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Towards OWL-based Knowledge Representation in Petrology

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Towards OWL-based Knowledge Representation in Petrology

  1. 1. Towards OWL-based Knowledge Representation in Petrology A.Shkotin, V.Ryakhovsky, D.Kudryavtsev GIS Department Vernadsky State Geological Museum Russian Academy of Sciences www.sgm.ru ashkotin@acm.org
  2. 2. Contents Introduction Fact formalization Dictionary formalization Formal definitions Conclusions and further plans Acknowledgments References 2
  3. 3. IntroductionPetrology is a science investigating rocks andtheir formation conditions.Large volume of petrological information requiringsystematization, integration and maintenance in aconsistent state is accumulated at present.These tasks can be solved through knowledgeformalization. 3
  4. 4. Knowledge FormalizationFinal goal: Create a formal theory for the keyconcepts of petrology and relationships amongthem.Ontologies, that is conceptual structuresorganized on the basis of mathematical logic, playa pivotal role in the process of creation.Definitions play a decisive role in a formal theory,as they specify exactly those concepts whoseproperties will be used and studied. 4
  5. 5. Formal TheoryBuilding a formal theory of the field of naturalscience similar of a mathematical one enables: Revealing primary concepts Giving definitions to other concepts Stating axioms and theorems 5
  6. 6. Fact Formalization 6
  7. 7. The ApproachDatabases are not a knowledge.They require an essential and thoroughprocessing to obtain a knowledge.DB conversion to the traditional form ofknowledge, i.e. knowledge in a natural language,is the direct way of obtaining knowledge fromdata.The natural language is limited to a CNL. CNL is auniversal means of formal knowledgepresentation. 7
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  9. 9. CNL Sentences. The ApproachCreate templates of a CNL sentences to presentall the facts contained in the Proba DB.Use local (‘internal’) proper names.Connect words in composite terms using ‘_’ letter.Global commonly known proper names such asIceland, Atlantic_Ocean can be found in a text. 9
  10. 10. CNL Sentences. ExamplePUB5633 is a publication.PUB5633 title is "A CONTRIBUTION TO THE GEOLOGY OF THE K...".SAM32994 is a sample. SAM32994 is a rhyolite.PLC32994 is a place. PLC32994 is a part of Iceland.SUB469812 is a substance.WPC469812 is a weight_percent. WPC469812 value is73.95.PUB5633 describes SAM32994.SAM32994 gathering_place is PLC32994.SAM32994 includes SUB469812.SUB469812 is a WPC469812 component. 10
  11. 11. OWL OntologyAll generated sentences are ACE* languagestatements.The sentences are so that the APE* translatortranslates them to OWL.The DB is converted to 1,174 ontologies.* Attempto Project. http://attempto.ifi.uzh.ch/site/ 11
  12. 12. OWL Ontology #5633 Classes: place,  Object properties: publication, rhyolite, component, sample, substance, gathering_place, weight_percent. includes, mixture, part... Data properties:  Individuails: Iceland, authorial_number, PLC32994..., chemical_formula, PUB5633, first_page, latitude, SAM32994..., longitude, reference, SUB469812..., title, value, year. WPC469812... 12
  13. 13. Dictionary Ontology andDefinition Concentrator 13
  14. 14. Definition Dictionaryis an important and specific type of knowledgecontains the terms of a subject area and informaldefinitions of these terms.Informal definitions are provided by expertsusually belonging to a scientific school.Tasks: Convert a definition dictionary into formal knowledge Gather definitions given by various schools 14
  15. 15. Dictionary Entry ExampleHARZBURGITE. An ultramafic plutonic rockcomposed essentially of olivine andorthopyroxene. Now defined modally in theultramafic rock classification (Fig. 2.9, p.28).(Rosenbusch, 1887, p.269; Harzburg, HarzMts, Lower Saxony, Germany; Tröger 732;Johannsen v.4, p.438; Tomkeieff p.247)[IRCGT], p.88 15
