phs.ttl

# baseURI: https://linked.data.gov.au/def/phs
# imports: http://datashapes.org/dash
# imports: http://rs.tdwg.org/dwc/terms/
# imports: http://www.w3.org/ns/sosa/

@prefix : <https://linked.data.gov.au/def/phs#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix dwc: <http://rs.tdwg.org/dwc/terms/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sdo: <https://schema.org/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix sosa: <http://www.w3.org/ns/sosa/> .
@prefix vann: <http://purl.org/vocab/vann/> .
@base <https://linked.data.gov.au/def/phs> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

dcterms:Dataset
  a owl:Class ;
.
dcterms:contributor
  a owl:AnnotationProperty ;
.
dcterms:created
  a owl:AnnotationProperty ;
.
dcterms:creator
  a owl:AnnotationProperty ;
.
dcterms:hasPart
  a owl:ObjectProperty ;
.
dcterms:modified
  a owl:AnnotationProperty ;
.
dcterms:publisher
  a owl:AnnotationProperty ;
.
dcterms:source
  a owl:DatatypeProperty ;
  skos:definition "Likely the model should use dcat but as at 10-Jun-2021 the existing dcterms:dataset is being used" ;
  rdfs:range dcterms:Dataset ;
  skos:prefLabel "source" ;
.
dcterms:type
  a owl:ObjectProperty ;
  skos:prefLabel "type"@en ;
.
vann:preferredNamespacePrefix
  a owl:AnnotationProperty ;
.
dwc:coordinateUncertaintyInMeters
  a owl:DatatypeProperty ;
  rdfs:domain :ObservationLocation ;
  skos:prefLabel "co-ordinate uncertainty in meters" ;
.
dwc:decimalLatitude
  a owl:DatatypeProperty ;
  rdfs:domain :ObservationLocation ;
  skos:prefLabel "decimal latitude" ;
.
dwc:decimalLongitude
  a owl:DatatypeProperty ;
  rdfs:domain :ObservationLocation ;
  skos:prefLabel "decimal longitude" ;
.
dwc:eventID
  a owl:DatatypeProperty ;
  rdfs:domain :SurveillanceEvent ;
  skos:prefLabel "event ID" ;
.
dwc:geodeticDatum
  a owl:DatatypeProperty ;
  rdfs:domain :ObservationLocation ;
  skos:prefLabel "geodetic datum" ;
.
dwc:recordedBy
  a owl:DatatypeProperty ;
  rdfs:domain :SurveillanceEvent ;
  skos:prefLabel "recorded by" ;
  skos:definition "It is a requirement of ISPM 6 that a pest record includes the name of the individual who performed the surveillance observation. There are no formatting requirements or requirements that the name unambiguously identifies a person. Thus, a name in the form of 'Surname, Initials' is acceptable."@en ;
.
dwc:scientificName
  a owl:DatatypeProperty ;
  skos:definition "The systematic name for an organism found by a Surveillance Event, and recorded as a TaxonPresence" ;
  rdfs:domain :TaxonPresence ;
  skos:example "Erwinia amylovora" ;
  skos:prefLabel "scientific name" ;
.

:openNomenclature
  a owl:DatatypeProperty ;
  skos:definition "An annotation that may be applied to a specimen to indicate the 'reason for stopping' where an identifaction to Rank species was not performed. " ;
  rdfs:domain :TaxonPresence ;
  skos:scopeNote "Open nomenclature annotations are recorded as latin abbreviations." ;
  skos:scopeNote "In a future version of the ontology, a Vocabulary of terms, along with defintions and business rules, will be created. It is recommended to follow the open nomenclature devised by Sigovini (see link)." ;
  rdfs:seeAlso <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12594> ;
  skos:example "sp." ;
  skos:example "stet." ;
  skos:prefLabel "open nomenclature" ;
.

dwc:taxonConceptID
  a owl:DatatypeProperty ;
  skos:definition "The unique identifier for a taxon, referenced by `taxonomicReferenceSource`" ;
  rdfs:domain :TaxonPresence ;
  skos:example "`3222012`, which when paired with `https://www.gbif.org/species`, prvides a link to Erwinia amylovora, Fire Blight." ;
  skos:prefLabel "taxon concept ID" ;
.

