The doce water quality ontology

Metadata

IRI

http://purl.org/nemo/doce#

Creator(s)

Almeida, João Paulo A.

License

https://creativecommons.org/licenses/by/4.0/legalcode

Ontology Source

RDF (Turtle)

Description

Usage Guide

Table of Contents

• 1. Overview
• 2. Research Activities
• 3. Agents and Devices
• 4. Location and Geographical Features
• 5. Material Entities of Interest
• 6. Water Qualities and their Types
• 7. Measurement (incl. units)

See also reference table of contents.

1. Overview

This section provides an introduction to doce as a primer to prospective users. Turtle is used as a syntax for RDF serialization for illustrative purposes.

An overview of the main fragments of the doce taxonomy is shown below, anchored in the gUFO implementation of UFO. gufo is a prefix for the namespace: http://purl.org/nemo/gufo#

The taxonomy of events of doce concerns research activities of interest:

• gufo:Event
  • ResearchActivity
    • Sampling
    • Preparation
    • Measurement

The taxonomy of objects concern the agents, devices, material entities and procedures that participate in research activities:

• gufo:Object
  • Agent
    • ResearchActivityAgent
    • ResearchActivityPrincipal
  • Device
  • MaterialEntity
    • AbioticEntity
      • AmountOfWater
        • WaterSample
          • SurfaceWaterSample
      • GeographicFeature
        • ArtificialGeographicFeature
          • Reservoir
        • HydrographicFeature
          • SurfaceWaterFeature
            • Lake
            • Reservoir
            • River
        • NaturalGeographicFeature
          • Lake
          • River
    • BioticEntity
    • Sample
      • WaterSample
        • SurfaceWaterSample
    • SampledEntity
  • ResearchActivityProcedure

Abstract individuals are used to establish units of measurement and geolocation coordinates:

• gufo:AbstractIndividual
  • Unit
  • gufo:QualityValue
    • GeographicPoint

The taxonomy of qualities concerns those aspects of the material entities that are subject to measurement and further investigation. A number of qualities are defined in doce to facilitate integration:

• gufo:Quality
  • MetereologicalQuality
    • AmbientTemperature
    • Rainfall
    • RelativeHumidity
  • PhysicalChemicalQuality
    • BiologicalOxygenDemand
    • Concentration
      • MetalConcentration
      • MetalloidConcentration
      • NonMetalConcentration
      • SolidsConcentration
    • Conductivity
    • Hardness_CalciumCarbonateEquivalence
    • pH
    • RedoxPotential
    • Salinity
    • SecchiDiskTransparency
    • Temperature
    • TotalAlkalinityAsCaCO3
    • TrueColor
    • Turbidity
  • SamplingDepth
  • VolumePerUnitTime
    • FlowRate

Additional (metereological, biological and physical-chemical) qualities may be defined instantiating the taxonomy of Quality Kinds:

• gufo:Type
  • gufo:RigidType
    • gufo:Kind
      • QualityKind
        • MetereologicalQualityKind
        • WaterQualityKind
          • BiologicalQualityKind
          • PhysicalChemicalQualityKind
            • ChemicalEntityConcentrationQualityKind
    • ChemicalEntityType

Doce is anchored in gUFO in the following ways:

1. Doce (as a UFO-based ontology) specializes gUFO classes in the gUFO taxonomy of individuals
   For example, doce:Device rdfs:subClassOf gufo:Object, doce:Measurement rdfs:subClassOf gufo:Event and doce:WaterQuality rdfs:subClassOf gufo:Quality.
2. Doce specializes gUFO classes in the gUFO taxonomy of types
   For example, doce:QualityKind rdfs:subClassOf gufo:Kind.
3. Doce instantiates gUFO classes in the taxonomy of types
   For example, doce:Agent rdf:type gufo:Category, doce:SampledEntity rdf:type gufo:Role.

Doce reuses some units of measurement QUDT 2.1 vocabularies. Correspondences are indicated when necessary, and the unit prefix is used for namespace http://qudt.org/vocab/unit/. Some correspondences to QUDT Quantity Kinds are also identified. Correspondences to Chemical Entities of Biological Interest (CHEBI) https://www.ebi.ac.uk/ols/ontologies/chebi are also indicated.

2. Research Activities

The taxonomy of research activities has the following overall structure:

• gufo:Event
  • ResearchActivity
    • Sampling
    • Preparation
    • Measurement

A doce:ResearchActivity is a gufo:Event which is conducted by one or more agents in order to investigate one or more aspects of a phenomenon of interest.

