A short story of geologic time ontologies and vocabularies
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A short story of
geologic time ontologies and vocabularies
Xiaogang (Marshall) Ma
Tetherless World Constellation
Rensselaer Polytechnic Institute
01-May-2013
TWC eScience presentation
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1 The topic
• Ontologies are being applied to harmonize distributed
geoscience data and improve functionalities of data
services on the Web
– Geologic time scale is one of the topics that have received the
most discussion and practices
• This review:
– Recent progress on geologic time ontologies and vocabularies
– Further works
– Recommendations for other geoscience ontology and vocabulary
works
2
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Geology
-- the scientific study of the
earth, including the origin
and history of the rocks and
soil of which the earth is
made
3
Image courtesy of Wikipedia Definition from Oxford Collocations Dictionary
Students examining the Wasatch
Fault near Salt Lake City, Utah
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GT -- the time which has
elapsed since the
formation of the earth and
the beginning of the
historical period
GTS -- a chronological
(i.e. timeline) framework
for studying the history of
the earth
4 Image courtesy of anonymous author
Geologic time & Geologic time scale
Definition from Oxford English Dictionary
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2 Models of geologic time scale
• International Commission on Stratigraphy (ICS)
– Targeting at establish a standard time scale for global correlations
– A primary output: International Stratigraphic Chart
5
2008
2010 2012
2009
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6 2013
The standardized nomenclature and hierarchy of
geologic time scale coordinated by ICS is widely
adopted in geological works across the world.
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Now let’s see a few models that describe the
primary concepts in geologic time scale
7
We will see some
UML connectors
in the following models
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8
Geologic time schema in the
North American Geologic Map
Data Model (NADM) (NADM
Steering Committee 2004)
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9
The basic geologic time scale
model of Cox and Richard (2005)
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10
The topological
temporal ordinal
reference system
of Michalak
(2005)
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11
The schema of geologic time ontology
by Perrin et al. (2011)
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Analysis
• The above models share two main concepts in the
geologic time scale: interval (i.e., a period of time) and
instant (i.e., a particular point in time).
– Interval: ‘AgeInterval’, ‘TimeOrdinalEra’, ‘GL_OrdinalTopolEra’ and
‘GeochronologicUnit’
– Instant: ‘AgeDate’, ‘TimeOrdinalEraBoundary’,
‘GL_OrdinalTopolNode’ and ‘GeochronologicBoundary’
• Each model also has feature of its own on some details
– For detailed analysis see Ma and Fox (2013)
12
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3 Ontologies and vocabularies of
geologic time scale
• The above-mentioned models describe high-level
concepts behind the nomenclature and hierarchy of
temporal intervals and boundaries
• Besides these abstract models, there are also works on
encodings that represent the contents of geologic time
scale in Semantic Web-compatible formats
13
