A short story of
geologic time ontologies and vocabularies
Xiaogang (Marshall) Ma
Tetherless World Constellation
Rensselae...
1 The topic
• Ontologies are being applied to harmonize distributed
geoscience data and improve functionalities of data
se...
Geology
-- the scientific study of the
earth, including the origin
and history of the rocks and
soil of which the earth is...
GT -- the time which has
elapsed since the
formation of the earth and
the beginning of the
historical period
GTS -- a chro...
2 Models of geologic time scale
• International Commission on Stratigraphy (ICS)
– Targeting at establish a standard time ...
6
2013
The standardized nomenclature and hierarchy of
geologic time scale coordinated by ICS is widely
adopted in geologic...
Now let’s see a few models that describe the
primary concepts in geologic time scale
7
We will see some
UML connectors
in ...
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
inst...
3 Ontologies and vocabularies of
geologic time scale
• The above-mentioned models describe high-level
concepts behind the ...
Table 1 Ontologies and vocabularies of geologic time
scale encoded in Web-compatible formats
14
ID Web address Related pub...
• Now we check the features of a few ontologies and
vocabularies in the above table by using the definition of
‘Lower Tria...
17
<gtime:Epoch rdf:about="#LowerTriassic">
<trela:hasEndTime rdf:resource="#245.9MYA" />
<trela:hasStartTime rdf:resource...
18
<skos:Concept rdf:about="urn:cgi:classifier:ICS:StratChart:200908:LowerTriassic">
<geosciml:from_Ma xml:lang="en">251 +...
19
isc:LowerTriassic
rdf:type gts:GeochronologicEra , skos:Concept ;
rdfs:comment "younger bound-245.9"@en , "older bound-...
Analysis
• SWEET geologic time ontology
– Reuses other ontologies in SWEET
– Quantitative time boundaries
– Less qualitati...
• The general idea of Cox (2011, 2012)
21
A geologic time scale ontology
A vocabulary for each version
of the Internationa...
22
isc:LowerTriassic
rdf:type gts:GeochronologicEra , skos:Concept ;
rdfs:comment "younger bound-245.9"@en , "older bound-...
SISSvoc
Vocabulary deployment
• Publish SKOS document at ‘vocabulary URI’
– http://def.seegrid.csiro.au/ontology/geotime/i...
4 Discussion on further works
• We are currently in a pragmatic situation
– Organizations and individuals are free to buil...
• Ontology/vocabulary evolution
– Geologic time concepts and their descriptions are not static but
continuously evolving, ...
• Ontology/vocabulary mapping
– e.g., Geologic time vocabulary by Cox (2011) makes mappings to
equivalent concepts in DBpe...
• Ontology/vocabulary governance
– the activities related to the directing, guiding, development,
evaluation and revision ...
• Ontology/vocabulary delivery
– Static service: release the RDF document
– A SPARQL endpoint: RESTful, content negotiatio...
5 Recommendations
• Refer to preceding vocabulary or conceptual schema
works
– There is an ontology spectrum
Glossary  Ta...
6 Wrap up
• The review shows that we are still in the beginning stage of using
Semantic Web technologies in the field of g...
Thanks
31
See also
Ma, X., Fox, P., 2013. Recent progress on geologic
time ontologies and considerations for future works....
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A short story of geologic time ontologies and vocabularies

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–Recent progress on geologic time ontologies and vocabularies;
–Their applications;
–Further works;
–Recommendations for other geoscience ontology and vocabulary works.

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A short story of geologic time ontologies and vocabularies

  1. 1. A short story of geologic time ontologies and vocabularies Xiaogang (Marshall) Ma Tetherless World Constellation Rensselaer Polytechnic Institute 01-May-2013 TWC eScience presentation
  2. 2. 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
  3. 3. 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
  4. 4. 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
  5. 5. 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. 6. 6 2013 The standardized nomenclature and hierarchy of geologic time scale coordinated by ICS is widely adopted in geological works across the world.
  7. 7. 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. 8. 8 Geologic time schema in the North American Geologic Map Data Model (NADM) (NADM Steering Committee 2004)
  9. 9. 9 The basic geologic time scale model of Cox and Richard (2005)
  10. 10. 10 The topological temporal ordinal reference system of Michalak (2005)
  11. 11. 11 The schema of geologic time ontology by Perrin et al. (2011)
  12. 12. 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
  13. 13. 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
  14. 14. 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)
  15. 15. • 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 Ordinal Period Epoch AgeEon Era
  16. 16. 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)
  17. 17. 18 <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:prefLa <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:Oleneki <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)
  18. 18. 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"@ "zgodnji/spodnji trias"@sl , "Spodní trias"@cs , "Раннен/долен Триаѿ"@bg , "Early/Lowe Triassic"@en , "Vroeg/Onder Trias"@nl , "raný/spodný trias"@sk , "早三叠世"@zh , "前期三 "@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)
  19. 19. 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
  20. 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
  21. 21. 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)
  22. 22. 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}
  23. 23. 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 visualizationVocabulary service (Cox 2012)
  24. 24. • 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)
  25. 25. • 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
  26. 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
  27. 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
  28. 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)
  29. 29. 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
  30. 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 More information

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