Since all research activities are events they can be given temporal boundaries. gUFO includes a number of data and object properties that can be used with events. For example, temporal aspects can be captured with the data properties gufo:hasBeginPointInXSDDate, gufo:hasBeginPointInXSDDateTimeStamp, gufo:hasEndPointInXSDDate and gufo:hasEndPointInXSDDateTimeStamp. These properties determine the time point when the event starts to take place or when it ends. (Instantaneous events can be represented with the same begin and end point.) (Temporal instants may also be reified using time:Instant in which case the gufo:hasBeginPoint and gufo:hasEndPoint object properties are applicable, see OWL-Time for details concerning time:Instant, including support for Allen relations, temporal reference systems, temporal precision.)

Further, a doce:ResearchActivity is a doce:GeographicallyLocatedEntity, and hence can be located in space (see the doce:locatedIn object property).

The following example shows a fragment representing the sampling of water in a geographic point named RCA-01, on 17th August 2009, 14:24 Brasília Time.

:WaterSampling314020-2017-1 rdf:type owl:NamedIndividual ,
                                    doce:Sampling ;
                            doce:locatedIn :RCA-01 ;
                            gufo:hasBeginPointInXSDDateTimeStamp "2009-08-17T14:24:00-03:00"^^xsd:dateTimeStamp ;
                            gufo:hasEndPointInXSDDateTimeStamp "2009-08-17T14:24:00-03:00"^^xsd:dateTimeStamp .

The following fragment shows the doce:Sample created in the sampling above. A doce:Sample represents a doce:SampledEntity. In this particular case, the sampled entity is the Rio Doce (which is previously defined in doce with the URI doce:RioDoce).

:WaterSample314020-2017-1 rdf:type owl:NamedIndividual ,
                                doce:SurfaceWaterSample ;
                        doce:represents doce:RioDoce ;
                        gufo:wasCreatedIn :WaterSampling314020-2017-1 .

The created Sample is typically subject to measurement later, which can be representing using doce:Measurement. A doce:Measurement is a doce:ResearchActivity whose purpose is to ascertain the value of a quality of an entity of interest (a gufo:Object).

The following example represents the (ex-situ) measurement of alkalinity (doce:TotalAlkalinityAsCaCO3) of the sample identified earlier (which is identified using the doce:measured object property). The measurement is expressed in milligrams per liter (unit:MilliGM-PER-L). (See more on units.) The measured value is represented with the gufo:hasQualityValue data property. In this case, the water sample is found to have a total alkalinity of 22.0 milligrams per liter:

:WaterMeasurementAlkalinity001 rdf:type owl:NamedIndividual ,
                                        doce:Measurement ;
                            doce:measured :WaterSample314020-2017-1 ;
                            doce:expressedIn unit:MilliGM-PER-L ;
                            doce:measuredQualityKind doce:TotalAlkalinityAsCaCO3 ;
                            gufo:hasQualityValue "22.0"^^xsd:double .

For an in-situ doce:Measurement (or a less detailed record of a measurement abstracting away from the sampling event and the sample), the measured gufo:Object is often a doce:GeographicFeature, such as a river (instance of doce:River) or a lake (instance of doce:Lake). Note that for the measurement of a doce:MetereologicalQuality, no specific gufo:Object is indicated.

The following fragment represents the (in-situ) measurement of water temperature (no sampling involved in this case.) The location of the measurement itself is now relevant (in this case point RCA-01). The quality kind measured is doce:Temperature and the measurement is expressed in degrees Celsius (unit:DEC_C). (See more on units.) The measured value is represented with the gufo:hasQualityValue data property. In this case, the water in point RCA-01 measured 21.21 degrees Celsius on the 17th August 2009 at 14:24 Brasília Time:

:WaterTemperatureMeasurement314020-2017-1 rdf:type owl:NamedIndividual ,
                                                doce:Measurement ;
                                        doce:locatedIn :RCA-01 ;
                                        doce:measured doce:RioDoce ;
                                        doce:measuredQualityKind doce:Temperature ;
                                        doce:expressedIn unit:DEG_C ;
                                        gufo:hasBeginPointInXSDDateTimeStamp "2009-08-17T14:24:00-03:00"^^xsd:dateTimeStamp ;
                                        gufo:hasEndPointInXSDDateTimeStamp "2009-08-17T14:24:00-03:00"^^xsd:dateTimeStamp ;
                                        gufo:hasQualityValue "21.21"^^xsd:double .

The following fragment represents the (in-situ) measurement of water transparency in the same location and time (again no sampling involved in this case.) Transparency is measured in meters (unit:M).

