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Plant Health Surveillance Ontology

Metadata

URI
https://linked.data.gov.au/def/phs
Publisher(s)
Department of Agriculture, Water and the Environment
Creator(s)
Nicholas J. Car Orcid logo (nicholas.car@surroundaustralia.com) of SURROUND Australia Pty Ltd
Stephen J. Pratt Orcid logo (stephen.pratt@awe.gov.au) of Department of Agriculture, Water and the Environment
Simon J. Opper Orcid logo (simon.opper@surroundaustralia.com) of SURROUND Australia Pty Ltd
Contributor(s)
Simon J.D. Cox Orcid logo (simon.cox@csiro.au) of CSIRO
Created
2020-02-11
Modified
2021-06-12
Version URI
https://linked.data.gov.au/def/phs/0.2.1
Imports
http://datashapes.org/dash
dwc:
sosa:
Ontology RDF
RDF (turtle)
Code Repository

Description

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.

Table of Contents

  1. Classes
  2. Object Properties
  3. Datatype Properties
  4. Annotation Properties
  5. Named Individuals
  6. Namespaces
  7. Legend

Overview

Overview Diagram
Figure 1: Ontology overview

Classes

Datasetc # Classes

URI http://purl.org/dc/terms/Dataset
In range of dcterms:sourcedp

Featurec # Classes

URI http://www.opengis.net/ont/geosparql#Feature

Geometryc # Classes

URI http://www.opengis.net/ont/geosparql#Geometry

dataPropertyc # Classes

URI http://www.w3.org/1999/02/22-rdf-syntax-ns#dataProperty

Collectionc # Classes

URI http://www.w3.org/2004/02/skos/core#Collection

Conceptc # Classes

URI http://www.w3.org/2004/02/skos/core#Concept
Sub-classes Lure Typec
Effort Unit Typec
Inspection Method Typec
Host Typec
Target Pest Group Typec
Trap Typec
Substrate Typec
Diagnostic Method Typec
Occurrence Status Typec

Samplerc # Classes

URI http://www.w3.org/ns/sosa/Sampler
Sub-classes Trapc

Diagnostic methodc # Classes

URI https://linked.data.gov.au/def/phs#DiagnosticMethod
Description

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.

Super-classes sosa:Procedurec
In domain of Identifies pestop

Diagnostic Method Typec # Classes

URI https://linked.data.gov.au/def/phs#DiagnosticMethodType
Description

The subtype of a Diagnostic Method

Super-classes skos:Conceptc

Effort Unit Typec # Classes

URI https://linked.data.gov.au/def/phs#EffortUnitType
Description

The unit by which surveillance effort is measured

Super-classes skos:Conceptc
In range of has effort unitop

Hostc # Classes

URI https://linked.data.gov.au/def/phs#Host
Description

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

Scope Notes

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.

Example(s)
Orange tree: host of the pathogen that causes citrus canker

Bee; a Varroa Mite may be found in a bee's trachea

Super-classes sosa:Platformc
In domain of hosts pestop

Host Typec # Classes

URI https://linked.data.gov.au/def/phs#HostType
Description

The subtype of a Host

Super-classes skos:Conceptc

Inspection Methodc # Classes

URI https://linked.data.gov.au/def/phs#InspectionMethod
Description

A technique used to carry out an act of surveillance

Scope Notes

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.

Super-classes sosa:Procedurec
In domain of detects pestop

Inspection Method Typec # Classes

URI https://linked.data.gov.au/def/phs#InspectionMethodType
Description

The subtype of an Inspection Method

Super-classes skos:Conceptc

Lure Typec # Classes

URI https://linked.data.gov.au/def/phs#LureType
Description

The subtype of a Lure

Super-classes skos:Conceptc
In range of has lure typeop

Observation Locationc # Classes

URI https://linked.data.gov.au/def/phs#ObservationLocation
Description

The point location at which a surveillance event occured.

