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Simon J D Cox, Jonathan Yu, Megan Williams, Fabrizio Giabardo, Dominic Lowe
16 April 2015
LAND AND WATER FLAGSHIP
Technologies and practices for maintaining and publishing earth science vocabularies
Are these the same?
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe
“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”
2 |
Why are vocabularies important?
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe3 |
OM_Observation
+ phenomenonTime
+ resultTime
+ validTime [0..1]
+ resultQuality [0..*]
+ parameter [0..*]
GFI_PropertyTypeGFI_Feature
OM_ProcessGFI_DomainFeature Any
+observedProperty
1+propertyValueProvider
0..*
+featureOfInterest
1
+generatedObservation
0..*
+procedure1 +result
Range
observed property
Parameter dictionary
procedure
Register of sensors, processes & algorithms
feature of interest
Feature-type catalogue
Feature service
result format:
GML, SWE, netCDF, JSON, SQLite...
O&M domain specialization
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe4 |
RDF Data Cube 101 - Slices and observations
Dimension d6
Dimension d7
Dimension d1
Dimension d2
Dimension d3
Dimension d4
Dimension d5
Measure m1, m2, …
Attribute a1, a2, …
Cube
Slice
Observation
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe5 |A linked sensor data cube, Lefort, 5th Intl. SSN workshop, 2012
W3C Data Cube ontology
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe6 |
Each axis or variable
specified as a skos:Concept
Values of coded-properties
selected from a
skos:ConceptScheme
Homogeneous observations,
common structure definition
The RDF Data Cube Vocabulary, Cyganiak & Reynolds, W3C Recommendation 2014
Standard ontology of chemicals
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe15 |
Vocabulary formalization
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe16 |
Formalization: RDF – SKOS for basic vocabularies
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe17 |
chem:sodium
a skos:Concept ;
rdfs:label "sodium"^^xsd:string ;
skos:broader chem:alkali ;
skos:exactMatch <http://dbpedia.org/resource/Sodium> ;
skos:inScheme skos:chemicals ;
skos:prefLabel "nátrium"@hu , "sodio"@it , "sodium"@fr , "sodium"@en .
RDFS
Semantic web dead long live semantic web | Simon Cox18 |
GeochronEraTemporalReference
System
componentmember
skos:ConceptSchemeskos:Concept
skos:hasTopConcept skos:narrowersubClassOf subClassOf
subPropertyOf subPropertyOf
domain
domain
domain
range
rangerange
domain range
Inferencing
• Entailments and reasoning
• What does this combination of axioms imply?
• Is there anything unexpected?
Phanerozoic
Cenozoic
Neogene
StratigraphicChart
GeochronEra
TemporalReferenceSystem
type
type
type
type
component member
member
hasTopConcept narrower
narrowernarrowerTransitive
Concept
ConceptScheme
broaderTransitive
Semantic web dead long live semantic web | Simon Cox19 |
Formalization and encoding process
Create order within existing excel spreadsheets
Every layout is different
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe20 |
Formalization and encoding process
RDF 123
Every mapping
is different
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe21 |
Formalization and encoding process
Turtle,
in text editor …
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe22 |
Vocabulary distribution
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe24 |
• Physical documents, PDF
• Tables on web pages
• Bespoke XML documents
• RDF documents, OWL documents
• Web services
• RESTful web resources, Linked data
Vocabulary services | Cox & Yu
Delivery
Publish as linked data
URI = web-scale foreign-key
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe26 |
Linked vocabularies can be shared and re-used
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe27 |
Governance issues, design flaws
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe31 |
Governance issues
What is the best way to re-use existing content already published as linked data?
Do we fix it for them? Do we re-claim it?
Vocabulary deployment and governance | Cox32 |
Modeling flaws
GCMD science keywords
• Same textual definition, same label
• Different parent, different URI
– are they the same concept?
Vocabulary deployment and governance | Cox33 |
Re-base the URI?
<http://registry.it.csiro.au/def/kwa/gcmd/ABRASION>
a skos:Concept ;
rdfs:label "ABRASION" ;
dct:description "Mechanical scraping of a rock surface by friction between rocks and moving particles."@en ;
owl:sameAs
<http://gcmdservices.gsfc.nasa.gov/kms/concept/8f57f4b0-5177-4362-81e8-ced75d37d1aa> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/fd29bf77-df38-4b80-8148-8184fa41d843> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/efacd4f6-59ea-4019-8265-8cc81ecc99c0> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/f6e19e2e-555a-4d40-9833-c7513d92c813> ;
skos:prefLabel "ABRASION"@en .
Vocabulary deployment and governance | Cox34 |
Versioning flaws
NASA SWEET
http://sweet.jpl.nasa.gov/1.1/time.owl#PLIOCENE
http://sweet.jpl.nasa.gov/2.0/timeGeologic.owl#Pliocene
http://sweet.jpl.nasa.gov/2.1/reprTimeGeologicPeriod.owl#Pliocene
http://sweet.jpl.nasa.gov/2.2/stateTimeGeologic.owl#Pliocene
http://sweet.jpl.nasa.gov/2.3/stateTimeGeologic.owll#Pliocene
• Same label, and same place in hierarchy
• Different URI
- are they the same concept?