dwc:taxonRank
  a owl:DatatypeProperty ;
  skos:definition "The taxonomic rank at which an identification was applied to a specimen" ;
  skos:scopeNote "In most cases, a 'full' identification will allow a specimen to be named to the rank of 'species'. However, in some cases this is not possible. These circumstances include a) lack of expertise by the diagnostician b) unclear nomenclature (i.e. the taxa have not been classified) c) time or importance constraints d) incomplete specimen e) incorrect life stage. The phs:openNomenclature property records 'reasons for stopping'." ;
  rdfs:domain :TaxonPresence ;
  skos:example "species" ;
  skos:example "family" ;
  skos:prefLabel "taxon rank" ;
.
dwc:vernacularName
  a owl:DatatypeProperty ;
  skos:definition "The vernacular (common) name for the host or pest" ;
  rdfs:domain :TaxonPresence ;
  skos:example "Fire Blight" ;
  skos:prefLabel "vernacular name" ;
.
<http://www.opengis.net/ont/geosparql#Feature>
  a owl:Class ;
.
<http://www.opengis.net/ont/geosparql#Geometry>
  a owl:Class ;
.
<http://www.opengis.net/ont/geosparql#hasGeometry>
  a owl:ObjectProperty ;
.
rdf:dataProperty
  a owl:Class ;
.
owl:cardinality
  a owl:AnnotationProperty ;
.
owl:minCardinality
  a owl:AnnotationProperty ;
.
skos:Collection
  a owl:Class ;
.
skos:Concept
  a owl:Class ;
.
skos:definition
  a owl:AnnotationProperty ;
.
skos:editorialNote
  a owl:AnnotationProperty ;
.
skos:member
  a owl:AnnotationProperty ;
.
skos:prefLabel
  a owl:AnnotationProperty ;
.
sosa:Sampler
  a owl:Class ;
.
sosa:phenomenonTime
  a owl:ObjectProperty ;
  skos:definition "The time that the Result of an Observation/Actuation applies to the FeatureOfInterest. Not necessarily the same as the result-time. May be an interval or an instant, or some other compound temporal entity." ;
  skos:prefLabel "phenomenon time"@en ;
.
<https://linked.data.gov.au/def/phs>
  a owl:Ontology ;
  dcterms:conformsTo <https://linked.data.gov.au/def/agop> ;
  dcterms:contributor <https://orcid.org/0000-0002-3884-3420> ;
  dcterms:created "2020-02-11"^^xsd:date ;
  dcterms:creator <https://orcid.org/0000-0002-8742-7730> ;
  dcterms:creator <https://orcid.org/0000-0003-3357-2307> ;
  dcterms:creator <https://orcid.org/0000-0003-3932-5614> ;
  dcterms:modified "2021-06-12"^^xsd:date ;
  dcterms:publisher <https://linked.data.gov.au/org/dawe> ;
  owl:imports <http://datashapes.org/dash> ;
  owl:imports dwc: ;
  owl:imports sosa: ;
  owl:versionIRI <https://linked.data.gov.au/def/phs/0.2.1> ;
  skos:definition "An ontology for surveillance events relating to plant pests. These events comprise field observations and associated diagnostic work (i.e. taxonomic identification) of samples taken as part of the observation. Surveillance is one of the core activities of national plant protection organizations (NPPOs). It provides NPPOs with a technical basis for many phytosanitary measures; including phytosanitary import requirements, pest free areas, pest reporting and eradication, and pest status in an area. All terms are defined by ISPM 5."@en ;
  skos:prefLabel "Plant Health Surveillance Ontology"@en ;
  sdo:codeRepository "<https://github.com/AGLDWG/phs>"^^xsd:anyURI ;
.
:DiagnosticMethod
  a owl:Class ;
  skos:definition "A procedure or method used to determine the taxonomic identity of a plant pest. May be carried out in the field, or more usually, in a laboratory." ;
  rdfs:subClassOf sosa:Procedure ;
  skos:prefLabel "Diagnostic method" ;
.
:DiagnosticMethodType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The subtype of a Diagnostic Method"@en ;
  skos:prefLabel "Diagnostic Method Type"@en ;
.
:EffortUnitType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The unit by which surveillance effort is measured"@en ;
  skos:prefLabel "Effort Unit Type" ;
.
:Host
  a owl:Class ;
  skos:definition "A living thing (usually a plant) from which a sample was taken for identification. In the case of trapping, the tree in which the trap was hung"@en ;
  skos:scopeNote "Particular pests are often associated with certain substrates or hosts. In the field, when targetting a pest, a surveyor will look for substrates or hosts that are more likely to harbour the target pest. Recording the substrate assists diagnosticians when they are identifying a specimen. It also aids analysis aimed at estimating pest prevalence based on absence records. Lastly, some protocols require the host or substrate to be recorded for each observation." ;
  rdfs:subClassOf sosa:Platform ;
  owl:disjointWith :Substrate ;
  skos:example "Orange tree: host of the pathogen that causes citrus canker" ;
  skos:example "Bee; a Varroa Mite may be found in a bee's trachea" ;
  sosa:hosts :Trap ;
  skos:prefLabel "Host" ;
.
:HostType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The subtype of a Host"@en ;
  skos:prefLabel "Host Type"@en ;
.
:InspectionMethod
  a owl:Class ;
  skos:definition "A technique used to carry out an act of surveillance"@en ;
  skos:scopeNote "Inspection Methods are chosen according to the target pest and/or host|substrate. The sensitivity of an observation may depend on the method that was used." ;
  skos:definition "The units used to record Surveillance Effort vary according to the Inspection method."@en ;
  rdfs:subClassOf sosa:Procedure ;
  skos:prefLabel "Inspection Method" ;
.
:InspectionMethodType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The subtype of an Inspection Method"@en ;
  skos:prefLabel "Inspection Method Type"@en ;
.
:LureType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The subtype of a Lure"@en ;
  skos:prefLabel "Lure Type"@en ;
.
:ObservationLocation
