@prefix dce: <http://purl.org/dc/elements/1.1/>.
@prefix foaf: <http://xmlns.com/foaf/0.1/>.
@prefix owl: <http://www.w3.org/2002/07/owl#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix skos: <http://www.w3.org/2004/02/skos/core#>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
@prefix agent: <http://eulersharp.sourceforge.net/2003/03swap/agent#>.
@prefix env: <http://eulersharp.sourceforge.net/2003/03swap/environment#>.
@prefix fos: <http://eulersharp.sourceforge.net/2003/03swap/foster#>.
@prefix event: <http://eulersharp.sourceforge.net/2003/03swap/event#>.
@prefix space: <http://eulersharp.sourceforge.net/2003/03swap/space#>.
@prefix time: <http://eulersharp.sourceforge.net/2003/03swap/time#>.
@prefix organism: <http://eulersharp.sourceforge.net/2003/03swap/organism#>.
@prefix quant: <http://eulersharp.sourceforge.net/2003/03swap/quantities#>.
@prefix bac: <http://www.agfa.com/w3c/2009/bacteria#>.
@prefix clinproc: <http://www.agfa.com/w3c/2009/clinicalProcedure#>.
@prefix clisko: <http://www.agfa.com/w3c/2009/clinicalSKOSSchemes#>.
@prefix clinspec: <http://www.agfa.com/w3c/2009/clinicalSpecimen#>.
@prefix hecaad: <http://www.agfa.com/w3c/2009/healthCareAdministration#>.
@prefix clinlabproc: <http://www.agfa.com/w3c/2009/clinicalLabProcedure#>.
@prefix abther: <http://www.agfa.com/w3c/2009/antibioticTherapy#>.
@prefix unit: <http://sweet.jpl.nasa.gov/2.3/reprSciUnits.owl#>.
@prefix screla: <http://sweet.jpl.nasa.gov/2.3/relaSci.owl#>.
@prefix units: <http://eulersharp.sourceforge.net/2003/03swap/units#>.
@prefix mic: <http://www.agfa.com/w3c/2009/microbiology#>.

<http://www.agfa.com/w3c/2009/microbiology>
	a owl:Ontology;
	dce:title """Microbiology"""@en;
	dce:creator """Hans Cools, MD; Agfa Healthcare/Belgium"""@en;
	dce:publisher """Agfa Healthcare/Belgium"""@en;
	dce:description """Formal general description of microbiology."""@en;
	dce:format """OWL Full"""@en;
	rdfs:comment """Copyright (c) 2009 Agfa-Gevaert Group. All Rights Reserved. THIS IS UNPUBLISHED PROPRIETARY SOURCE CODE OF Agfa-Gevaert Group. The copyright notice above does not evidence any actual or intended publication of such source code."""@en.

#
# CLASSES
#

mic:Microorganism
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """microorganism"""@en;
	skos:definition """Organism too small to be viewed by the unaided human eye."""@en;
	rdfs:subClassOf organism:Organism.

mic:UnicellularOrganism
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """unicellular organism"""@en;
	skos:definition """Organism consisting of a single cell."""@en;
	rdfs:subClassOf mic:Microorganism.

mic:Examining
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """microbiological examining"""@en;
	rdfs:subClassOf clinlabproc:Examining;
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "19851009"^^clisko:sct20080731DT].

mic:Examination
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """microbiological examination"""@en;
	rdfs:subClassOf clinlabproc:Examination.

mic:Culturing
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """microbial culturing"""@en;
	skos:definition """Propagation of microorganisms in special media conducive to their growth."""@en; # or of living tissue cells
	rdfs:subClassOf mic:Examining;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty time:after; owl:someValuesFrom clinspec:Collecting], [
		a owl:Restriction; owl:onProperty event:hasInput; owl:someValuesFrom clinspec:Specimen];
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "61594008"^^clisko:sct20080731DT].