:WaterTransparencyMeasurement314020-2017-1 rdf:type owl:NamedIndividual ,
                                                    doce:Measurement ;
                                        doce:locatedIn :RCA-01 ;
                                        doce:measured doce:RioDoce ;
                                        doce:measuredQualityKind doce:SecchiDiskTransparency ;
                                        doce:expressedIn unit:M ;
                                        gufo:hasBeginPointInXSDDateTimeStamp "2009-08-17T14:24:00-03:00"^^xsd:dateTimeStamp ;
                                        gufo:hasEndPointInXSDDateTimeStamp "2009-08-17T14:24:00-03:00"^^xsd:dateTimeStamp ;
                                        gufo:hasQualityValue "0.43"^^xsd:double .

Finally, a doce:Preparation activity is a doce:ResearchActivity whose purpose is to prepare a sample for further analysis. For example, consider activities such as "extractions" in the preparation for measuring the concentration of metals in a water sample. In many cases, preparation is not explicitly modeled, and the preparation activities are encompassed in measurement. When preparation is explicit, a doce:Preparation terminates an original doce:Sample, creating a newly prepared doce:Sample. (See gufo:wasTerminatedIn and gufo:wasCreatedIn.) Explicit preparation creates the opportunity to track the agents involved in handling preparation, the procedures and devices employed.

3. Agents and Devices

Example of a doce:ResearchActivityPrincipal responsible for delegating the sampling and measurement activities discussed earlier:

:Renova rdf:type owl:NamedIndividual ,
                doce:Agent ;
        doce:delegated :WaterMeasurementAlkalinity001 ,
                    :WaterSampling314020-2017-1 ,
                    :WaterTemperatureMeasurement314020-2017-1 ,
                    :WaterTransparencyMeasurement314020-2017-1 .

4. Location and Geographical Features

Example of a doce:GeographicPoint where the sampling and in-situ measurements exemplified above took place:

:RCA-01 rdf:type owl:NamedIndividual ,
                doce:GeographicPoint ;
        wgs:lat "-20.3471"^^xsd:float ;
        wgs:long "-43.1127"^^xsd:float ;
        rdfs:comment "Ponte férrea sobre o rio do Carmo, em Acaiaca (MG). Não atingido pelo rejeito. Área de pastagem." ;
        rdfs:label "Acaiaca - Carmo 01" .

Latitude and longitude are expressed in decimal degrees using datum WGS84, with data properties wgs:lat and wgs:long with xsd:float values. Note that doce:GeographicPoint corresponds to http://www.w3.org/2003/01/geo/wgs84_pos#Point and "coordinate tuple" in ISO 19111:2007. Altitude information can also be included with wgs:alt. See http://www.w3.org/2003/01/geo/ for further information.

5. Material Entities of Interest

The taxonomy of material entities has the following overall structure:

• MaterialEntity
  • AbioticEntity
    • AmountOfWater
      • WaterSample
        • SurfaceWaterSample
    • GeographicFeature
      • ArtificialGeographicFeature
        • Reservoir
      • NaturalGeographicFeature
        • Lake
        • River
      • HydrographicFeature
        • SurfaceWaterFeature
          • Lake
          • Reservoir
          • River

Example of an instance of doce:River:

:RioDoce rdf:type owl:NamedIndividual ,
                :River .

See example of doce:SurfaceWaterSample above under activities.

6. Water Qualities and their Types

The taxonomy of qualities concerns those aspects of the material entities that are subject to measurement and further investigation.

The following metereological qualities have been defined:

• MetereologicalQuality
  • AmbientTemperature
  • Rainfall
  • RelativeHumidity

The following physical-chemical qualities that apply to water have been defined:

• PhysicalChemicalQuality
  • BiologicalOxygenDemand
  • Concentration
    • MetalConcentration
    • MetalloidConcentration
    • NonMetalConcentration
    • SolidsConcentration
  • Conductivity
  • Hardness_CalciumCarbonateEquivalence
  • pH
  • RedoxPotential
  • Salinity
  • SecchiDiskTransparency
  • Temperature
  • TotalAlkalinityAsCaCO3
  • TrueColor
  • Turbidity

The following qualities characterize the point of the body of water in which measurement or sampling takes place.

• SamplingDepth
• VolumePerUnitTime
  • FlowRate

Additional (metereological, biological and physical-chemical) qualities may be defined instantiating the taxonomy of Quality Kinds which are special types of kinds. Instances of these MetereologicalQualityKind and PhysicalChemicalQualityKind should be defined as subclasses of MetereologicalQuality, PhysicalChemicalQuality.

