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Plant Health Surveillance Ontology

IRI: https://linked.data.gov.au/def/phs
Publisher(s): Department of Agriculture, Water and the Environment
Creator(s): Stephen J. Pratt of Department of Agriculture, Water and the Environment
Nicholas J. Car of SURROUND Australia Pty Ltd
Simon J. Opper of SURROUND Australia Pty Ltd
Contributors(s): Simon J.D. Cox of CSIRO
Created: 2020-02-11
Modified: 2021-06-12
Version IRI: https://linked.data.gov.au/def/phs/0.2.1
Imports: http://datashapes.org/dash
sosa:
dwc:
Ontology Source: 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

Classes
Object Properties
Datatype Properties
Annotation Properties
Namespaces
Legend

Overview

Overview Diagram

Figure 1:Ontology overview, showing the major classes and their relationships to higher ontologies. Refer to descriptions of classes to see their datatype and object properties (aka 'data elements').

Classes ↑

Dataset^c

IRI	`http://purl.org/dc/terms/Dataset`
In range of	dcterms:source^dp

Feature^c

IRI	`http://www.opengis.net/ont/geosparql#Feature`

Geometry^c

IRI	`http://www.opengis.net/ont/geosparql#Geometry`

dataProperty^c

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

Collection^c

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

Concept^c

IRI	`http://www.w3.org/2004/02/skos/core#Concept`
Sub-classes	DiagnosticMethodType^c TargetPestType^c EffortUnitType^c InspectionMethodType^c LureType^c OccurrenceStatusType^c HostType^c TrapType^c SubstrateType^c

Sampler^c

IRI	`http://www.w3.org/ns/sosa/Sampler`
Sub-classes	Trap^c

Diagnostic method^c

IRI	`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:Procedure^c
In domain of	identifiesPest^op

Diagnostic Method Type^c

IRI	`https://linked.data.gov.au/def/phs#DiagnosticMethodType`
Description	The subtype of a Diagnostic Method
Super-classes	skos:Concept^c

Effort Unit Type^c

IRI	`https://linked.data.gov.au/def/phs#EffortUnitType`
Description	The unit by which surveillance effort is measured
Super-classes	skos:Concept^c
In range of	hasEffortUnit^op

Host^c

IRI	`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
Usage Note	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.
Super-classes	sosa:Platform^c
In domain of	hostsPest^op

Host Type^c

IRI	`https://linked.data.gov.au/def/phs#HostType`
Description	The subtype of a Host
Super-classes	skos:Concept^c

Inspection Method^c

IRI	`https://linked.data.gov.au/def/phs#InspectionMethod`
Description	The units used to record Surveillance Effort vary according to the Inspection method.
Usage Note	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:Procedure^c
In domain of	detectsPest^op targetsPest^op

Inspection Method Type^c

IRI	`https://linked.data.gov.au/def/phs#InspectionMethodType`
Description	The subtype of an Inspection Method
Super-classes	skos:Concept^c

Lure Type^c

IRI	`https://linked.data.gov.au/def/phs#LureType`
Description	The subtype of a Lure
Super-classes	skos:Concept^c
In range of	hasLureType^op

Observation Location^c

IRI	`https://linked.data.gov.au/def/phs#ObservationLocation`
Description	The point location at which a surveillance event occured.
Super-classes	dwc:Location^c sosa:FeatureOfInterest^c
In domain of	dwc:coordinateUncertaintyInMeters^dp dwc:geodeticDatum^dp dwc:decimalLongitude^dp dwc:decimalLatitude^dp

Occurrence Status Type^c

IRI	`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:Concept^c

Pest Occurrence Status^c

IRI	`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.
Usage Note	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:Result^c
Restrictions	dcterms:type^op exactly 1 OccurrenceStatusType^c

Substrate^c

IRI	`https://linked.data.gov.au/def/phs#Substrate`
Description	Thing or material on or in which a sample was taken for identification.
Usage Note	A Substrate is a Stratum that is not a Host. Usually non-living, such as a rock or leaf litter.
Super-classes	sosa:Platform^c
In domain of	supportsPest^op

Substrate Type^c

IRI	`https://linked.data.gov.au/def/phs#SubstrateType`
Description	The subtype of a Substrate
Super-classes	skos:Concept^c

SurveillanceEvent^c

IRI	`https://linked.data.gov.au/def/phs#SurveillanceEvent`
Description	An act of surveillance for a target pest, performed according to a specified procedure
Usage Note	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:Observation^c
Restrictions	targetsPest^op min 1 TargetPest^c sosa:usedProcedure exactly 1 InspectionMethod^c sosa:phenomenonTime^op value xsd:date^c sosa:hasFeatureOfInterest exactly 1 ObservationLocation^c
In domain of	dwc:recordedBy^dp hasEffortUnit^op dwc:eventID^dp effortValue^dp