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Table 1 Ontologies and vocabularies of geologic time
scale encoded in Web-compatible formats
14
ID Web address Related publication/webpage
1 http://sweet.jpl.nasa.gov/2.3/stateTimeGeologic.owl (Assessed on 21 March 2012) Raskin and Pan (2005);
http://sweet.jpl.nasa.gov (Assessed on 21 March 2012)
2 http://resource.geolba.ac.at/GeologicTimeScale/GeologicTimeScale/export/GeologicTimeScale.rdf
(Assessed on 21 March 2012)
Ebner (2011);
http://planet.lod2.eu/post/134091850/Marcus-Ebner-In-a-globalized-science-
world (Assessed on 21 March 2012)
3 http://srvgeosciml.brgm.fr/eXist2010/brgm/1GE201001index.html (Assessed on 21 March 2012)
Select “1GE_Ages.xml” in the combo box “GetVocabulary” and click the button “GetVocabulary” to
browse the file
Asch et al. (2010)
4 http://resource.geosciml.org/ISC2009/CGI2011TimeScale.rdf (Assessed on 21 March 2012) https://www.seegrid.csiro.au/wiki/bin/view/CGIModel/ConceptDefinitionsTG
(Assessed on 21 March 2012)
5 https://www.seegrid.csiro.au/subversion/CGI_CDTGVocabulary/tags/SKOSVocabularies/ICS_TimeSc
ale2008.rdf (Assessed on 21 March 2012)
https://www.seegrid.csiro.au/wiki/bin/view/CGIModel/ConceptDefinitionsTG
(Assessed on 21 March 2012)
6 https://www.seegrid.csiro.au/subversion/xmml/ontologies/TBCME/GeologicTimeScale/geologictimesc
ale.rdf (Assessed on 05 February 2011)
The original link is not available now. A copy of the file was archived at:
https://sites.google.com/site/mltgts/mltgts-for-download/geologictimescale.rdf (Assessed on 21 March
2012)
Cox and Richard (2005);
https://www.seegrid.csiro.au/wiki/CGIModel/GeologicTime (Assessed on 21
March 2012)
7 http://def.seegrid.csiro.au/ontology/geotime/isc-2010.ttl (Assessed on 27 June 2012) Cox (2011);
https://www.seegrid.csiro.au/wiki/CGIModel/GeologicTime (Assessed on 21
March 2012)
8 https://sites.google.com/site/mltgts/mltgts-for-download/mtgtsMa2010.rdf (Assessed on 21 March
2012)
Ma et al. (2011)
9 https://sites.google.com/site/mltgts/mltgts-for-download/gtsOwlMa2011.rdf (Assessed on 21 March
2012)
Ma et al. (2012)
10 http://www-
sop.inria.fr/edelweiss/projects/ewok/ontology/dateTimeData/ontologies/GeologicalTimeScale20-1.owl
(Assessed on 03 April 2012)
Perrin et al. (2011);
http://www-sop.inria.fr/edelweiss/projects/ewok/ontologyview/ontologies.html
(Assessed on 03 April 2012)
11 http://resource.geosciml.org/vocabulary/timescale/isc-2012.ttl (Assessed on 14 January 2013) https://www.seegrid.csiro.au/wiki/Siss/VocabularyFormalizationInSKOS
(Assessed on 14 January 2013)
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• Now we check the features of a few ontologies and
vocabularies in the above table by using the definition of
‘Lower Triassic’ as an example
16
Ordinal hierarchical structure
hierarchical
Ord
inal
Period Epoch Age Eon Era
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<gtime:Epoch rdf:about="#LowerTriassic">
<trela:hasEndTime rdf:resource="#245.9MYA" />
<trela:hasStartTime rdf:resource="#251.0MYA" />
<trela:temporalPartOf rdf:resource="#Triassic" />
</gtime:Epoch>
<gtime:Age rdf:about="#Olenekian">
<trela:hasEndTime rdf:resource="#245.9MYA" />
<trela:hasStartTime rdf:resource="#249.5MYA" />
<trela:temporalPartOf rdf:resource="#LowerTriassic" />
</gtime:Age>
<gtime:Age rdf:about="#Induan">
<trela:hasEndTime rdf:resource="#249.5MYA" />
<trela:hasStartTime rdf:resource="#251.0MYA" />
<trela:temporalPartOf rdf:resource="#LowerTriassic" />
</gtime:Age>
<owlt:Instant rdf:about="#245.9MYA">
<screla:hasNumericValue
rdf:datatype="&xsd;double">245.9</screla:hasNumericValue>
</owlt:Instant>