  16. 16. From Dictionary Text to OntologyDictionary“Dictionary of Terms of Igneous Rocks. 1,567entries, the overwhelming majority of them beingrock names.OwnerInter-Departmental Petrographic Committee in theGeoscience Division of the Russian Academy ofSciences.Texthttp://www.igem.ru/site/petrokomitet/slovar.htmOntology http://earth.jscc.ru/ontologies/dic.owl 16
  17. 17. Definition ConcentratorThe goal is to collectively maintain definitions ofscientific terms, including formal definitions.The ontology of igneous rocks is contained inwebProtege under the dic name.Some terms are complemented with definitionsfrom other dictionaries.Address at Geology portal:http://earth.jscc.ru/webprotege/ 17
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  19. 19. Name Spacesprefix pgc: <http://www.igem.ru/site/petrokomitet/slovar#>prefix dic: <http://earth.jscc.ru/ontologies/dic.owl#>prefix gwr: <http://wiki.web.ru/wiki#>prefix pgcc: <http://www.igem.ru/site/petrokomitet/code#> 19
  20. 20. Formal Term Meaning Definitionabessedite isperidotite and mineral_mixture andcontains_mineral only (olivine or hornblende orphlogopite)OWL syntax – Manchester. 20
  21. 21. Formal Definitions 21
  22. 22. Primary SourceLe Maitre, L.E., ed. 2002. Igneous Rocks: AClassification and Glossary of Terms 2nd edition,Cambridge.http://amigoreader.com/book/?b=29372 22
  23. 23. Building an AlgorithmThe classification rules described inmethodologies and recommendations have to beused to obtain precise definitions and to formalizethem.We start with a revision of all parts of thealgorithm. 23
  24. 24. VPC DefinitionsModal content of pyroxenesVPC_Px(x) = VPC_Opx(x)+VPC_Cpx(x)Mineral groups for diagramsVPC_OOC(x) = VPC_Ol(x)+VPC_Opx(x)+VPC_Cpx(x)VPC_OPH(x) = VPC_Ol(x)+VPC_Px(x)+VPC_hornblende(x)Modal content of mafic mineralsVPC_M(x) = 100 - (VPC_Q(x)+VPC_A(x)+VPC_P(x)+VPC_F(x)) 24
  25. 25. Qualitative CharacteristicsPredicatespyroclastic, kimberlite, lamproite, lamprophyre,charnockite, plutonic, volcanic.Definitionpyroclastic(x) = clastic(x) and(∀y clast(y) ⋀ part_of(y,x)→ volcanic_eruption_result(y))DLPyroclastic ≡ clastic⊓∀(part_of∘id(clast))-.volcanic_eruption_result 25
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  28. 28. The Use of ReasonersThe described properties can be automaticallyverified by loading definitions into a reasonerworking with linear inequalities.Such reasoners do exist (e.g. Racer), and linearinequalities can be written using the OWL 2extension [OWL2LE]. 28
  29. 29. harzburgiteharzburgite(x) =plutonic(x) andnot (pyroclastic(x) or kimberlite(x) or lamproite(x)or lamprophyre(x) or charnockite(x))and VPC_carbonates(x)≤50 andVPC_melilite(x)≤10 and VPC_M(x) ≥ 90 andVPC_kalsilite(x)=0 and VPC_leucite(x)=0 andVPC_hornblende(x)=0 and0.4*VPC_OOC(x)≤VPC_Ol(x)≤0.9*VPC_OOC(x)and VPC_Cpx(x)<0.05*VPC_OOC(x) 29
  30. 30. Conclusions and Further Plans A formula is possible Ontology project in The construction of a petrology: formal theory started  Definition Tools of formal concentrator knowledge  Formalization of maintenance tested [IRCGT] A definition  GIS formalization concentrator  CRL (Controlled prototype created Russian language) 30
  31. 31. AcknowledgmentsWe would like to thank Dr. Stephen M. Richard from Arizona GeologicalSurvey for comments on the report [otch10], ahelpful discussion and a reference to [BGSRCS] Pavel Klinov from University of Manchester fornumerous invaluable comments Dr. Kaarel Kaljurand from Attempto group for theidea of using proper names 31
  32. 32. References[IRCGT] Le Maitre, L.E., ed. 2002. Igneous Rocks: AClassification and Glossary of Terms 2nd edition, Cambridge.url[BGSRCS] Gillespie, M R, and Styles, M T. 1999. BGS RockClassification Scheme, Volume 1, Classification of igneousrocks. British Geological Survey Research Report, (2ndedition), RR 99–06. url[OWL2LE] OWL 2 Web Ontology Language. Data RangeExtension: Linear Equations. url 32

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