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Parameter Usage Vocabulary ontology

Metadata

IRI
https://w3id.org/env/puv
Creator(s)
Simon J D Cox (simon.cox@csiro.au) of CSIRO
Contributors(s)
Jonathan Yu (Jonathan.Yu@csiro.au) of CSIRO
Roy Lowry of BODC
Alexandra Kokkinaki (alexk@bodc.ac.uk) of BODC
Gwenaëlle Moncoiffé (gmon@bodc.ac.uk) of BODC
Created
2021-03-17
Modified
2021-05-21
Imports
http://purl.org/dc/elements/1.1/
sosa:
License
https://creativecommons.org/publicdomain/zero/1.0/
Ontology Source
RDF (turtle)

Description

A simple ontology which implements the Parameter Usage Vocabulary semantic model, as described at https://github.com/nvs-vocabs/P01

Table of Contents

  1. Classes
  2. Object Properties
  3. Namespaces
  4. Legend

Overview

Figure 1: Ontology overview

Classes ↑

Analytical method (S04)c

IRI https://w3id.org/env/puv#AnalyticalMethod
Description Controlled vocabulary defining the terms that may be used for an analytical method entity (part of the how theme) in the BODC parameter semantic model
Super-classes skos:Conceptc
puv:Methodc
In range of puv:analyticalMethodop

Biological entity (S25)c

IRI https://w3id.org/env/puv#BiologicalEntity
Description Also see S09 (size), S10 (gender), S11 (stage), S12 (sub-component), S13 (sub-group), S14 (shape), S15 (colour)
Super-classes skos:Conceptc
puv:Entityc
Restrictions puv:isComposedOfop only puv:BiologicalEntityComponentc
In range of puv:biologicalObjectop

Biological entity colour (S15)c

IRI https://w3id.org/env/puv#BiologicalEntityColour
Description Controlled vocabulary defining the terms that may be used for colour or optical appearance of a biological entity (component of the what theme) in the BODC parameter semantic model
Super-classes puv:BiologicalEntityComponentc
skos:Conceptc

Biological entity componentc

IRI https://w3id.org/env/puv#BiologicalEntityComponent
Description Also see S09 (size), S10 (gender), S11 (stage), S12 (sub-component), S13 (sub-group), S14 (shape), S15 (colour)
Super-classes skos:Conceptc
Sub-classes puv:BiologicalEntitySubGroupc
puv:BiologicalEntitySizec
puv:BiologicalEntityStagec
puv:BiologicalEntityShapec
puv:BiologicalEntityGenderc
puv:BiologicalEntityColourc
puv:BiologicalEntitySubComponentc

Biological entity gender (S10)c

IRI https://w3id.org/env/puv#BiologicalEntityGender
Description Controlled vocabulary defining terms used to refer to a biological entity sex category (part of the what theme) in the BODC parameter semantic model
Super-classes skos:Conceptc
puv:BiologicalEntityComponentc

Biological entity shape (S14)c

IRI https://w3id.org/env/puv#BiologicalEntityShape
Description Controlled vocabulary defining the terms that may be used for morphology of a biological entity (component of the what theme) in the BODC parameter semantic model
Super-classes skos:Conceptc
puv:BiologicalEntityComponentc

Biological entity size (S09)c

IRI https://w3id.org/env/puv#BiologicalEntitySize
Description Controlled vocabulary defining the terms that may be used for biological entity size (part of the what theme) in the BODC parameter semantic model
Super-classes skos:Conceptc
puv:BiologicalEntityComponentc

Biological entity stage (S11)c

IRI https://w3id.org/env/puv#BiologicalEntityStage
Description Controlled vocabulary defining the terms that may be used to specify the development or life cycle stage of a biological entity (part of the 'what' theme) in the BODC parameter semantic model
Super-classes puv:BiologicalEntityComponentc
skos:Conceptc

Biological entity sub-component (S12)c

IRI https://w3id.org/env/puv#BiologicalEntitySubComponent
Description Controlled vocabulary defining the terms that may be used for biological entity (component of the what theme) plant or animal parts in the BODC parameter semantic model
Super-classes skos:Conceptc
puv:BiologicalEntityComponentc

