Developing and publishing vocabularies

Simon Cox, Bruce Simons, Jonathan Yu | Environmental Information Systems4 December 2013

LAND AND WATER

Are we talking about the same thing? - Beer glasses in Australia

Glass Size

115 ml 4 oz

140 ml 5 oz

170 ml 6 oz

200 ml 7 oz

225 ml 8 oz

255 ml 9 oz

285 ml 10 oz

425 ml 15 oz

575 ml 20 oz

NSW - Pony - Seven - - Middy Schooner Pint

NT - - - Seven - - Handle Schooner -

QLD - Small Beer - - Glass - Pot - -

SA - Pony - Butcher - - Schooner Pint -

TAS Small Beer - A Beer or

Six - Eight - Ten orPot - -

VIC - Pony Small Glass - - Pot Schooner -

WA Shetland Pony Pony Bobbie Glass - - Middy Schooner Pot

Source: http://www.liquormerchants.org.au/Q&A.html

Linked Vocabularies | Simon Cox2 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Healthy Headwater - NGIS Termscas_rnnumber

ANGDTS Code ANGDTS Description Units_used

WDTF Parameter chemical name

ADWG name

IUPAC name Group Ion

EC ECease at which conduction current can be caused to flow through material in microSiemens/centimetre

us/cm ms/cm mg/L

ElectricalConductivityAt25C_uScm

Electrical Conductivity Conductivity

PH pH negative logarithm of hydrogen ion concentration in ph units pH units WaterpH_pH

pH pHpH, alkalinity, acidity

16887-00-6

16887-00-6

concentration of chloride as Cl in milligrams/litre

mg/L mg/kg Chloride Chloride Chloride Anion

TDS TDSthe portion of total solids that passes through filter and deemed to have been dissolved in sample in milligrams/litre

mg/LTotal Dissolved Solids

Total Dissolved Solids Salinity

TOTALALKALINITY ALKT

concentration in milligrams/litre CaCO3 of titratable bases using a methyl-orange endpoint of about pH 4.3

mg/LTotal Alkalinity (as CaCO3)

pH, alkalinity, acidity

HARDNESS_CACO3

HARDthe ability of water to precipitate soap and is sum of calcium and magnesium concentrations as milligrams/litre CaCO3

mg/LHardness (as CaCO3)

Hardness (as calcium carbonate)

Hardness (as calcium carbonate)

SAR SARratio of sodium to magnesium and calcium and used to assess risk of excess sodium in irrigation water Ratio

Sodium Adsorption Ratio Salinity

3812-32-6 ALKC alkalinity ascribed to carbonate in

milligrams/litre CO3mg/L %MOL

Carbonate Alkalinity (as CaCO3) Carbonate

pH, alkalinity, acidity

NITRATE 14797-55-8

concentration of nitrate as N in milligrams/litre

mg/L mg/kg Nitrate

Nitrate and Nitrite

Nitrate and Nitrite Anion

7439-89-6

7439-89-6

concentration of iron as Fe in milligrams/litre

mg/L mg/kg

ug/LIron Iron Metal Cation

collectionalt names hierarchy

Are these the same?

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

“nitrogen”“dissolved nitrogen”“Total nitrogen, water, filtered, milligrams per liter”“Concentration of nitrogen (total) per unit volume of the water body [dissolved plus reactive particulate phase] by oxidation and colorimetric autoanalysis““Concentration of nitrogen (total) per unit mass of the water body [dissolved plus reactive particulate <GF/F phase] by filtration and high temperature Pt catalytic oxidation”“Concentration (moles or mass) of total nitrogen (i.e. nitrogen in all chemical forms) in suspended particulate material per unit volume of the water column.”“Concentration of nitrogen (total) {'PON'} per unit volume of the water body [particulate 2-10um phase] by filtration, acidification and elemental analysis”“Dissolved total and organic nitrogen concentrations in the water column”