Super-classes dwc:Locationc
sosa:FeatureOfInterestc
In domain of dwc:coordinateUncertaintyInMetersdp
dwc:decimalLongitudedp
dwc:decimalLatitudedp
dwc:geodeticDatumdp

Occurrence Status Typec # Classes

URI https://linked.data.gov.au/def/phs#OccurrenceStatusType
Description

The name of the Occurrence Status of a Target Pest, associated with a single Observation

Super-classes skos:Conceptc

Pest Occurrence Statusc # Classes

URI https://linked.data.gov.au/def/phs#PestOccurrenceStatus
Description

A statement of whether a pest, which was the target of a surveillance event, was detected or not by a specified Inspection Method.

Scope Notes

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.

Super-classes sosa:Resultc
Restrictions dcterms:typeop exactly 1 Occurrence Status Typec

Substratec # Classes

URI https://linked.data.gov.au/def/phs#Substrate
Description

Thing or material on or in which a sample was taken for identification.

Scope Notes

A Substrate is a Stratum that is not a Host. Usually non-living, such as a rock or leaf litter.

Super-classes sosa:Platformc
In domain of supports pestop

Substrate Typec # Classes

URI https://linked.data.gov.au/def/phs#SubstrateType
Description

The subtype of a Substrate

Super-classes skos:Conceptc

SurveillanceEventc # Classes

URI https://linked.data.gov.au/def/phs#SurveillanceEvent
Description

An act of surveillance for a target pest, performed according to a specified procedure

Scope Notes

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.

Super-classes sosa:Observationc
Restrictions sosa:phenomenonTimeop value xsd:datec
sosa:usedProcedure exactly 1 Inspection Methodc
sosa:hasFeatureOfInterest exactly 1 Observation Locationc
sosa:hasFeatureOfInterest min 1 Target Pest Groupc
In domain of dwc:recordedBydp
dwc:eventIDdp
has effort unitop
effort valuedp

Target Pest Groupc # Classes

URI https://linked.data.gov.au/def/phs#TargetPestGroup
Description

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 Group according to an Inspection Method. Thus the Target Pest Group 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.

Scope Notes

The IPPC definition of Pest is 'Any species, strain or biotype of plant, animal or pathogenic agent injurious to plants or plant products.'

Super-classes sosa:FeatureOfInterestc
In range of hosts pestop
catches pestop
Identifies pestop
detects pestop
supports pestop
lures pestop

Target Pest Group Typec # Classes

URI https://linked.data.gov.au/def/phs#TargetPestGroupType
Description

The subtype of a Target Pest Group. Perhaps a single Taxon or perhaps a Group

Super-classes skos:Conceptc

Taxon Identityc # Classes

URI https://linked.data.gov.au/def/phs#TaxonOccurrence
Description

The identity of an organism whose occurrence was detected during a surveillance event.

Scope Notes

A record of the identity of a taxon that was observed or taken as a sample by a Surveillance Event

Super-classes dwc:Occurrencec
sosa:ObservablePropertyc
In domain of taxonomic reference sourcedp
dwc:taxonRankdp
dwc:taxonConceptIDdp
dwc:scientificNamedp
dwc:vernacularNamedp

Trapc # Classes

URI https://linked.data.gov.au/def/phs#Trap
Description

A device that catches or collects organisms or evidence of them.

Super-classes sosa:Samplerc
Restrictions dcterms:typeop min 0 Lure Typec
dcterms:typeop exactly 1 Trap Typec
has lure typeop only Lure Typec
In domain of catches pestop
has trap typeop
has lure typeop

Trap Typec # Classes

URI https://linked.data.gov.au/def/phs#TrapType
Description

The make, model or design of a Trap

Scope Notes

Trap Type must not to be confused with Trap ID, which is an identifier assigned to a single trap.

Example(s)
Patten; Bucket

Super-classes skos:Conceptc
In range of has trap typeop

Organizationc # Classes

URI https://schema.org/Organization
Members https://linked.data.gov.au/org/dawe
https://surroundaustralia.com
https://www.csiro.au

Personc # Classes

URI https://schema.org/Person
Members https://orcid.org/0000-0002-3884-3420
https://orcid.org/0000-0003-3932-5614
https://orcid.org/0000-0003-3357-2307
https://orcid.org/0000-0002-8742-7730

Object Properties

hasPartop # OPs

URI http://purl.org/dc/terms/hasPart

typeop # OPs

URI http://purl.org/dc/terms/type

hasGeometryop # OPs

URI http://www.opengis.net/ont/geosparql#hasGeometry

phenomenon timeop # OPs

URI http://www.w3.org/ns/sosa/phenomenonTime
Description

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.

