Infixowl fix

examples/infixowl_ontology_creation.py

@@ -0,0 +1,280 @@
+from rdflib import Graph, Literal, Namespace, URIRef
+from rdflib.extras.infixowl import Class, Ontology, Property, min, only, some
+
+CPR = Namespace("http://purl.org/cpr/0.75#")
+INF = Namespace("http://www.loa-cnr.it/ontologies/InformationObjects.owl#")
+EDNS = Namespace("http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#")
+DOLCE = Namespace("http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#")
+REL = Namespace("http://www.geneontology.org/owl#")
+GALEN = Namespace("http://www.co-ode.org/ontologies/galen#")
+TIME = Namespace("http://www.w3.org/2006/time#")
+CYC = Namespace("http://sw.cyc.com/2006/07/27/cyc/")
+
+
+def infixowl_example():
+    g = Graph()
+    g.bind("cpr", CPR, override=False)
+    g.bind("ro", REL, override=False)
+    g.bind("inf", INF, override=False)
+    g.bind("edns", EDNS, override=False)
+    g.bind("dol", DOLCE, override=False)
+    g.bind("time", TIME, override=False)
+    g.bind("galen", GALEN, override=False)
+
+    Class.factoryGraph = g
+    Property.factoryGraph = g
+    Ontology.factoryGraph = g
+
+    cprOntology = Ontology(URIRef("http://purl.org/cpr/owl"))  # noqa: N806
+    cprOntology.imports = [
+        URIRef("http://obo.sourceforge.net/relationship/relationship.owl"),
+        URIRef(DOLCE),
+        URIRef(EDNS),
+        URIRef("http://www.w3.org/2006/time#"),
+    ]
+    cprOntology.comment = [
+        Literal(
+            """This OWL ontology was generated by Fuxi 0.85b.dev-r107
+               (with newly added Infix OWL syntax library).  It imports the
+               OBO relationship ontology, DOLCE, and OWL time. It formally
+               defines a focused, core set of archetypes [Jung, C.]
+               replicated in various patient record terminology. This core is
+               defined in RDF and follows the normalization principles
+               of "rigorous formal ontologies" [Rector, A.]."""
+        )
+    ]
+    cprOntology.setVersion(Literal("0.75"))
+
+    # Relations
+    # represented-by
+    representationOf = Property(  # noqa: N806
+        CPR["representation-of"],
+        inverseOf=Property(CPR["represented-by"]),
+        comment=[
+            Literal(
+                """Patient records stand in the cpr:representation-of relation
+                   with patients"""
+            )
+        ],
+    )
+    representedBy = Property(  # noqa: F841, N806
+        CPR["represented-by"], inverseOf=representationOf
+    )
+    # description-of
+    descrOf = Property(  # noqa: N806
+        CPR["description-of"],
+        comment=[
+            Literal(
+                """Clinical descriptions stand in the cpr:description-of
+                   relation with various clinical phenomenon"""
+            )
+        ],
+        domain=[Class(CPR["clinical-description"])],
+    )
+    # cpr:interpreted-by
+    interpretedBy = Property(  # noqa: F841, N806
+        CPR["interpreted-by"],
+        comment=[
+            Literal(
+                """Signs and symptoms are interpreted by rational physical
+                   objects (people)"""
+            )
+        ],
+        domain=[Class(CPR["medical-sign"]) | Class(CPR["symptom"])],
+        range=[Class(CPR.person)],
+    )
+    # cpr:realized-by
+    realizedBy = Property(  # noqa: N806
+        CPR["realized-by"],
+        comment=[
+            Literal(
+                """The epistemological relation in which screening acts and
+                   the problems they realize stand to each other"""
+            )
+        ],
+        inverseOf=Property(CPR["realizes"]),
+        domain=[Class(CPR["medical-problem"])],
+        range=[Class(CPR["screening-act"])],
+    )
+    # cpr:realizes
+    realizes = Property(CPR["realizes"], inverseOf=realizedBy)  # noqa: F841
+
+    # Classes
+    # cpr:person
+    person = Class(CPR.person)
+    person.comment = [
+        Literal(
+            """A class which directly corresponds with the “Person” class in
+               both GALEN and Cyc"""
+        )
+    ]
+    person.subClassOf = [Class(EDNS["rational-physical-object"])]
+    person.equivalentClass = [Class(GALEN.Person), Class(CYC.Person)]
+
+    # cpr:patient
+    patient = Class(CPR.patient)
+    patient.comment = [
+        Literal(
+            """A class which directly corresponds with the “Patient”
+               and “MedicalPatient” classes in GALEN / Cyc"""
+        )
+    ]
+    # patient.equivalentClass = [Class(GALEN.Patient),Class(CYC.MedicalPatient)]
+    patient.subClassOf = [CPR["represented-by"] @ some @ Class(CPR["patient-record"])]
+    person += patient
+
+    # cpr:clinician
+    clinician = Class(CPR.person)
+    clinician.comment = [
+        Literal(
+            """A person who plays the clinician role (typically Nurse,
+               Physician / Doctor, etc.)"""