Biological entity sub-group (S13)c

IRI https://w3id.org/env/puv#BiologicalEntitySubGroup
Description Controlled vocabulary defining the terms that may be used for ad-hoc qualification of a biological entity (component of the what theme) in the BODC parameter semantic model
Super-classes skos:Conceptc
puv:BiologicalEntityComponentc

Chemical substance (S27)c

IRI https://w3id.org/env/puv#ChemicalEntity
Description Terms for chemicals whose quantity in a matrix is determined to generate measurements in the BODC parameter usage vocabulary semantic model. Includes elements, compounds, isotopes and mixtures
Super-classes skos:Conceptc
puv:Entityc
In range of puv:chemicalObjectop

Data processing method (S05)c

IRI https://w3id.org/env/puv#DataProcessingMethod
Description Controlled vocabulary defining the terms that may be used for data processing description (part of the how theme) in the BODC parameter semantic model
Super-classes puv:Methodc
skos:Conceptc
In range of puv:dataProcessingop

Entity that bears the parameterc

IRI https://w3id.org/env/puv#Entity
Sub-classes puv:BiologicalEntityc
puv:PhysicalEntityc
puv:ChemicalEntityc
In range of puv:objectOfInterestop

Measurement-matrix relationship (S02)c

IRI https://w3id.org/env/puv#MMRel
Description Terms used to describe the relationship between the 'where theme' and the 'what theme' in the BODC semantic model for measured phenomena descriptions
Super-classes skos:Conceptc
In range of puv:matrixRelationshipop

Matrix (S26)c

IRI https://w3id.org/env/puv#Matrix
Description Terms used to describe the medium in which a measurement was made in the semantic model that underpins the BODC parameter discovery vocabulary
Super-classes skos:Conceptc
Restrictions puv:isComposedOfop only puv:MatrixComponentc
In range of puv:matrixop

Matrix componentc

IRI https://w3id.org/env/puv#MatrixComponent
Description Also see S21 (sphere), S22 (sphere sub-group), S23 (phase), S24 (phase sub-group)
Super-classes skos:Conceptc
Sub-classes puv:MatrixPhasec
puv:MatrixSphereSubGroupc
puv:MatrixPhaseSubGroupc
puv:MatrixSpherec

Sphere phase (S23)c

IRI https://w3id.org/env/puv#MatrixPhase
Description Controlled vocabulary defining the terms for phase (dissolved, particulate etc.) within a sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme
Super-classes skos:Conceptc
puv:MatrixComponentc

Sphere phase sub-group (S24)c

IRI https://w3id.org/env/puv#MatrixPhaseSubGroup
Description Concepts describing physical or logical (i.e. categories) subdivisions of a phase (i.e. subcomponent) of a sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme
Super-classes puv:MatrixComponentc
skos:Conceptc

Matrix sphere (S21)c

IRI https://w3id.org/env/puv#MatrixSphere
Description Controlled vocabulary defining the terms that may be used to describe the sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme
Super-classes skos:Conceptc
puv:MatrixComponentc

Matrix sphere sub-group (S22)c

IRI https://w3id.org/env/puv#MatrixSphereSubGroup
Description Controlled vocabulary defining the terms that may be used to describe subgroupings of the sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme
Super-classes skos:Conceptc
puv:MatrixComponentc

Method usedc

IRI https://w3id.org/env/puv#Method
Sub-classes puv:PrepMethodc
puv:AnalyticalMethodc
puv:DataProcessingMethodc
In range of puv:methodop

Parameter (P01)c

IRI https://w3id.org/env/puv#Parameter
Description Scientific variable in databases and data files
Usage Note Remember that a P01 label is always constructed from the following association of concepts: The property or attribute 'of' an object of interest in relation to an environmental matrix 'by' a method (optional) All fields apart from 'of' and 'by' are populated from NVS controlled vocabularies (see this diagram for simple visualisation or download it to use as a tool for quick access to the semantic components of a P01 concept).
Super-classes sosa:ObservablePropertyc
skos:Conceptc
Restrictions skos:broader min 1 puv:ParameterDiscoveryc
In domain of puv:samplePreparationop
puv:dataProcessingop
puv:propertyop
puv:matrixop
puv:analyticalMethodop
puv:chemicalObjectop
puv:statisticop
puv:biologicalObjectop
puv:matrixRelationshipop
puv:physicalObjectop