4 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Standards

5 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

We are not alone!OKFN Linked Open

Vocabularies

6 |

http://lov.okfn.org/dataset/lov/

Conceptual Model of QUDT

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

7

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Standard ontology of chemicals

http://purl.obolibrary.org/obo/chebi.owl

>36 000 chemical entities

8 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Dissolved nitrogen concentration objects

dissolved nitrogen

concentration

nitrogen

elemental nitrogen

(CHEBI_33267)

Concentration

MolePercent

MilliGramsPerLitre

AmountOfSubstancePerUnitVolume

nitrogen concentration

+qudt:generalization

+objectOfInterest

+exactMatch

+qudt:quantityKind

+qudt:quantityKind

+qudt:generalization

+qudt:unit

+qudt:unit

+qudt:generalization

ScaledQuantityKindSubstanceOrTaxon

Unit

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Extension to QUDT

QUDT WQOP

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Linked to SKOS

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use12 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Linked vocabulary items

• http://environment.data.gov.au/water/quality/def/object/

• http://environment.data.gov.au/water/quality/def/object/anthracene

• http://environment.data.gov.au/water/quality/def/property/anthracene_concentration

13 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Underneath

• SPARQL endpoint http://sissvoc.ereefs.info/ereefs/sparql(test with this tool http://yasgui.laurensrietveld.nl/ )

• SISSvoc servicehttp://sissvoc.ereefs.info/sissvoc/ereefs/collection

• SISSvoc searchhttp://sissvoc.ereefs.info/search

14 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

NERC Vocabulary Service

• 60+ collections• 30,000+ terms (most in P01!)• Scope: geography, instruments, organizations, properties ...

15 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

NVS implementation/interfaces

• SQL storehttp://vocab.nerc.ac.uk/

• View item as SKOS Concepthttp://vocab.nerc.ac.uk/collection/C18/current/72/

• SPARQL endpoint http://vocab.nerc.ac.uk/sparql

• SISSvoc servicehttp://auscope-services-test.arrc.csiro.au/elda-demo/nerc

• SISSvoc searchhttp://sissvoc.ereefs.info/search#

16 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Harmonization

• WQOP Model extends QUDT

• Items refer to ChEBI• http://environment.data.gov.au/water/quality/def/object/anthracene

• Mappings to NVS• http://environment.data.gov.au/water/quality/def/property/air_pressure• http://environment.data.gov.au/water/quality/def/property/anthracene_con

centration

17 |

Linked Vocabularies | Simon Cox

[ODIP-1] Conflation

• Property/parameter vocabularies have 100s-1000s entries• each definition includes

– Semantics – the quantity being observed e.g. ‘Nitrogen’Plus one or more of– Procedure – the instrument or method used– Sampling protocol e.g. Weekly-mean– Units of measure– Aggregation with other primitive parameters

• This makes it difficult to discover and combine data from different projects

18 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Harmonization challenges

• Even standard mapping props have no effect without reasoning (sameAs/exactMatch/equivalentClass)

• items may be conceptualised as both classes and individuals: complicates mapping mechanics

• URIs generally reflect ownership/maintenance• re-use of items across vocabularies may lead to surprises

• versioning complicates cross-eferences and re-usehttp://sweet.jpl.nasa.gov/2.2/matrRock.owl#Serpentinite vs.http://sweet.jpl.nasa.gov/2.1/matrRock.owl#Serpentinite

???19 |

SUMMARY

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Summary

• Vocabularies should be• Standardized• Published• Harmonized

• Extend / re-use existing vocabularies where possible

http://environment.data.gov.au/water/quality/def/property/ http://sissvoc.ereefs.info/search

21 |

AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use

Acknowledgements

This work was undertaken as part of CSIRO’s contribution to eReefs – a National Environmental Information Infrastructure project.

22 |

LAND AND WATER

Thank youCSIRO Land and WaterSimon CoxResearch Scientistt +61 3 9252 6342e simon.cox@csiro.auw www.csiro.au/people/simon.cox