mic:BacterialCulturing
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacterial culturing"""@en;
	rdfs:subClassOf mic:Culturing, [
		a owl:Restriction; owl:onProperty time:after; owl:someValuesFrom clinspec:Collecting], [
		a owl:Restriction; owl:onProperty env:hasEnvironment; owl:someValuesFrom mic:BacterialCulture], [
		a owl:Restriction; owl:onProperty event:hasInput; owl:allValuesFrom clinspec:Specimen], [
		a owl:Restriction; owl:onProperty event:hasOutput; owl:allValuesFrom mic:BacteriaCultured];
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "104178000"^^clisko:sct20080731DT].

mic:BacterialCulture
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacterial culture"""@en;
	skos:definition """Medium to grow bacteria."""@en;
	rdfs:subClassOf clinproc:Substance, env:Environment.

mic:AgarCulture
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:subClassOf mic:BacterialCulture.

mic:LiquidCulture
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:subClassOf mic:BacterialCulture.

mic:BacteriumRole
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	skos:definition """Role a bacterium can play"""@en;
	rdfs:subClassOf agent:Role.

mic:BacteriaCultured # identification, measurement of growth: concentration, count
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacteria cultured"""@en;
	skos:definition """Bacteria multiplicated in culture."""@en;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty event:outputOf; owl:someValuesFrom mic:BacterialCulturing], [
		a owl:Restriction; owl:onProperty space:contains; owl:someValuesFrom bac:BacterialColony]; # also bac:Bacterium by chain space:contains-foaf:member
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "54082009"^^clisko:sct20080731DT].

mic:CultureEvaluating
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """evaluating cultured bacteria"""@en;
	#skos:definition """."""@en;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty time:after; owl:allValuesFrom mic:BacterialCulturing], [
		a owl:Restriction; owl:onProperty event:whereinEvaluated; owl:allValuesFrom mic:BacteriaCultured], [ # bac:BacterialColony
		a owl:Restriction; owl:onProperty event:hasOutput; owl:allValuesFrom mic:CultureEvaluation].

mic:CultureEvaluation
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacteria culture evaluation"""@en;
	skos:definition """Outcome of evaluating cultured bacteria."""@en;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty event:outputOf; owl:someValuesFrom mic:CultureEvaluating], [
		a owl:Restriction; owl:onProperty event:hasObject; owl:allValuesFrom bac:BacterialColony]. # taxon + quantifier

mic:NeisseriaMeningitidisCulturing
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """neisseria meningitidis culturing"""@en;
	rdfs:subClassOf mic:BacterialCulturing;
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "122387006"^^clisko:sct20080731DT].
	
mic:NeisseriaMeningitidisCultured
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:subClassOf mic:BacteriaCultured;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty event:outputOf; owl:allValuesFrom mic:NeisseriaMeningitidisCulturing], [
		a owl:Restriction; owl:onProperty event:outputOf; owl:minCardinality """1"""^^xsd:nonNegativeInteger].
    
mic:EColiCulturing
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """Escherichia coli culturing"""@en;
	rdfs:subClassOf mic:BacterialCulturing.

mic:EColiCultured
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """E. coli cultured"""@en;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty event:outputOf; owl:allValuesFrom mic:EColiCulturing].

mic:BacterialStrain
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacterial strain"""@en;
	skos:definition """
#strain is "a population of organisms that descends from a single organism or pure culture isolate. Strains within a species may differ slightly from one another in many ways.
#A group of organisms of the same species, having distinctive characteristics but not usually considered a separate breed or variety"""@en.

mic:BacterialStrainTyping
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacterial strain typing"""@en;
	rdfs:subClassOf mic:Examining;
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "76208001"^^clisko:sct20080731DT].