SeaDataNet Parameter Discovery (P02)c

IRI https://w3id.org/env/puv#ParameterDiscovery
Description Terms describing fine-grained related groups of measurement phenomena designed to be used in dataset discovery interfaces
Super-classes skos:Conceptc

Parameter statistic (S07)c

IRI https://w3id.org/env/puv#ParameterStatistic
Description Controlled vocabulary defining the terms that may be used for a parameter statistic (part of the what theme) in the BODC parameter semantic model
Super-classes skos:Conceptc
In range of puv:statisticop

Physical entity (S29)c

IRI https://w3id.org/env/puv#PhysicalEntity
Description Terms used to describe physical entities in the BODC Parameter Usage Vocabulary
Super-classes puv:Entityc
skos:Conceptc
Restrictions puv:isComposedOfop only puv:PhysicalEntityComponentc
In range of puv:physicalObjectop

Physical entity componentc

IRI https://w3id.org/env/puv#PhysicalEntityComponent
Description Also see S18 (name), S19 (sub-group), S20 (datum)
Super-classes skos:Conceptc
Sub-classes puv:PhysicalEntityNamec
puv:PhysicalEntityDatumc
puv:PhysicalEntitySubGroupc

Physical entity datum (S20)c

IRI https://w3id.org/env/puv#PhysicalEntityDatum
Description Controlled vocabulary defining the terms that may be used to describe the reference with respect to which a physical entity (part of the what theme) in the BODC parameter. semantic model is specified
Super-classes skos:Conceptc
puv:PhysicalEntityComponentc

Physical entity name (S18)c

IRI https://w3id.org/env/puv#PhysicalEntityName
Description Controlled vocabulary defining the terms that may be used for a physical entity (part of the what theme) in the BODC parameter semantic model
Super-classes puv:PhysicalEntityComponentc
skos:Conceptc

Physical entity sub-group (S19)c

IRI https://w3id.org/env/puv#PhysicalEntitySubGroup
Description Controlled vocabulary defining the terms that may be used to qualify a generic physical entity (part of the what theme) in the BODC parameter semantic model
Super-classes skos:Conceptc
puv:PhysicalEntityComponentc

Sample preparation method (S03)c

IRI https://w3id.org/env/puv#PrepMethod
Description Controlled vocabulary defining the terms that may be used for a sample preparation entity (part of the how theme) in the BODC parameter semantic model
Super-classes puv:Methodc
skos:Conceptc
In range of puv:samplePreparationop

Property (S06) c

IRI https://w3id.org/env/puv#Property
Description Controlled vocabulary defining the terms that may be used to specify the property element of a parameter (part of the 'what' theme) in the BODC parameter semantic model
Super-classes sosa:ObservablePropertyc
skos:Conceptc
In range of puv:propertyop

Unit of Measurement (P06)c

IRI https://w3id.org/env/puv#UnitOfMeasurement
Description Terms approved for use by BODC to describe the measurement units for data held in its repositories
Super-classes skos:Conceptc
In range of puv:uomop

Object Properties ↑

analytical methodop

IRI https://w3id.org/env/puv#analyticalMethod
Super-properties puv:methodop
Domain(s) puv:Parameterc
Range(s) puv:AnalyticalMethodc

biological object of interestop

IRI https://w3id.org/env/puv#biologicalObject
Super-properties puv:objectOfInterestop
Domain(s) puv:Parameterc
Range(s) puv:BiologicalEntityc

chemical object of interestop

IRI https://w3id.org/env/puv#chemicalObject
Super-properties puv:objectOfInterestop
Domain(s) puv:Parameterc
Range(s) puv:ChemicalEntityc

data processing methodop

IRI https://w3id.org/env/puv#dataProcessing
Super-properties puv:methodop
Domain(s) puv:Parameterc
Range(s) puv:DataProcessingMethodc