catches pestop # OPs

URI https://linked.data.gov.au/def/phs#catchesPest
Description

An object which provides refuge to the target pest, and can thus be used as a trap

Domain(s) Trapc
Range(s) https://linked.data.gov.au/def/phs#TargetPestGroupc

detects pestop # OPs

URI https://linked.data.gov.au/def/phs#detectsPest
Description

The pest for which the inspection method is useful

Domain(s) Inspection Methodc
Range(s) https://linked.data.gov.au/def/phs#TargetPestGroupc

has effort unitop # OPs

URI https://linked.data.gov.au/def/phs#hasEffortUnit
Description

Effort is the amount of time, number of plants inspected, or area surveyed while carrying out a Surveillance Event

Scope Notes

Always used in conjunction with effortValue. Effort is recorded with a value and a Unit that is an EffortUnitType

Example(s)
Visual inspection of 1 square metre of ground: effortUnit='square metre' ; effortValue='1'.

Domain(s) SurveillanceEventc
Range(s) https://linked.data.gov.au/def/phs#EffortUnitTypec

has lure typeop # OPs

URI https://linked.data.gov.au/def/phs#hasLureType
Description

Names of lures are selected from the LureTypes vocabulary

Super-properties dcterms:hasPartop
Domain(s) Trapc
Range(s) https://linked.data.gov.au/def/phs#LureTypec

has trap typeop # OPs

URI https://linked.data.gov.au/def/phs#hasTrapType
Description

The make or model of a trap, selected from the TrapTypes vocabulary

Domain(s) Trapc
Range(s) https://linked.data.gov.au/def/phs#TrapTypec

hosts pestop # OPs

URI https://linked.data.gov.au/def/phs#hostsPest
Description

A living thing (usually a plant) on which the target pest may be found

Domain(s) Hostc
Range(s) https://linked.data.gov.au/def/phs#TargetPestGroupc

Identifies pestop # OPs

URI https://linked.data.gov.au/def/phs#identifiesPest
Description

This diagnostic method is appropriate for the target pest

Domain(s) Diagnostic methodc
Range(s) https://linked.data.gov.au/def/phs#TargetPestGroupc

lures pestop # OPs

URI https://linked.data.gov.au/def/phs#luresPest
Description

The target pest which is attracted by this lure

Range(s) https://linked.data.gov.au/def/phs#TargetPestGroupc

supports pestop # OPs

URI https://linked.data.gov.au/def/phs#supportsPest
Description

A substrate on which the target pest is likely be found, if it were present

Domain(s) Substratec
Range(s) https://linked.data.gov.au/def/phs#TargetPestGroupc

Datatype Properties

sourcedp # DPs

URI http://purl.org/dc/terms/source
Description

Likely the model should use dcat but as at 10-Jun-2021 the existing dcterms:dataset is being used

Range(s) dcterms:Datasetc

co-ordinate uncertainty in metersdp # DPs

URI http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters
Domain(s) Observation Locationc

decimal latitudedp # DPs

URI http://rs.tdwg.org/dwc/terms/decimalLatitude
Domain(s) Observation Locationc

decimal longitudedp # DPs

URI http://rs.tdwg.org/dwc/terms/decimalLongitude
Domain(s) Observation Locationc

event IDdp # DPs

URI http://rs.tdwg.org/dwc/terms/eventID
Domain(s) SurveillanceEventc

geodetic datumdp # DPs

URI http://rs.tdwg.org/dwc/terms/geodeticDatum
Domain(s) Observation Locationc

recorded bydp # DPs

URI http://rs.tdwg.org/dwc/terms/recordedBy
Description

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 is acceptable.

Domain(s) SurveillanceEventc

scientific namedp # DPs

URI http://rs.tdwg.org/dwc/terms/scientificName
Description

The systematic name for an organism found by a Surveillance Event, and recorded as a TaxonOccurrence

Example(s)
Erwinia amylovora

Domain(s) Taxon Identityc

taxon concept IDdp # DPs

URI http://rs.tdwg.org/dwc/terms/taxonConceptID
Description

The unique identifier for a taxon, referenced by taxonomicReferenceSource

Example(s)
`3222012`, which when paired with `https://www.gbif.org/species`, prvides a link to Erwinia amylovora, Fire Blight.

