from rdflib import Namespace from rdflib import plugin,RDF,RDFS,URIRef,BNode,Literal,Variable from FuXi.Syntax.InfixOWL import * from rdflib.Graph import Graph 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/') XML = Namespace('http://www.w3.org/2001/04/infoset#') def main(): namespace_manager = NamespaceManager(Graph()) namespace_manager.bind('xml', CPR, override=False) namespace_manager.bind('cpr', CPR, override=False) namespace_manager.bind('ro', REL, override=False) namespace_manager.bind('inf', INF, override=False) namespace_manager.bind('edns', EDNS, override=False) namespace_manager.bind('owl', OWL_NS, override=False) namespace_manager.bind('dol', DOLCE, override=False) namespace_manager.bind('time', TIME, override=False) namespace_manager.bind('galen', GALEN, override=False) g = Graph() g.namespace_manager = namespace_manager Class.factoryGraph = g Property.factoryGraph = g Ontology.factoryGraph = g cprOntology = Ontology("http://purl.org/cpr/owl") # cprOntology.imports = ["http://obo.sourceforge.net/relationship/relationship.owl", # DOLCE, # EDNS, # "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("0.75") ##Relations #represented-by representationOf = Property(CPR['representation-of'], inverseOf=Property(CPR['represented-by']), comment=[Literal("Patient records stand in the cpr:representation-of relation with patients")]) representedBy = Property(CPR['represented-by'], inverseOf=representationOf) #description-of descrOf = Property(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(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(CPR['realized-by'], comment=[Literal("The epistemological relation in which screening acts and the problems they realize stand to each other in")], inverseOf=Property(CPR['realizes']), domain=[Class(CPR['medical-problem'])], range=[Class(CPR['screening-act'])]) ##cpr:realizes realizes = Property(CPR['realizes'], inverseOf=realizedBy) ##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']) 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']) 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(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(CPR['medical-therapy'],disjointWith=[CPR['physical-therapy'], CPR['psychological-therapy']]) therapy+=medicalTherapy medicalTherapy+=Class(CPR['substance-administration']) diagnosticAct = Class(CPR['diagnostic-act'],subClassOf=[clinicalAct]) diagnosticAct.disjointWith = [CPR['therapeutic-act']] screeningAct = Class(CPR['screening-act']) 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(CPR['medical-device'],subClassOf=[Class(GALEN.Device)]) print g.serialize(format='pretty-xml') if __name__ == '__main__': main()