is composed ofop

IRI https://w3id.org/env/puv#isComposedOf
Description link to component concepts

matrix op

IRI https://w3id.org/env/puv#matrix
Description environmental matrix that the measurement is in relation to
Usage Note What is the environmental matrix? - Do I need one? You will for most environmental measurements. - Why? This is to remove any ambiguity about what the value reported relates to. - Take for example "Concentration of cadmium" - This is an ambiguous label if used to define a variable because it does not say concentration of cadmium in what? In the sediment? a water body? the atmosphere? a biological organism? If the former was it in the liquid phase or attached to particles? If the latter was it in the whole organism or one of its organs? - If the measurement relates to a water body or the atmosphere one needs to ask: Was the sample filtered? If it were, then the filter type or filter size is an important information to be stored close to the measurement value. In the P01 semantic model this is captured as part of the matrix definition. For example, when a dissolved quantity is measured in a water body, we apply the following rules - Use "water body [dissolved plus reactive particulate phase]" if the sample was not filtered - Use "water body [dissolved plus reactive particulate
Domain(s) puv:Parameterc
Range(s) puv:Matrixc

measurement-matrix relationshipop

IRI https://w3id.org/env/puv#matrixRelationship
Domain(s) puv:Parameterc
Range(s) puv:MMRelc

methodop

IRI https://w3id.org/env/puv#method
Description method used to measure the value
Usage Note Do I need to specify the method? - This can be important for some measurements or if one wants to distinguish between quantities measured using different methods - The method is specified to avoid ambiguity and minimise the need to refer to free-text documentation - It can help with automated data compilation and aggregation and decrease the risk of data being misinterpreted Take for example, chlorophyll-a. The output from an in situ fluorometer is often labelled as "Concentration of chlorophyll-a". However the values cannot be guaranteed to be an accurate representation of the real amount of chlorophyll-a in a water body without access to textual information about the method and knowing whether the data have been validated against chlorophyll-a measured by filtration, extracted in a solvent and analysed using either HPLC, fluorometry or photometric methods. Most users would require that an automated search of chlorophyll-a data be able to distinguish between these different methods. The P01 semantic model is built so that this information can be captured in the parameter code.
Range(s) puv:Methodc

object of interest op

IRI https://w3id.org/env/puv#objectOfInterest
Description object of interest can be a chemical object, a biological object, a physical phenomenon, or a material object
Usage Note What are the objects of interest? Are they chemical substances? biological organisms? material objects? physical phenomena? none of these? Note that if the property is the property of the environment under study (e.g. "pH of the water body" or "Temperature of the atmosphere") then the object of interest is the environmental matrix and the field "object of interest" can be ignored.
Range(s) puv:Entityc

physical object of interestop

IRI https://w3id.org/env/puv#physicalObject
Super-properties puv:objectOfInterestop
Domain(s) puv:Parameterc
Range(s) puv:PhysicalEntityc

propertyop

IRI https://w3id.org/env/puv#property
Description property or attribute that is being measured, which must be associated with either an object of interest or a matrix or both
Usage Note What are the properties measured or observed? What kind of properties are they? Concentrations? Abundances? Temperature? Uptake rates? pH?
Domain(s) puv:Parameterc
Range(s) puv:Propertyc

sample-preparation methodop

IRI https://w3id.org/env/puv#samplePreparation
Super-properties puv:methodop
Domain(s) puv:Parameterc
Range(s) puv:PrepMethodc

statistic op

IRI https://w3id.org/env/puv#statistic
Description statistical treatment
Domain(s) puv:Parameterc
Range(s) puv:ParameterStatisticc

unit-of-measurement op

IRI https://w3id.org/env/puv#uom
Description scale or unit of measurement
Range(s) puv:UnitOfMeasurementc

Namespaces ↑

default (:)
https://w3id.org/env/puv#
dcterms
http://purl.org/dc/terms/
owl
http://www.w3.org/2002/07/owl#
puv
https://w3id.org/env/puv#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
schema
https://schema.org/
sdo
http://schema.org/
skos
http://www.w3.org/2004/02/skos/core#
sosa
http://www.w3.org/ns/sosa/
time
http://www.w3.org/2006/time#
xml
http://www.w3.org/XML/1998/namespace
xsd
http://www.w3.org/2001/XMLSchema#

Legend

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