+        )
+    ]
+    person += clinician
+
+    # bytes
+    bytes = Class(CPR.bytes)
+    bytes.comment = [
+        Literal(
+            """The collection of physical objects which constitute a stream of
+               bytes in memory, disk, etc."""
+        )
+    ]
+    bytes.subClassOf = [DOLCE["non-agentive-physical-object"]]
+
+    # cpr:patient-record
+    patientRecord = Class(CPR["patient-record"])  # noqa: N806
+    patientRecord.comment = [
+        Literal(
+            """a class (a representational artifact [REFTERM]) depicting
+               relevant clinical information about a specific patient and is
+               primarily comprised of one or more
+               cpr:clinical-descriptions."""
+        )
+    ]
+    patientRecord.seeAlso = [URIRef("")]
+    patientRecord.subClassOf = [
+        bytes,
+        # Class(CYC.InformationBearingThing),
+        CPR["representation-of"] @ only @ patient,
+        REL.OBO_REL_has_proper_part @ some @ Class(CPR["clinical-description"]),
+    ]
+
+    # cpr:medical-problem
+    problem = Class(
+        CPR["medical-problem"],
+        subClassOf=[
+            Class(DOLCE.quality),
+            realizedBy @ only @ Class(CPR["screening-act"]),
+        ],
+    )
+    problem.comment = [
+        Literal(
+            """.. problems that clearly require the intervention of a health
+                  care professional. These include acute problems requiring
+                  hospitalization and chronic problems requiring long-term
+                  management."""
+        )
+    ]
+
+    # cpr:clinical-description
+    clinDescr = Class(CPR["clinical-description"])  # noqa: N806
+    clinDescr.disjointWith = [CPR["patient-record"]]
+    clinDescr.comment = [
+        Literal(
+            """A class which corresponds (at least syntactically) with the HL7
+               RIM Act Class, insofar as its members consist of clinical
+               recordings (representational artifacts) of natural phenomena
+               of clinical significance"""
+        )
+    ]
+    clinDescr.subClassOf = [
+        bytes,
+        # Class(CYC.InformationBearingThing),
+        DOLCE["has-quality"] @ some @ Class(TIME.TemporalEntity),
+        descrOf @ min @ Literal(1),
+    ]
+
+    # cpr:medical-sign
+    sign = Class(
+        CPR["medical-sign"],
+        subClassOf=[
+            problem,
+            Property(CPR["interpreted-by"]) @ only @ clinician,
+            Property(CPR["interpreted-by"]) @ some @ clinician,
+        ],
+        disjointWith=[CPR.symptom],
+    )
+    sign.comment = [
+        Literal(
+            """A cpr:medical-problem which are specifically interpreted by a
+               clinician. As such, this class is informally defined as an
+               objective indication of a quality typically detected by a
+               physician during a physical examination of a patient."""
+        )
+    ]
+
+    symptom = Class(
+        CPR["symptom"],
+        subClassOf=[
+            problem,
+            Property(CPR["interpreted-by"]) @ only @ patient,
+            Property(CPR["interpreted-by"]) @ some @ patient,
+        ],
+        disjointWith=[sign],
+    )
+    symptom.comment = [
+        Literal(
+            """(Medicine) any sensation or change in bodily function that is
+               experienced by a patient and is associated with a particular
+               disease."""
+        )
+    ]
+
+    # clinical-act heriarchy
+    clinicalAct = Class(  # noqa: N806
+        CPR["clinical-act"], subClassOf=[Class(EDNS.activity)]
+    )
+
+    therapy = Class(CPR["therapeutic-act"], subClassOf=[clinicalAct])
+    therapy += Class(CPR["physical-therapy"], disjointWith=[CPR["medical-therapy"]])
+    therapy += Class(
+        CPR["psychological-therapy"],
+        disjointWith=[CPR["medical-therapy"], CPR["physical-therapy"]],
+    )
+
+    medicalTherapy = Class(  # noqa: N806
+        CPR["medical-therapy"],
+        disjointWith=[CPR["physical-therapy"], CPR["psychological-therapy"]],
+    )
+    therapy += medicalTherapy
+    medicalTherapy += Class(CPR["substance-administration"])
+
+    diagnosticAct = Class(CPR["diagnostic-act"], subClassOf=[clinicalAct])  # noqa: N806
+    diagnosticAct.disjointWith = [CPR["therapeutic-act"]]
+
+    screeningAct = Class(CPR["screening-act"])  # noqa: N806
+    screeningAct += Class(CPR["laboratory-test"])
+
+    diagnosticAct += screeningAct
+
+    screeningAct += Class(
+        CPR["medical-history-screening-act"],
+        disjointWith=[CPR["clinical-examination"], CPR["laboratory-test"]],
+    )
+
+    screeningAct += Class(
+        CPR["clinical-examination"],
+        disjointWith=[CPR["laboratory-test"], CPR["medical-history-screening-act"]],
+    )
+
+    device = Class(  # noqa: F841
+        CPR["medical-device"], subClassOf=[Class(GALEN.Device)]
+    )
+
+    print(g.serialize(format="turtle"))
+
+
+if __name__ == "__main__":
+    infixowl_example()