• QualityKind
  • MetereologicalQualityKind
  • WaterQualityKind
    • BiologicalQualityKind
    • PhysicalChemicalQualityKind
      • ChemicalEntityConcentrationQualityKind

7. Measurement (incl. units)

Declarations in doce are provided to establish the units that are applicable to the various quality kinds. For example, the specification states that oxygen saturation is measured with percentages and that conductivity can be measured with μS/cm or mS/cm:

:OxygenSaturation rdf:type owl:NamedIndividual ,
                       :ChemicalEntityConcentrationQualityKind ;
              :hasApplicableUnit unit:PERCENT .

:Conductivity rdf:type owl:NamedIndividual ,
                   :PhysicalChemicalQualityKind ;
          :hasApplicableUnit unit:MicroS-PER-CentiM ,
                             unit:MilliS-PER-CentiM .

Doce reuses some units of measurement QUDT 2.1 vocabularies with the unit prefix denoting the namespace http://qudt.org/vocab/unit/, as follows:

#  http://qudt.org/vocab/unit/CentiM
unit:CentiM rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/DEG_C
unit:DEG_C rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/M
unit:M rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/M3-PER-SEC
unit:M3-PER-SEC rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/MicroGM-PER-L
unit:MicroGM-PER-L rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/MicroS-PER-CentiM
unit:MicroS-PER-CentiM rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/MilliGM-PER-L
unit:MilliGM-PER-L rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/MilliM
unit:MilliM rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/MilliS-PER-CentiM
unit:MilliS-PER-CentiM rdf:type owl:NamedIndividual, :Unit .    
#  http://qudt.org/vocab/unit/MilliV
unit:MilliV rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/NTU
unit:NTU rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/PERCENT
unit:PERCENT rdf:type owl:NamedIndividual, :Unit .
#  http://qudt.org/vocab/unit/PH
unit:PH rdf:type owl:NamedIndividual, :Unit .

Other units not available for reuse for QUDT have been defined. They are particularly relevant to the domain of water quality.

For example, doce:MPN-PER-Decil refers to Most Probable Number per deciliter (in Portuguese NMP/100ml) which can be used to measure total coliforms, doce:HazenUnit refers to units for color measurement following ISO 2211:1973 and doce:PSU to Practical Salinity Units.

:MPN-PER-DeciL rdf:type owl:NamedIndividual ,
                    :Unit .
:HazenUnit rdf:type owl:NamedIndividual ,
                    :Unit .
:PSU rdf:type owl:NamedIndividual ,
                    :Unit .

doce:HazenUnit is used as applicable unit for the doce:TrueColor quality kind:

:TrueColor rdf:type owl:NamedIndividual ,
                :PhysicalChemicalQualityKind ;
       :hasApplicableUnit :HazenUnit .

