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A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
A short story of geologic time ontologies and vocabularies
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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; …

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

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  • 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. 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. 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. 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. 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 2013 The standardized nomenclature and hierarchy of geologic time scale coordinated by ICS is widely adopted in geological works across the world.
  • 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 Geologic time schema in the North American Geologic Map Data Model (NADM) (NADM Steering Committee 2004)
  • 9. 9 The basic geologic time scale model of Cox and Richard (2005)
  • 10. 10 The topological temporal ordinal reference system of Michalak (2005)
  • 11. 11 The schema of geologic time ontology by Perrin et al. (2011)
  • 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. 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. 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. • 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. 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. 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. 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. 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. • 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. 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. 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. 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. • 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. • 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. • 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. • 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. 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. 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. 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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