mic:BacterialSusceptibilityTesting
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacterial susceptibility testing"""@en;
	skos:definition """In vitro susceptibility testing of an isolated bacterial strain to antibiotics."""@en;
	rdfs:subClassOf mic:Examining, [
		a owl:Restriction; owl:onProperty time:after; owl:someValuesFrom mic:BacterialCulturing], [
		a owl:Restriction; owl:onProperty event:examiningOf; owl:someValuesFrom mic:BacteriaCultured], [ # also bac:Bacterium by chain space:contains-foaf:member
		a owl:Restriction; owl:onProperty event:examiningOf; owl:someValuesFrom [
			a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic]], [
		a owl:Restriction; owl:onProperty agent:hasAgent; owl:someValuesFrom mic:BacteriaCultured], [
		a owl:Restriction; owl:onProperty agent:hasAgent; owl:someValuesFrom [
			a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic]], [
		a owl:Restriction; owl:onProperty event:hasOutput; owl:allValuesFrom mic:Antibiogram];
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "275754001"^^clisko:sct20080731DT].

# mic:DiffusionTesting rdfs:subClassOf mic:BacterialSusceptibilityTesting -> MIC
# mic:DilutionTesting rdfs:subClassOf mic:BacterialSusceptibilityTesting -> MIC

mic:Antibiogram
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """antibiogram"""@en;
	skos:definition """Output of a bacterial susceptibility testing."""@en;
	rdfs:subClassOf mic:Examination, [
		a owl:Restriction; owl:onProperty event:outputOf; owl:someValuesFrom mic:BacterialSusceptibilityTesting].

# clearing zone diameter, MIC measuring -> measurement -> evaluating

mic:AntibiogramEvaluating
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """antibiogram evaluating"""@en;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty time:after; owl:someValuesFrom mic:BacterialSusceptibilityTesting], [
		a owl:Restriction; owl:onProperty event:whereinEvaluated; owl:someValuesFrom mic:Antibiogram], [
		a owl:Restriction; owl:onProperty event:hasOutput; owl:allValuesFrom mic:AntibiogramEvaluation];
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "82106000"^^clisko:sct20080731DT].

mic:AntibiogramEvaluation
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """antibiogram evaluation"""@en;
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty event:outputOf; owl:someValuesFrom mic:AntibiogramEvaluating], [
		a owl:Restriction; owl:onProperty event:evaluationOf; owl:someValuesFrom [
			a owl:Restriction; owl:onProperty mic:hasSusceptibilityStateFor; owl:someValuesFrom [
				a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic]]].
	
mic:BacterialSerotype
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacterial serotype"""@en;
	owl:intersectionOf (<http://purl.uniprot.org/taxonomy/2> clinlabproc:Serotype);
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty event:outputOf; owl:allValuesFrom mic:BacterialSerotyping].

mic:BacterialSerotyping
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacterial serotyping"""@en;
	skos:definition """."""@en;
	rdfs:subClassOf clinlabproc:Serotyping;
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "57906000"^^clisko:sct20080731DT].

mic:NeisseriaMeningitidisW135
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """neisseria meningitidis serogroup W135"""@en;
	skos:definition """Neisseria meningitidis serogroup W135 as identified by serotyping."""@en;
	rdfs:subClassOf mic:BacterialSerotype;
	rdfs:subClassOf bac:NeisseriaMeningitidis;
	rdfs:subClassOf <http://purl.uniprot.org/taxonomy/295996>;
	skos:exactMatch [
		a skos:Concept; skos:inScheme clisko:sct20080731; skos:notation "103483006"^^clisko:sct20080731DT].
	
mic:MinimumInhibitoryConcentration
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """minimum inhibitory concentration"""@en;
	skos:definition """Lowest concentration of an antimicrobial that will inhibit the visible growth of a test microorganism after incubation."""@en;
	rdfs:subClassOf quant:Concentration.

mic:MinimumInhibitoryConcentrationMeasurement
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """minimum inhibitory concentration measurement"""@en;
	skos:definition """Measurement of a lowest concentration of an antimicrobial that will inhibit the visible growth of a test microorganism after incubation."""@en;
	rdfs:subClassOf clinlabproc:Examination, [
		a owl:Restriction; owl:onProperty quant:measurementOf; owl:someValuesFrom mic:MinimumInhibitoryConcentration].