<owlt:Instant rdf:about="#251.0MYA">
<screla:hasNumericValue
rdf:datatype="&xsd;double">251.0</screla:hasNumericValue>
<mrela:hasError rdf:datatype="&xsd;double">0.4</mrela:hasError>
</owlt:Instant>
Geologic time ontology in
SWEET v. 2.3
(ID 1 in Table 1)
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<skos:Concept rdf:about="urn:cgi:classifier:ICS:StratChart:200908:LowerTriassic">
<geosciml:from_Ma xml:lang="en">251 +/-0.4</geosciml:from_Ma>
<geosciml:to_Ma xml:lang="en">245.9</geosciml:to_Ma>
<skos:notation xml:lang="en">a1.1.2.3.3</skos:notation>
<skos:prefLabel xml:lang="bg">Раннен/долен Триас</skos:prefLabel>
<skos:prefLabel xml:lang="cs">Spodní trias</skos:prefLabel>
<skos:prefLabel xml:lang="da">Tidlig/Nedre Triassisk</skos:prefLabel>
<skos:prefLabel xml:lang="de">Frühe/Untere Trias (Buntsandstein)</skos:prefLabel>
<skos:prefLabel xml:lang="en">Early/Lower Triassic</skos:prefLabel>
<skos:prefLabel xml:lang="es">Triásico Inferior</skos:prefLabel>
<skos:prefLabel xml:lang="et">Vara/Alam-Triias</skos:prefLabel>
<skos:prefLabel xml:lang="fi">Varhais/Ala-Trias</skos:prefLabel>
<skos:prefLabel xml:lang="fr">Trias inférieur</skos:prefLabel>
<skos:prefLabel xml:lang="hu">kora/alsó-triász</skos:prefLabel>
<skos:prefLabel xml:lang="it">triassico inferiore</skos:prefLabel>
<skos:prefLabel xml:lang="lt">Ankstyvasis/Apatinis Triasas</skos:prefLabel>
<skos:prefLabel xml:lang="no">Tidlig/undre trias</skos:prefLabel>
<skos:prefLabel xml:lang="nl">Vroeg/Onder Trias</skos:prefLabel>
<skos:prefLabel xml:lang="pl">Wczesny/Dolny Trias</skos:prefLabel>
<skos:prefLabel xml:lang="pt">Triásico Inferior</skos:prefLabel>
<skos:prefLabel xml:lang="sk">rany/spodny trias</skos:prefLabel>
<skos:prefLabel xml:lang="sl">zgodnji/spodnji trias</skos:prefLabel>
<skos:prefLabel xml:lang="sv">äldre/undre trias</skos:prefLabel>
<skos:narrower rdf:resource="urn:cgi:classifier:ICS:StratChart:200908:Induan"/>
<skos:narrower rdf:resource="urn:cgi:classifier:ICS:StratChart:200908:Olenekian"/>
<skos:broader rdf:resource="urn:cgi:classifier:ICS:StratChart:200908:Triassic"/>
</skos:Concept>
Geologic time vocabulary in OneGeology-Europe (1G-E)
(ID 3 in Table 1)
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isc:LowerTriassic
rdf:type gts:GeochronologicEra , skos:Concept ;
rdfs:comment "younger bound-245.9"@en , "older bound-251 +/-0.4"@en ;
rdfs:label "Lower Triassic Epoch"@en ;
gts:rank gts:Epoch ;
gtrs:end isc:BaseMiddleTriassic ;
gtrs:member isc:Induan , isc:Olenekian ;
gtrs:start isc:BaseMesozoic ;
owl:sameAs <http://dbpedia.org/resource/LowerTriassic> ;
skos:altLabel "下三叠统"@zh , "三畳紀前期"@ja ;
skos:broader isc:Triassic ;
skos:broaderTransitive
isc:Mesozoic , isc:Triassic , isc:Phanerozoic ;
skos:inScheme <http://resource.geosciml.org/classifierscheme/ics/ischart/2010> ;
skos:narrower isc:Olenekian , isc:Induan ;
skos:narrowerTransitive
isc:Induan , isc:Olenekian ;
skos:notation "a1.1.2.3.3"^^gts:EraCode ;
skos:prefLabel "Trias inférieur"@fr , "äldre/undre trias"@sv , "Tidlig/undre
trias"@no , "Tidlig/Nedre Triassisk"@da , "Varhais/Ala-Trias"@fi , "kora/alsó-triász"@hu ,
"zgodnji/spodnji trias"@sl , "Spodní trias"@cs , "Раннен/долен Триаѿ"@bg , "Early/Lower
Triassic"@en , "Vroeg/Onder Trias"@nl , "raný/spodný trias"@sk , "早三叠世"@zh , "前期三畳紀"@ja , "Frühe/Untere Trias (Buntsandstein)"@de , "Wczesny/Dolny Trias"@pl , "Vara/Alam-
Triias"@et , "Ankstyvasis/Apatinis Triasas"@lt , "triassico inferiore"@it , "Triásico
Inferior"@pt , "Triásico Inferior"@es ;
foaf:isPrimaryTopicOf
<http://sweet.jpl.nasa.gov/2.2/stateTimeGeologic.owl#LowerTriassic> .