  a owl:Class ;
  rdfs:subClassOf dwc:Location ;
  rdfs:subClassOf sosa:FeatureOfInterest ;
  skos:definition "The point location at which a surveillance event occured."@en ;
  skos:prefLabel "Observation Location"@en ;
  sosa:isFeatureOfInterestOf :SurveillanceEvent ;
.
:OccurrenceStatusType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The name of the Occurrence Status of a Target Pest, associated with a single Observation"@en ;
  skos:prefLabel "Occurrence Status Type"@en ;
.
:PestOccurrenceStatus
  a owl:Class ;
  rdfs:subClassOf sosa:Result ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:onClass :OccurrenceStatusType ;
      owl:onProperty dcterms:type ;
      owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
    ] ;
  skos:scopeNote "If an organism that is a pest, but not the target of the specified Inspection Method, were detected, a new record would have to be created to register the 'bycatch' pest's status." ;
  skos:definition "A statement of whether a pest, which was the target of a surveillance event, was detected or not by a specified Inspection Method."@en ;
  skos:prefLabel "Pest Occurrence Status"@en ;
  sosa:isResultOf :SurveillanceEvent ;
.
:Substrate
  a owl:Class ;
  skos:scopeNote "A Substrate is a Stratum that is not a Host. Usually non-living, such as a rock or leaf litter." ;
  skos:definition "Thing or material on or in which a sample was taken for identification." ;
  rdfs:subClassOf sosa:Platform ;
  skos:prefLabel "Substrate" ;
.
:SubstrateType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The subtype of a Substrate"@en ;
  skos:prefLabel "Substrate Type"@en ;
.
:SurveillanceEvent
  a owl:Class ;
  rdfs:subClassOf sosa:Observation ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:hasValue xsd:date ;
      owl:onProperty sosa:phenomenonTime ;
      owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
    ] ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:minQualifiedCardinality "1"^^xsd:nonNegativeInteger ;
      owl:onClass :TargetPest ;
      owl:onProperty :targetsPest ;
    ] ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:onClass :InspectionMethod ;
      owl:onProperty sosa:usedProcedure ;
      owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
    ] ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:onClass :ObservationLocation ;
      owl:onProperty sosa:hasFeatureOfInterest ;
      owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
    ] ;
  skos:PrefLabel "Surveillance Event"@en ;
  skos:definition "An act of surveillance for a target pest, performed according to a specified procedure"@en ;
  skos:scopeNote "Also called 'Targetted' or 'Active' surveillance. The observation/s made during a Surveillance Event are directed towards establishing whether a Pest is present or not, insofar that the inspection method is capable of detecting the pest."@en ;
  sosa:hasFeatureofInterest :TargetPest ;
  sosa:usedProcedure :InspectionMethod ;
.
:TargetPest
  a owl:Class ;
  a [
      a owl:Restriction ;
      owl:onProperty dcterms:type ;
      owl:someValuesFrom :TargetPestType ;
    ] ;
  skos:scopeNote "The IPPC definition of Pest is 'Any species, strain or biotype of plant, animal or pathogenic agent injurious to plants or plant products.'"@en ;
  skos:definition "Pest or Pests that are the subject of a surveillance event. The primary goal of a surveillance event is to determine the presence or absence of a Target Pest according to an Inspection Method. Thus the Target Pest is the thing whose prorty is being estimated in the course of a Surveillance Event, to arrive at an Occurrence Status for the target pest."@en ;
  skos:prefLabel "Target Pest"@en ;
.
:TargetPestType
  a owl:Class ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The subtype of a Target Pest. Perhaps a single Taxon or perhaps a Group"@en ;
  skos:prefLabel "Target Pest Type"@en ;
.
:TaxonPresence
  a owl:Class ;
  rdfs:subClassOf sosa:ObservableProperty ;
  skos:scopeNote "A record of the identity of a taxon that was observed or taken as a sample by a Surveillance Event" ;
  skos:definition "The identity of an organism whose occurrence was detected during a surveillance event."@en ;
  skos:prefLabel "Taxon Presence"@en ;
  sosa:observedProperty :SurveillanceEvent ;
.
:Trap
  a owl:Class ;
  skos:definition "A device that catches or collects organisms or evidence of them." ;
  rdfs:subClassOf sosa:Sampler ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:allValuesFrom :LureType ;
      owl:onProperty :hasLureType ;
    ] ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ;
      owl:onClass :LureType ;
      owl:onProperty dcterms:type ;
    ] ;
  rdfs:subClassOf [
      a owl:Restriction ;
      owl:onClass :TrapType ;
      owl:onProperty dcterms:type ;
      owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
    ] ;
  skos:prefLabel "Trap" ;
.
:TrapType
  a owl:Class ;
  skos:scopeNote "Trap Type must not to be confused with Trap ID, which is an identifier assigned to a single trap." ;
  rdfs:subClassOf skos:Concept ;
  skos:definition "The make, model or design of a Trap"@en ;
  skos:example "Patten; Bucket" ;
  skos:prefLabel "Trap Type" ;
.
:catchesPest
  a owl:ObjectProperty ;
  skos:definition "An object which provides refuge to the target pest, and can thus be used as a trap"@en ;
  rdfs:domain :Trap ;
  rdfs:range :TargetPest ;
  skos:prefLabel "catches pest"@en ;
.
:detectsPest
  a owl:ObjectProperty ;
  skos:definition "The pest for which the inspection method is useful"@en ;
  rdfs:domain :InspectionMethod ;
  rdfs:range :TargetPest ;
  skos:prefLabel "detects pest"@en ;
.