Reference Table of Contents

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

Classes ↑

• AbioticEntity
• AbstractIndividual
• Agent
• AmbientTemperature
• AmmoniacalNitrogenConcentration
• AmountOfWater
• ArtificialGeographicFeature
• BiologicalOxygenDemand
• BiologicalQualityKind
• BioticEntity
• Category
• ChemicalEntityConcentrationQualityKind
• ChemicalEntityType
• ChlorophyllAConcentration
• Concentration
• ConcreteIndividual
• Conductivity
• CyanideConcentration
• Device
• DissolvedAluminiumConcentration
• DissolvedAntimonyConcentration
• DissolvedArsenicConcentration
• DissolvedBariumConcentration
• DissolvedBerylliumConcentration
• DissolvedBoronConcentration
• DissolvedCadmiumConcentration
• DissolvedCalciumConcentration
• DissolvedChromiumConcentration
• DissolvedCobaltConcentration
• DissolvedCopperConcentration
• DissolvedIronConcentration
• DissolvedLeadConcentration
• DissolvedMagnesiumConcentration
• DissolvedManganeseConcentration
• DissolvedMercuryConcentration
• DissolvedMolybdenumConcentration
• DissolvedNickelConcentration
• DissolvedOrganicCarbonConcentration
• DissolvedOxygenConcentration
• DissolvedPhosphorusConcentration
• DissolvedPotassiumConcentration
• DissolvedSeleniumConcentration
• DissolvedSilicaConcentration
• DissolvedSilverConcentration
• DissolvedSodiumConcentration
• DissolvedVanadiumConcentration
• DissolvedZincConcentration
• Event
• FerricIronIIIConcentration
• FerrousIronIIConcentration
• FlourideConcentration
• FlowRate
• GeographicFeature
• GeographicPoint
• GeographicallyLocatedEntity
• Geometry
• Hardness_CalciumCarbonateEquivalence
• HydrogenSulfideConcentration
• HydrographicFeature
• Kind
• KjeldahlMethodNitrogenConcentration
• Lake
• MaterialEntity
• Measurement
• MetalConcentration
• MetalloidConcentration
• MetereologicalQuality
• MetereologicalQualityKind
• MethylmercuryConcentration
• NaturalGeographicFeature
• NitrateConcentration
• NitriteConcentration
• NonMetalConcentration
• Object
• OrganicNitrogenConcentration
• OxygenSaturation
• PheophytinConcentration
• PhosphateConcentration
• PhysicalChemicalQuality
• PhysicalChemicalQualityKind
• PolyphosphateConcentration
• Preparation
• Quality
• QualityKind
• QualityValue
• Rainfall
• RedoxPotential
• RelativeHumidity
• ResearchActivity
• ResearchActivityAgent
• ResearchActivityPrincipal
• ResearchActivityProcedure
• Reservoir
• RigidType
• River
• Salinity
• Sample
• SampledEntity
• Sampling
• SamplingDepth
• SecchiDiskTransparency
• SettleableSolids
• SolidsConcentration
• SulphateConcentration
• SurfaceWaterFeature
• SurfaceWaterSample
• Temperature
• TotalAlkalinityAsCaCO3
• TotalAluminiumConcentration
• TotalAntimonyConcentration
• TotalArsenicConcentration
• TotalBariumConcentration
• TotalBerylliumConcentration
• TotalBoronConcentration
• TotalCadmiumConcentration
• TotalCalciumConcentration
• TotalChlorideConcentration
• TotalChromiumConcentration
• TotalCobaltConcentration
• TotalCopperConcentration
• TotalDissolvedSolids
• TotalIronConcentration
• TotalLeadConcentration
• TotalMagnesiumConcentration
• TotalManganeseConcentration
• TotalMercuryConcentration
• TotalMolybdenumConcentration
• TotalNickelConcentration
• TotalOrganicCarbonConcentration
• TotalPhosphorousConcentration
• TotalSeleniumConcentration
• TotalSilverConcentration
• TotalSodiumConcentration
• TotalSolids
• TotalSulfideConcentration
• TotalSuspendedSolids
• TotalVanadiumConcentration
• TotalZincConcentration
• TrueColor
• Turbidity
• Type
• Unit
• VolumePerUnitTime
• WaterQualityKind
• WaterSample
• pH

Object Properties ↑

• delegated
• expressedIn
• hasApplicableUnit
• hasAssociatedChemicalEntityType
• locatedIn
• measured
• measuredQualityKind
• performed
• represents
• wasAdoptedIn
• wasMeasuredIn
• wasUsedIn
• hasReifiedQualityValue
• participatedIn

Datatype Properties ↑

• lat
• long

Namespaces ↑

default (:)

http://purl.org/nemo/doce#

:

http://purl.org/nemo/doce#

brick

https://brickschema.org/schema/Brick#

csvw

http://www.w3.org/ns/csvw#

dc

http://purl.org/dc/elements/1.1/

dcam

http://purl.org/dc/dcam/

dcat

http://www.w3.org/ns/dcat#

dcmitype

http://purl.org/dc/dcmitype/

dct

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

doap

http://usefulinc.com/ns/doap#

foaf

http://xmlns.com/foaf/0.1/

geo

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

gufo

http://purl.org/nemo/gufo#

odrl

http://www.w3.org/ns/odrl/2/

org

http://www.w3.org/ns/org#

owl

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

prof

http://www.w3.org/ns/dx/prof/

prov

http://www.w3.org/ns/prov#

qb

http://purl.org/linked-data/cube#

rdf

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

rdfs

http://www.w3.org/2000/01/rdf-schema#

schema

https://schema.org/

sh

http://www.w3.org/ns/shacl#

skos

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

sosa

http://www.w3.org/ns/sosa/

ssn

http://www.w3.org/ns/ssn/

time

http://www.w3.org/2006/time#

unit

http://qudt.org/vocab/unit/

vann

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

void

http://rdfs.org/ns/void#

wgs

https://www.w3.org/2003/01/geo/wgs84_pos#

wgs1

http://www.w3.org/2003/01/geo/wgs84_pos#

xml

http://www.w3.org/XML/1998/namespace

xsd

http://www.w3.org/2001/XMLSchema#