Domain(s) Taxon Identityc

scientific namedp # DPs

URI http://rs.tdwg.org/dwc/terms/taxonRank
Description

The stematic name for an organism found by a Surveillance Event

Example(s)
Erwinia amylovora

Domain(s) Taxon Identityc

vernacular namedp # DPs

URI http://rs.tdwg.org/dwc/terms/vernacularName
Description

The vernacular (common) name for the host or pest

Example(s)
Fire Blight

Domain(s) Taxon Identityc

effort valuedp # DPs

URI https://linked.data.gov.au/def/phs#effortValue
Description

Amount or quantity of 'effort' expended in the making of an observation.

Scope Notes

Always used in conjunction with effortUnit

Example(s)
A fruitfly trap is emptied after two weeks in a lemon tree: effortUnit='week' ; effortValue='2'.

Domain(s) SurveillanceEventc

occurrence IDdp # DPs

URI https://linked.data.gov.au/def/phs#occurrenceID
Scope Notes

This ID must be locally unique within the surveillance event

taxonomic reference sourcedp # DPs

URI https://linked.data.gov.au/def/phs#taxonomicReferenceSource
Description

The online taxonomic reference source

Example(s) https://www.gbif.org/species
Domain(s) Taxon Identityc

Annotation Properties

contributorap # APs

URI http://purl.org/dc/terms/contributor

createdap # APs

URI http://purl.org/dc/terms/created

creatorap # APs

URI http://purl.org/dc/terms/creator

modifiedap # APs

URI http://purl.org/dc/terms/modified

publisherap # APs

URI http://purl.org/dc/terms/publisher

preferredNamespacePrefixap # APs

URI http://purl.org/vocab/vann/preferredNamespacePrefix

cardinalityap # APs

URI http://www.w3.org/2002/07/owl#cardinality

minCardinalityap # APs

URI http://www.w3.org/2002/07/owl#minCardinality

definitionap # APs

URI http://www.w3.org/2004/02/skos/core#definition

editorialNoteap # APs

URI http://www.w3.org/2004/02/skos/core#editorialNote

memberap # APs

URI http://www.w3.org/2004/02/skos/core#member

prefLabelap # APs

URI http://www.w3.org/2004/02/skos/core#prefLabel

affiliationap # APs

URI https://schema.org/affiliation

codeRepositoryap # APs

URI https://schema.org/codeRepository

emailap # APs

URI https://schema.org/email

jobTitleap # APs

URI https://schema.org/jobTitle

nameap # APs

URI https://schema.org/name

urlap # APs

URI https://schema.org/url

Named Individuals

Department of Agriculture, Water and the Environmentni

Class(es)
sdo:Organization
URI https://linked.data.gov.au/org/dawe

Simon J.D. Coxni

Class(es)
sdo:Person
URI https://orcid.org/0000-0002-3884-3420

Nicholas J. Carni

Class(es)
sdo:Person
URI https://orcid.org/0000-0002-8742-7730

Stephen J. Prattni

Class(es)
sdo:Person
URI https://orcid.org/0000-0003-3357-2307

Simon J. Opperni

Class(es)
sdo:Person
URI https://orcid.org/0000-0003-3932-5614

SURROUND Australia Pty Ltdni

Class(es)
sdo:Organization
URI https://surroundaustralia.com

CSIROni

Class(es)
sdo:Organization
URI https://www.csiro.au

Namespaces

default (:)
https://linked.data.gov.au/def/phs
dcterms
http://purl.org/dc/terms/
dwc
http://rs.tdwg.org/dwc/terms/
geosparql
http://www.opengis.net/ont/geosparql#
owl
http://www.w3.org/2002/07/owl#
prov
http://www.w3.org/ns/prov#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sdo
https://schema.org/
skos
http://www.w3.org/2004/02/skos/core#
sosa
http://www.w3.org/ns/sosa/
vann
http://purl.org/vocab/vann/
xsd
http://www.w3.org/2001/XMLSchema#

Legend

cClasses
opObject Properties
fpFunctional Properties
dpData Properties
dpAnnotation Properties
pProperties
niNamed Individuals