+
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+ The following reasoner options are supported:
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+ - [ELK](https://code.google.com/p/elk-reasoner/) (elk)
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+ - [Expression Materializing Reasoner](http://static.javadoc.io/org.geneontology/expression-materializing-reasoner/0.1.3/org/geneontology/reasoner/ExpressionMaterializingReasoner.html) (emr)
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+ - [HermiT](http://www.hermit-reasoner.com/) (hermit)
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+ - [JFact](http://jfact.sourceforge.net/) (jfact)
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+ - [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural)
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+ - [Whelk](https://github.com/balhoff/whelk) (whelk)
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+
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+ ### Produce output graph
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+
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+ If enabled, an explanation graph is created.
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+
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+ ### Output graph IRI
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+
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+ The IRI of the output graph for the reasoning result.
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+
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+ ⚠️ Existing graphs will be overwritten.
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+
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+ ### Write markdown explanation file
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+
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+ If enabled, an explanation markdown file is written to the project.
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+
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+ ### Output filename
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+
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+ The filename of the Markdown file with the explanation of inconsistencies.
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+
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+ ⚠️ Existing files will be overwritten.
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+
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+ ### Stop at inconsistencies
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+ Raise an error if inconsistencies are found. If enabled, the plugin does not output entities.
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+
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+ ### Validate OWL2 profiles
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+
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+ Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph.
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+
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+ ### Mode
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+ Mode _inconsistency_ generates an explanation for an inconsistent ontology.
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+ Mode _unsatisfiability_ generates explanations for many unsatisfiable classes at once.
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+
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+ ### Output entities
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+
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+ Output entities. The plugin outputs the explanation as text in Markdown format on the path "markdown", the ontology IRI
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+ on the path "ontology_graph_iri", the reasoner option on the path "reasoner", and, if enabled, the valid OWL2 profiles
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+ on the path "valid_profiles".
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+
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+ ### Maximum RAM Percentage
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+
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+ Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
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+
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+ ⚠️ Setting the percentage too high may result in an out of memory error.
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