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# `` infixowl_ontology_creation

Functions:

- `infixowl_example` –

Attributes:

- `CPR` –
- `CYC` –
- `DOLCE` –
- `EDNS` –
- `GALEN` –
- `INF` –
- `REL` –
- `TIME` –

## `` CPR `module-attribute`

    CPR = Namespace('http://purl.org/cpr/0.75#')

## `` CYC `module-attribute`

    CYC = Namespace('http://sw.cyc.com/2006/07/27/cyc/')

## `` DOLCE `module-attribute`

    DOLCE = Namespace('http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#')

## `` EDNS `module-attribute`

    EDNS = Namespace('http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#')

## `` GALEN `module-attribute`

    GALEN = Namespace('http://www.co-ode.org/ontologies/galen#')

## `` INF `module-attribute`

    INF = Namespace('http://www.loa-cnr.it/ontologies/InformationObjects.owl#')

## `` REL `module-attribute`

    REL = Namespace('http://www.geneontology.org/owl#')

## `` TIME `module-attribute`

    TIME = Namespace('http://www.w3.org/2006/time#')

## `` infixowl_example

    infixowl_example()

Source code in `examples/infixowl_ontology_creation.py`

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    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"])  # noqa: N806

        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"])  # noqa: N806

        diagnosticAct += screeningAct  # noqa: N806

        screeningAct += Class(  # noqa: N806
            CPR["medical-history-screening-act"],
            disjointWith=[CPR["clinical-examination"], CPR["laboratory-test"]],
        )

        screeningAct += Class(  # noqa: N806
            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"))