Publishing earth science vocabularies for semantic technologies

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_PropertyType
GFI_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

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
A linked sensor data cube, Lefort, 5th Intl. SSN workshop, 2012

W3C Data Cube ontology
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

What is available?

AGU

Thomson-Reuters

ANZSRC

ICS
Publishing earth science vocabularies |
Cox, Yu, Williams, Giabardo, Lowe
12 |

GSSP

GCMD

Standard ontology
of chemicals

Vocabulary formalization

Formalization: RDF – SKOS for basic vocabularies
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 |
GeochronEra
TemporalReference
System
component
member
skos:ConceptScheme
skos:Concept
skos:hasTopConcept skos:narrowersubClassOf
subClassOf
subPropertyOf
subPropertyOf
domain
domain
domain
range
range
range
domain range

Inferencing
• Entailments and reasoning
• What does this combination of axioms
imply?
• Is there anything unexpected?
Phanerozoic
Cenozoic
Neogene
Stratigraphic
Chart
GeochronEra
TemporalReference
System
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

RDF 123
Every mapping
is different

Turtle,
in text editor …

People + judgement

Vocabulary distribution

• 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

Linked vocabularies can be shared and re-used

Status and lifecycle

Governance issues, design flaws

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?

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 .

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?

Governance issues
Who is the expert? - Wikipedia??

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"^^xsd: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"^^xsd: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> .

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 .

Summary and conclusions

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)

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

LAND AND WATER FLAGSHIP
Thank youEnvironmental Informatics Infrastructure
Simon J D Cox
Research Scientist
t +61 3 9252 6342
e simon.cox@csiro.au
w people.csiro.au/C/S/Simon-Cox
Jonathan Yu
Research Engineer
t +61 3 9252 6440
e jonathan.yu@csiro.au
w people.csiro.au/C/S/Jonathan-Yu

SISSVoc UI & API for vocabulary query
Publishing earth science vocabularies
| Cox, Yu, Williams, Giabardo, Lowe
45 |

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

• 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 |

Governance
Clear roles:
• Content is determined by the experts
• Formalization may uncover inconsistencies
• History and status must be visible
• No deletions! - retirement or supercession

Publishing earth science vocabularies for semantic technologies

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