mic:AntibiogramReport
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """antibiogram report"""@en;
	skos:definition """Report on an antibiogram of bacteria."""@en; # from a specimen from a patient
	rdfs:subClassOf hecaad:LaboratoryReport.
	
mic:Bacteriuria
	a rdfs:Class;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """bacteriuria"""@en;
	skos:definition """Presence of bacteria in urine, not due to contamination from urine sample collection."""@en.

mic:colonyFormingUnitsPerMilliliter
	a units:Unit, unit:ComplexUnit;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """colony-forming units per milliliter"""@en;
	skos:definition """Unit for measurement of concentration of viable number of microorganism in liquid."""@en;
	screla:hasSymbol """CFU/mL""";
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty quant:unitOf; owl:someValuesFrom [
			a owl:Restriction; owl:onProperty quant:measurementOf; owl:someValuesFrom quant:Concentration]].

mic:colonyFormingUnitsPerGram
	a units:Unit, unit:ComplexUnit;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """colony-forming units per gram"""@en;
	skos:definition """Unit for measurement of concentration of viable number of microorganism in solid."""@en;
	screla:hasSymbol """CFU/g""";
	rdfs:subClassOf [
		a owl:Restriction; owl:onProperty quant:unitOf; owl:someValuesFrom [
			a owl:Restriction; owl:onProperty quant:measurementOf; owl:someValuesFrom quant:Concentration]].

#
# PROPERTIES
#

mic:wherefromCultured
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	skos:definition """Specifying a cultured microorganism from a specimen."""@en;
	rdfs:domain clinspec:Specimen;
	rdfs:range mic:Microorganism.

mic:culturedFrom
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	skos:definition """Specifying a specimen a microorganism is cultured from."""@en;
	owl:inverseOf mic:wherefromCultured;
	rdfs:domain mic:Microorganism;
	rdfs:range clinspec:Specimen.

mic:examinationOfBacterium
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """examination of bacterium"""@en;
	skos:definition """Specifying a bacterium of an antibiogram."""@en;
	rdfs:subPropertyOf event:examinationOf;
	rdfs:domain mic:Antibiogram;
	rdfs:range bac:Bacterium.

mic:examinationOfAntibiotic
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """examination of antibiotic"""@en;
	skos:definition """Specifying an antibiotic of an antibiogram."""@en;
	rdfs:subPropertyOf event:examinationOf;
	rdfs:domain mic:Antibiogram;
	rdfs:range [a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic].

mic:hasSusceptibilityStateFor
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """has susceptibility state for"""@en;
	skos:definition """Specifying an antibiotic for which a bacterium has a susceptibility state."""@en;
	rdfs:domain bac:Bacterium;
	rdfs:range [a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic].

mic:resistantTo
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """resistant to"""@en;
	skos:definition """Specifying an antibiotic a bacterium is resistant to."""@en;
	rdfs:subPropertyOf event:resistantTo, mic:hasSusceptibilityStateFor;
	rdfs:domain bac:Bacterium;
	rdfs:range [a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic].

mic:susceptibleTo
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """susceptible to"""@en;
	skos:definition """Specifying an antibiotic a bacterium is susceptible to."""@en;
	rdfs:subPropertyOf event:susceptibleTo, mic:hasSusceptibilityStateFor;
	rdfs:domain bac:Bacterium;
	rdfs:range [a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic].

mic:intermediatelySusceptibleTo
	a owl:ObjectProperty;
	rdfs:isDefinedBy <http://www.agfa.com/w3c/2009/microbiology#>;
	rdfs:label """intermediately susceptible to"""@en;
	skos:definition """Specifying an antibiotic a bacterium is intermediately susceptible to."""@en;
	rdfs:subPropertyOf event:intermediatelySusceptibleTo, mic:hasSusceptibilityStateFor;
	rdfs:domain bac:Bacterium;
	rdfs:range [a owl:Restriction; owl:onProperty agent:playsRole; owl:someValuesFrom abther:Antibiotic].