:targetsPest
  a owl:ObjectProperty ;
  skos:definition "The pest that is the target of the surveillance event"@en ;
  rdfs:domain :InspectionMethod ;
  rdfs:range :TargetPest ;
  skos:prefLabel "targets pest"@en ;
.

:effortValue
  a owl:DatatypeProperty ;
  skos:scopeNote "Always used in conjunction with effortUnit" ;
  skos:definition "Amount or quantity of 'effort' expended in the making of an observation." ;
  rdfs:domain :SurveillanceEvent ;
  rdfs:range [
      a rdfs:Datatype ;
      owl:onDatatype xsd:decimal ;
      owl:withRestriction [
          xsd:minInclusive 0 ;
        ] ;
    ] ;
  skos:example "A fruitfly trap is emptied after two weeks in a lemon tree: effortUnit='week' ; effortValue='2'." ;
  skos:prefLabel "effort value" ;
.
:hasEffortUnit
  a owl:ObjectProperty ;
  skos:scopeNote "Always used in conjunction with effortValue. Effort is recorded with a value and a Unit that is an EffortUnitType"@en ;
  rdfs:domain :SurveillanceEvent ;
  rdfs:range :EffortUnitType ;
  skos:definition "Effort is the amount of time, number of plants inspected, or area surveyed while carrying out a Surveillance Event"@en ;
  skos:example "Visual inspection of 1 square metre of ground: effortUnit='square metre' ; effortValue='1'." ;
  skos:prefLabel "has effort unit" ;
.
:hasLureType
  a owl:ObjectProperty ;
  rdfs:domain :Trap ;
  rdfs:subPropertyOf dcterms:hasPart ;
  rdfs:range :LureType ;
  skos:scopeNote ""@en ;
  skos:definition "Names of lures are selected from the LureTypes vocabulary"@en ;
  skos:prefLabel "has lure type"@en ;
.
:hasTrapType
  a owl:ObjectProperty ;
  skos:definition "The make or model of a trap, selected from the TrapTypes vocabulary" ;
  rdfs:domain :Trap ;
  rdfs:range :TrapType ;
  skos:prefLabel "has trap type" ;
.
:hostsPest
  a owl:ObjectProperty ;
  skos:definition "A living thing (usually a plant) on which the target pest may be found"@en ;
  rdfs:domain :Host ;
  rdfs:range :TargetPest ;
  skos:prefLabel "hosts pest"@en ;
.
:identifiesPest
  a owl:ObjectProperty ;
  skos:definition "This diagnostic method is appropriate for the target pest"@en ;
  rdfs:domain :DiagnosticMethod ;
  rdfs:range :TargetPest ;
  skos:prefLabel "identifies pest"@en ;
.
:luresPest
  a owl:ObjectProperty ;
  skos:definition "The target pest which is attracted by this lure"@en ;
  rdfs:range :TargetPest ;
  skos:prefLabel "lures pest"@en ;
.
:occurrenceID
  a owl:DatatypeProperty ;
  skos:scopeNote "This ID must be locally unique within the surveillance event" ;
  skos:prefLabel "occurrence ID" ;
.
:supportsPest
  a owl:ObjectProperty ;
  skos:definition "A substrate on which the target pest is likely be found, if it were present"@en ;
  rdfs:domain :Substrate ;
  rdfs:range :TargetPest ;
  skos:prefLabel "supports pest"@en ;
.
:identificationID
  a owl:DatatypeProperty ;
  skos:definition "Identifier assigned to specimen or sample by diagnostician or LIMS" ;
  rdfs:domain :TaxonPresence ;
  skos:prefLabel "identification ID" ;
.
:taxonomicReferenceSource
  a owl:DatatypeProperty ;
  skos:definition "The online taxonomic reference source" ;
  rdfs:domain :TaxonPresence ;
  skos:example "https://www.gbif.org/species" ;
  skos:prefLabel "taxonomic reference source" ;
.
<https://linked.data.gov.au/org/dawe>
  a owl:NamedIndividual ;
  a sdo:Organization ;
  sdo:name "Department of Agriculture, Water and the Environment" ;
  sdo:url "https://www.awe.gov.au"^^xsd:anyURI ;
.
<https://orcid.org/0000-0002-3884-3420>
  a owl:NamedIndividual ;
  a sdo:Person ;
  sdo:affiliation <https://www.csiro.au> ;
  sdo:email "simon.cox@csiro.au"^^xsd:anyURI ;
  sdo:jobTitle "Research Scientist" ;
  sdo:name "Simon J.D. Cox" ;
.