Target Pest^c

IRI	`https://linked.data.gov.au/def/phs#TargetPest`
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 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.
Usage Note	The IPPC definition of Pest is 'Any species, strain or biotype of plant, animal or pathogenic agent injurious to plants or plant products.'
In range of	targetsPest^op catchesPest^op detectsPest^op identifiesPest^op hostsPest^op supportsPest^op luresPest^op

Target Pest Type^c

IRI	`https://linked.data.gov.au/def/phs#TargetPestType`
Description	The subtype of a Target Pest. Perhaps a single Taxon or perhaps a Group
Super-classes	skos:Concept^c

Taxon Presence^c

IRI	`https://linked.data.gov.au/def/phs#TaxonPresence`
Description	The identity of an organism whose occurrence was detected during a surveillance event.
Usage Note	A record of the identity of a taxon that was observed or taken as a sample by a Surveillance Event
Super-classes	sosa:ObservableProperty^c
In domain of	dwc:taxonRank^dp identificationID^dp taxonomicReferenceSource^dp dwc:taxonConceptID^dp dwc:vernacularName^dp dwc:scientificName^dp

Trap^c

IRI	`https://linked.data.gov.au/def/phs#Trap`
Description	A device that catches or collects organisms or evidence of them.
Super-classes	sosa:Sampler^c
Restrictions	dcterms:type^op exactly 1 TrapType^c hasLureType^op only LureType^c dcterms:type^op min 0 LureType^c
In domain of	hasTrapType^op hasLureType^op catchesPest^op

Trap Type^c

IRI	`https://linked.data.gov.au/def/phs#TrapType`
Description	The make, model or design of a Trap
Usage Note	Trap Type must not to be confused with Trap ID, which is an identifier assigned to a single trap.
Super-classes	skos:Concept^c
In range of	hasTrapType^op

Organization^c

IRI	`https://schema.org/Organization`

Person^c

IRI	`https://schema.org/Person`

Object Properties ↑

hasPart
type
hasGeometry
phenomenon time
catches pest
detects pest
has effort unit
has lure type
has trap type
hosts pest
Identifies pest
lures pest
supports pest
targets pest

hasPart^op

IRI	`http://purl.org/dc/terms/hasPart`

type^op

IRI	`http://purl.org/dc/terms/type`

hasGeometry^op

IRI	`http://www.opengis.net/ont/geosparql#hasGeometry`

phenomenon time^op

IRI	`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 pest^op

IRI	`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)	Trap^c
Range(s)	TargetPest^c

detects pest^op

IRI	`https://linked.data.gov.au/def/phs#detectsPest`
Description	The pest for which the inspection method is useful
Domain(s)	InspectionMethod^c
Range(s)	TargetPest^c

has effort unit^op

IRI	`https://linked.data.gov.au/def/phs#hasEffortUnit`
Description	Units of effort are selected from the EffortUnitType vocabulary
Usage Note	Always used in conjunction with effortValue. Effort is recorded with a value and a Unit that is an EffortUnitType
Domain(s)	SurveillanceEvent^c
Range(s)	EffortUnitType^c

has lure type^op

IRI	`https://linked.data.gov.au/def/phs#hasLureType`
Description	Names of lures are selected from the LureTypes vocabulary
Super-properties	dcterms:hasPart^op
Domain(s)	Trap^c
Range(s)	LureType^c

has trap type^op

IRI	`https://linked.data.gov.au/def/phs#hasTrapType`
Description	The make or model of a trap, selected from the TrapTypes vocabulary
Domain(s)	Trap^c
Range(s)	TrapType^c

hosts pest^op

IRI	`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)	Host^c
Range(s)	TargetPest^c

Identifies pest^op

IRI	`https://linked.data.gov.au/def/phs#identifiesPest`
Description	This diagnostic method is appropriate for the target pest
Domain(s)	DiagnosticMethod^c
Range(s)	TargetPest^c

lures pest^op

IRI	`https://linked.data.gov.au/def/phs#luresPest`
Description	The target pest which is attracted by this lure
Range(s)	TargetPest^c

supports pest^op

IRI	`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)	Substrate^c
Range(s)	TargetPest^c

targets pest^op

IRI	`https://linked.data.gov.au/def/phs#targetsPest`
Description	The pest that is the target of the surveillance event
Domain(s)	InspectionMethod^c
Range(s)	TargetPest^c

