Ocean Data Interoperability Platform - Vocabularies: DOIs for NVS Controlled Vocabularies
Developing and publishing vocabularies
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Transcript of Developing and publishing vocabularies
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”
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AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use
Standards
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AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use
We are not alone!OKFN Linked Open
Vocabularies
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http://lov.okfn.org/dataset/lov/
Conceptual Model of QUDT
AGU Fall 2013 | IN52B-08 | Cox, Simons, Yu | Vocabulary re-use
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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
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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
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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
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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 ...
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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#
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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
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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
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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
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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
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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.
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LAND AND WATER
Thank youCSIRO Land and WaterSimon CoxResearch Scientistt +61 3 9252 6342e [email protected] www.csiro.au/people/simon.cox