Post on 06-May-2015
description
transcript
A short story of
geologic time ontologies and vocabularies
Xiaogang (Marshall) Ma
Tetherless World Constellation
Rensselaer Polytechnic Institute
01-May-2013
TWC eScience presentation
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
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
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
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
6 2013
The standardized nomenclature and hierarchy of
geologic time scale coordinated by ICS is widely
adopted in geological works across the world.
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
8
Geologic time schema in the
North American Geologic Map
Data Model (NADM) (NADM
Steering Committee 2004)
9
The basic geologic time scale
model of Cox and Richard (2005)
10
The topological
temporal ordinal
reference system
of Michalak
(2005)
11
The schema of geologic time ontology
by Perrin et al. (2011)
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
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
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)
• 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
17
<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)
19
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)
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
• 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
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)
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}
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)
• 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)
• 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
26
• 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
• 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)
28
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)
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
30
Thanks
31
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
max7@rpi.edu
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