Geologic time vocabulary by
Cox (2011)
(ID 7 in Table 1)
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Analysis
• SWEET geologic time ontology
– Reuses other ontologies in SWEET
– Quantitative time boundaries
– Less qualitative descriptions (but some can be inferred from the
time boundaries, e.g., Induan is a subset of Lower Triassic)
• 1G-E geologic time vocabulary
– A typical application of SKOS
– A point of interest is using multilingual labels for translating
distributed geologic map services in Europe (1G-E portal)
• Geologic time vocabulary by Cox (2011)
– Reuses OWL and SKOS: a overlaid structure
– A point of interest is the SISSVoc vocabulary service
let’s see more about Cox’s work, details in next slides
20
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• The general idea of Cox (2011, 2012)
21
A geologic time scale ontology
A vocabulary for each version
of the International Stratigraphic
Chart
Reuse the ontology
2010
2009
2012
2013
2008
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22
isc:LowerTriassic
rdf:type gts:GeochronologicEra , skos:Concept ;
rdfs:comment "younger bound-245.9"@en , "older bound-251 +/-0.4"@en ;
rdfs:label "Lower Triassic Epoch"@en ;
gts:rank gts:Epoch ;
gtrs:end isc:BaseMiddleTriassic ;
gtrs:member isc:Induan , isc:Olenekian ;
gtrs:start isc:BaseMesozoic ;
owl:sameAs <http://dbpedia.org/resource/LowerTriassic> ;
skos:altLabel "下三叠统"@zh , "三畳紀前期"@ja ;
skos:broader isc:Triassic ;
skos:broaderTransitive
isc:Mesozoic , isc:Triassic , isc:Phanerozoic ;
skos:inScheme <http://resource.geosciml.org/classifierscheme/ics/ischart/2010>
;
skos:narrower isc:Olenekian , isc:Induan ;
skos:narrowerTransitive
isc:Induan , isc:Olenekian ;
skos:notation "a1.1.2.3.3"^^gts:EraCode ;
skos:prefLabel "Trias inférieur"@fr , "äldre/undre trias"@sv , "Tidlig/undre
trias"@no , "Tidlig/Nedre Triassisk"@da , "Varhais/Ala-Trias"@fi , "kora/alsó-
triász"@hu , "zgodnji/spodnji trias"@sl , "Spodní trias"@cs , "Раннен/долен
Триаѿ"@bg , "Early/Lower Triassic"@en , "Vroeg/Onder Trias"@nl , "raný/spodný
trias"@sk , "早三叠世"@zh , "前期三畳紀"@ja , "Frühe/Untere Trias (Buntsandstein)"@de , "Wczesny/Dolny Trias"@pl , "Vara/Alam-Triias"@et , "Ankstyvasis/Apatinis Triasas"@lt
, "triassico inferiore"@it , "Triásico Inferior"@pt , "Triásico Inferior"@es ;
foaf:isPrimaryTopicOf
<http://sweet.jpl.nasa.gov/2.2/stateTimeGeologic.owl#LowerTriassic> .
Geologic time vocabulary by
Cox (2011)
(ID 7 in Table 1)
OWL and SKOS are overlaid. This
will necessarily be OWL Full
Can you see the difference between: twc:X rdf:type owl:Class;
rdf:type skos:Concept.
and twc:X rdf:type owl:Class;
rdfs:subClassOf skos:Concept.
