@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 THIS IS UNPUBLISHED PROPRIETARY SOURCE CODE OF Agfa-Gevaert Group.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.
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;
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
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];
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;
rdfs:subClassOf [
a owl:Restriction; owl:onProperty time:after; owl:allValuesFrom mic:BacterialCulturing], [
a owl:Restriction; owl:onProperty event:whereinEvaluated; owl:allValuesFrom mic:BacteriaCultured], [
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].
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], [
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: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].
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;
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]].
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].