<https://orcid.org/0000-0003-3932-5614>
  rdf:type owl:NamedIndividual ;
  rdf:type sdo:Person ;
  sdo:affiliation <https://surroundaustralia.com> ;
  sdo:email "simon.opper@surroundaustralia.com"^^xsd:anyURI ;
  sdo:jobTitle "Chief Data Scientist" ;
  sdo:name "Simon J. Opper" ;
.
<https://orcid.org/0000-0002-8742-7730>
  a owl:NamedIndividual ;
  a sdo:Person ;
  sdo:affiliation <https://surroundaustralia.com> ;
  sdo:email "nicholas.car@surroundaustralia.com"^^xsd:anyURI ;
  sdo:jobTitle "Data Systems Architect" ;
  sdo:name "Nicholas J. Car" ;
.
<https://orcid.org/0000-0003-3357-2307>
  a owl:NamedIndividual ;
  a sdo:Person ;
  sdo:affiliation <https://linked.data.gov.au/org/dawe> ;
  sdo:email "stephen.pratt@awe.gov.au"^^xsd:anyURI ;
  sdo:jobTitle "Project Manager: Implementation of Plant Health Surveillance Data Store" ;
  sdo:name "Stephen J. Pratt" ;
.
sdo:Organization
  a owl:Class ;
.
sdo:Person
  a owl:Class ;
.
sdo:affiliation
  a owl:AnnotationProperty ;
.
sdo:codeRepository
  a owl:AnnotationProperty ;
.
sdo:email
  a owl:AnnotationProperty ;
.
sdo:jobTitle
  a owl:AnnotationProperty ;
.
sdo:name
  a owl:AnnotationProperty ;
.
sdo:url
  a owl:AnnotationProperty ;
.
<https://surroundaustralia.com>
  a owl:NamedIndividual ;
  a sdo:Organization ;
  sdo:name "SURROUND Australia Pty Ltd" ;
  sdo:url "https://surroundaustralia.com"^^xsd:anyURI ;
.
<https://www.csiro.au>
  a owl:NamedIndividual ;
  a sdo:Organization ;
  sdo:name "CSIRO" ;
  sdo:url "https://www.csiro.au"^^xsd:anyURI ;
.