Datatype Properties ↑

source
co-ordinate uncertainty in meters
decimal latitude
decimal longitude
event ID
geodetic datum
recorded by
scientific name
taxon concept ID
scientific name
vernacular name
effort value
identification ID
occurrence ID
taxonomic reference source

source^dp

IRI	`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:Dataset^c

co-ordinate uncertainty in meters^dp

IRI	`http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters`
Domain(s)	ObservationLocation^c

decimal latitude^dp

IRI	`http://rs.tdwg.org/dwc/terms/decimalLatitude`
Domain(s)	ObservationLocation^c

decimal longitude^dp

IRI	`http://rs.tdwg.org/dwc/terms/decimalLongitude`
Domain(s)	ObservationLocation^c

event ID^dp

IRI	`http://rs.tdwg.org/dwc/terms/eventID`
Domain(s)	SurveillanceEvent^c

geodetic datum^dp

IRI	`http://rs.tdwg.org/dwc/terms/geodeticDatum`
Domain(s)	ObservationLocation^c

recorded by^dp

IRI	`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)	SurveillanceEvent^c

scientific name^dp

IRI	`http://rs.tdwg.org/dwc/terms/scientificName`
Description	The systematic name for an organism found by a Surveillance Event, and recorded as a TaxonPresence
Domain(s)	TaxonPresence^c

taxon concept ID^dp

IRI	`http://rs.tdwg.org/dwc/terms/taxonConceptID`
Description	The unique identifier for a taxon, referenced by `taxonomicReferenceSource`
Domain(s)	TaxonPresence^c

scientific name^dp

IRI	`http://rs.tdwg.org/dwc/terms/taxonRank`
Description	The stematic name for an organism found by a Surveillance Event
Domain(s)	TaxonPresence^c

vernacular name^dp

IRI	`http://rs.tdwg.org/dwc/terms/vernacularName`
Description	The vernacular (common) name for the host or pest
Domain(s)	TaxonPresence^c

effort value^dp

IRI	`https://linked.data.gov.au/def/phs#effortValue`
Description	Amount or quantity of 'effort' expended in the making of an observation.
Usage Note	Always used in conjunction with effortUnit
Domain(s)	SurveillanceEvent^c

identification ID^dp

IRI	`https://linked.data.gov.au/def/phs#identificationID`
Description	Identifier assigned to specimen or sample by diagnostician or LIMS
Domain(s)	TaxonPresence^c

occurrence ID^dp

IRI	`https://linked.data.gov.au/def/phs#occurrenceID`
Usage Note	This ID must be locally unique within the surveillance event

taxonomic reference source^dp

IRI	`https://linked.data.gov.au/def/phs#taxonomicReferenceSource`
Description	The online taxonomic reference source
Domain(s)	TaxonPresence^c

Annotation Properties ↑

contributor
created
creator
modified
publisher
preferredNamespacePrefix
cardinality
minCardinality
definition
editorialNote
member
prefLabel
affiliation
codeRepository
email
jobTitle
name
url

contributor^ap

IRI	`http://purl.org/dc/terms/contributor`

created^ap

IRI	`http://purl.org/dc/terms/created`

creator^ap

IRI	`http://purl.org/dc/terms/creator`

modified^ap

IRI	`http://purl.org/dc/terms/modified`

publisher^ap

IRI	`http://purl.org/dc/terms/publisher`

preferredNamespacePrefix^ap

IRI	`http://purl.org/vocab/vann/preferredNamespacePrefix`

cardinality^ap

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

minCardinality^ap

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

definition^ap

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

editorialNote^ap

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

member^ap

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

prefLabel^ap

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

affiliation^ap

IRI	`https://schema.org/affiliation`

codeRepository^ap

IRI	`https://schema.org/codeRepository`

email^ap

IRI	`https://schema.org/email`

jobTitle^ap

IRI	`https://schema.org/jobTitle`

name^ap

IRI	`https://schema.org/name`

url^ap

IRI	`https://schema.org/url`

Namespaces ↑

default (:): https://linked.data.gov.au/def/phs#
:: https://linked.data.gov.au/def/phs#
dcterms: http://purl.org/dc/terms/
dwc: http://rs.tdwg.org/dwc/terms/
owl: http://www.w3.org/2002/07/owl#
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/
xml: http://www.w3.org/XML/1998/namespace
xsd: http://www.w3.org/2001/XMLSchema#

Legend

^c	Classes
^op	Object Properties
^fp	Functional Properties
^dp	Data Properties
^dp	Annotation Properties
^p	Properties
ⁿⁱ	Named Individuals