(cf. Bechhofer and Miles 2008)
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SISSvoc
Vocabulary deployment
• Publish SKOS document at ‘vocabulary URI’
– http://def.seegrid.csiro.au/ontology/geotime/isc-2010
• Load SKOS document in triple-store to provide SPARQL
endpoint
– http://def.seegrid.csiro.au/sparql/isc2010
• Configure SISSvoc API
– http://def.seegrid.csiro.au/sissvoc/isc2010/concept
• Configure redirects
– http://resource.geosciml.org/classifier/ics/ischart/LowerTriassic
−http 303→
– http://def.seegrid.csiro.au/sissvoc/isc2012/resource?uri=http://resource.ge
osciml.org/classifier/ics/ischart/LowerTriassic
(Cox, 2012) {URI} vs http://{service}/resource?uri={URI}
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4 Discussion on further works
• We are currently in a pragmatic situation
– Organizations and individuals are free to build ontologies,
vocabularies and develop innovative functions
– As long as the developed ontologies/vocabularies and application
functions can be used to tackle research and/or application
problems in efficient ways
24
Geodata harmonization
(Laxton et al. 2010) (Ma et al. 2012)
Exploratory visualization Vocabulary service
(Cox 2012)
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• Ontology/vocabulary evolution
– Geologic time concepts and their descriptions are not static but
continuously evolving, e.g., the time boundaries in the geologic
time scale are being updated continuously
– Ontologies/vocabularies with ID ‘4’, ‘5’, ‘7’ and ‘11’ are
corresponding to the International Stratigraphic Charts 2009, 2008,
2010 and 2012, respectively
– Cox discussed the difference between changes made to a concept
and those made to the description of a concept: if a concept is
changed, then it is a new concept, and if only the description of a
concept is changed, the concept remains. See: https://www.seegrid.csiro.au/wiki/Siss/VocabularyFormalizationInSKOS
25
(cf. Ding and Foo 2002; Noy and Klein 2004; Pavel and Euzenat 2012)
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• Ontology/vocabulary mapping
– e.g., Geologic time vocabulary by Cox (2011) makes mappings to
equivalent concepts in DBpedia and SWEET by using owl:sameAs and foaf:isPrimaryTopicOf
– e.g., Brodaric and Probst (2009) used the DOLCE foundational
ontology to aid the mapping and integration between two individual
works: the SWEET ontology and the GeoSciML schema
– Need to maintain persistent Uniform Resource Identifiers (URIs)
and metadata for concepts in developed ontologies and
vocabularies, and thus benefit the mappings between ontologies
and vocabularies
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• Ontology/vocabulary governance
– the activities related to the directing, guiding, development,
evaluation and revision of ontologies on certain topics
• involves interactions and collaborations, e.g., in summer 2012 we (i.e., as the
ontology users) did some inference tests with the ‘isc-2010.ttl’ ontology (ID 7 in
Table 1) created by Cox (i.e., as the ontology manager), and we found some inconsistencies in that ontology, such as ‘isc:MiddleTriassic
skos:broader isc:MiddleTriassic’ and ‘isc:MiddleTriassic
skos:narrower isc:MiddleTriassic’. We then contacted Cox and he
revised the ontology.
– Gruber (1995): guidelines for evaluating an ontology: clarity,
coherence, extendibility, minimal encoding bias, and minimal
ontological commitment
– Fox and Lynnes: evaluation guidelines w.r.t. the use of an
ontology: contextual relevance, maturity, intended use, and fit for
use http://tw.rpi.edu/web/project/SeSF/workinggroups/OntologyEvaluation 27
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• Ontology/vocabulary delivery
– Static service: release the RDF document
– A SPARQL endpoint: RESTful, content negotiation
– User-friendly web pages using Application Programming Interfaces
(APIs, e.g., ELDA)
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5 Recommendations
• Refer to preceding vocabulary or conceptual schema
works
– There is an ontology spectrum
Glossary Taxonomy Thesaurus Conceptual schema Ontology
• Collaborative works to improve the interoperability of
geoscience ontologies/vocabularies and the geodata
underpinned by them
• Expressivity, implementability and maintainability of
geoscience ontology/vocabulary works and applications
29
(McGuinness 2003; Uschold and Gruninger 2004)
(Fox 2012)
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6 Wrap up
• The review shows that we are still in the beginning stage of using
Semantic Web technologies in the field of geoscience
• Those items discussed for geologic time ontologies, such as ontology
evolution, ontology mapping, ontology governance, ontology delivery
and multilingual labels are also applicable to other geoscience
ontologies
• More general recommendations:
– Linking current geoscience ontology/vocabulary works to preceding works by
referring to an ontology spectrum
– Collaborative working to improve the interoperability of ontologies and data within
the geoscience community
– Balancing the expressivity, implementability and maintainability to achieve prioritized
applications of geoscience ontologies
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Thanks
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See also
Ma, X., Fox, P., 2013. Recent progress on geologic
time ontologies and considerations for future works.
Earth Science Informatics 6 (1), 31–46.
http://dx.doi.org/10.1007/s12145-013-0110-x
Marshall X Ma
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