Vocabulary deployment and governance | Cox35 |
Collection sub-set?
<http://registry.it.csiro.au/def/kwa/gcmd/GCMD-keywords-subset_newnames>
a skos:Collection ;
rdfs:label "Subset of GCMD keywords - re-based"̂ x̂sd:string ;
skos:member <http://registry.it.csiro.au/def/kwa/gcmd/ABLATION> , <http://registry.it.csiro.au/def/kwa/gcmd/ABRASION> , <http://registry.it.csiro.au/def/kwa/gcmd/ABLATION-ZONES-ACCUMULATION-ZONES> .
- Or -
<http://registry.it.csiro.au/def/kwa/gcmd/GCMD-keywords-subset>
a skos:Collection ;
rdfs:label "Subset of GCMD keywords"̂ x̂sd:string ;
skos:member
<http://gcmdservices.gsfc.nasa.gov/kms/concept/8f57f4b0-5177-4362-81e8-ced75d37d1aa> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/95fbaefd-1afe-4887-a1ba-fc338a8109bb> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/99db4dca-4d07-48fd-8ba3-393532d04aa6> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/a994a6f6-cfcd-45d2-95a4-0f8455a9454d> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/efacd4f6-59ea-4019-8265-8cc81ecc99c0> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/fd29bf77-df38-4b80-8148-8184fa41d843> , <http://gcmdservices.gsfc.nasa.gov/kms/concept/f6e19e2e-555a-4d40-9833-c7513d92c813> .
Vocabulary deployment and governance | Cox37 |
More complex constraints?
OWL classes vs instances
cgi-lith-instance:carbonate_rich_mudstone a skos:Concept ;
rdfs:label "carbonate-rich mudstone" ;skos:broader cgi-lith-instance:rock_material ;CGI_Lith:ConsolDegree CGI_Lith:consolidated ;CGI_Lith:Constituents CGI_Lith:carbonateBearing ;CGI_Lith:GeneticCateg CGI_Lith:sedimentary ;CGI_Lith:GrainSize CGI_Lith:mud_size ;CGI_Lith:ParticleType CGI_Lith:grain .
Vocabulary deployment and governance | Cox38 |
Summary and conclusions
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe39 |
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe40 |
Source Vocabulary
(csv, html, txt)
Database (triple-store)
Formalized vocabulary
(skos/rdf)
Vocab service
LDR API SPARQL
SISSVoc
Summary
• Term vocabularies can be formalized in RDF (SKOS, OWL) and published as linked data
• Much content available, but needs converting (‘lifting’) to semantic technologies
• Excel, RDF123, Text editor, SKOS, LDR and SISSVoc are our enablers (but people are essential)
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe41 |
Applications and published vocabularies
• GeoSciML vocabularies
• http://def.seegrid.csiro.au/sissvoc/cgi201211/collection
• http://resource.geosciml.org/classifier/ics/ischart/
• Environmental observations vocabularies
• http://environment.data.gov.au/def/
• http://registry.it.csiro.au/environment/def
• Bioregional assessments glossary
• http://registry.it.csiro.au/test1/ba-glossary
• Agriculture definitions
• http://registry.it.csiro.au/agriculture/def
• Australian Government definitions - AGIFT 2014, ANZSRC 2008 …
• http://registry.it.csiro.au/agldwg/def
• CSIRO Keyword aggregator … • Coming soon
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe42 |
LAND AND WATER FLAGSHIP
Thank youEnvironmental Informatics InfrastructureSimon J D CoxResearch Scientist
t +61 3 9252 6342e [email protected] people.csiro.au/C/S/Simon-Cox
Jonathan YuResearch Engineer
t +61 3 9252 6440e [email protected] people.csiro.au/C/S/Jonathan-Yu
SISSVoc UI & API for vocabulary query
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe45 |
Simplified Knowledge Organization System SKOS: a W3C Standard
Focus on the concept rather than the term
• Web/Linked data principle: Concept is identified by a URI
• Concept is annotated with text labels (i.e. the traditional ‘term’)
• Structured using hierarchical relations within a vocabulary• broader, narrower
• Matching relations between vocabularies• broadMatch, closeMatch, exactMatch
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe47 |
• Physical documents, PDF
• Tables on web pages
• Bespoke XML documents
• RDF documents, OWL documents
• Web services
• RESTful web resources, Linked data
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, Lowe
Delivery
O&M
OM_Observation
+ phenomenonTime
+ resultTime
+ validTime [0..1]
+ resultQuality [0..*]
+ parameter [0..*]
GF_PropertyType
GFI_Feature
OM_Process Any
+observedProperty
1
0..*
+featureOfInterest 1
0..*
+procedure1 +result
Publishing earth science vocabularies | Cox, Yu, Williams, Giabardo, LoweISO 19156:2011 Geographic Information – Observations and measurements – ed. S Cox49 |