A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data

1. A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data Rathachai Chawuthai Hideaki Takeda Vilas Wuwongse Utsugi Jinbo rathachai.c@gmail.com Professor Professor Entomologist Montpellier, France S4BIODIV - ESWC 2013 May 27th, 2013

2. Overview Millions of species throughout the world have been classified and named by different perspectives among taxonomists. For example, the Northern Orioles named Icterus galbulaand Icterus bullockiihave been reclassified many times. The up-to-date information may not be enough for researchers to learn from a single taxonomic name, whereas, the history of change and linked data of it can expand more knowledge about taxon concepts. A logical model for taxon concepts in RDF has been proposed in order to record the change of taxon concepts and publish in LOD.

3. Agenda • Introduction • Logical Model • Prototype • Future works

4. Introduction

5. Background

6. Background Chinese Yellow Swallowtail Butterfly Papilio xuthus, also known as the Asian Swallowtail, Chinese Yellow Swallowtail, or as the Xuthus swallowtail, is a middle to large sized swallowtail butterfly found in northeast Asia, Korea, Japan, and Hawaii.

7. Background Papilio xuthus Linnaeus, 1767 Papilio xuthulus Bremer, 1861 Papilio chinensis Neuburger, 1900 Papilio koxinga Fruhstorfer, 1908

8. Background Papilio xuthus Linnaeus, 1767 Papilio xuthulus Bremer, 1861 Papilio chinensis Neuburger, 1900 Papilio koxinga Fruhstorfer, 1908

9. Challenge These birds are found in the Nearctic in summer, primarily the eastern United States. Northern Oriole

10. Challenge Icterus galbula (Linnaeus, 1758) “Baltimore Oriole” Icterus bullockii (Swainson, 1827) “Bullock’s Oriole”

11. 1758 1827 I. galbula I. bullockii

12. 1758 1827 1964 I. galbula I. galbula I. bullockii I. bullockii

13. 1758 1827 1964 Merged Into I. galbula I. galbula I. bullockii

14. 1758 1827 1964 1995 Merged Into I. galbula I. galbula I. galbula I. bullockii I. bullockii

15. 1758 1827 1964 1995 Split Into Merged Into I. galbula I. galbula I. galbula I. bullockii I. bullockii

16. Goals Propose a logical model to manage the change of Taxon Concept. Implement a prototypeto ensure the feasibility of the model.

17. LogicalModel

18. Change of Taxon Concept

19. Change of Taxon Concept ltk:TaxonSplitter ltk:TaxonMerger

20. Change of Taxon Concept cka:ConceptEvolution rdfs:subClassOf rdfs:subClassOf ltk:TaxonSplitter ltk:TaxonMerger

21. Change of Taxon Concept cka:ConceptEvolution rdfs:subClassOf rdfs:subClassOf ltk:TaxonSplitter ltk:TaxonMerger cka:linkingProperty cka:linkingProperty ltk:splitInto ltk:mergedInto

22. Change of Taxon Concept cka:ConceptEvolution rdfs:subClassOf rdfs:subClassOf ltk:TaxonSplitter ltk:TaxonMerger cka:linkingProperty cka:linkingProperty ltk:splitInto ltk:mergedInto rdfs:subPropertyOf rdfs:subPropertyOf skos:relatedMatch

23. Scenario The change of the genera of Snowy Owl Nyctea + Bubo = Bubo ?

24. Scene 1 Merging of genus Nyctea and Bubo into Bubo ltk:TaxonMerger

25. Scene 1 Merging of genus Nyctea and Bubo into Bubo ltk:TaxonMerger rdf:type ex:merge1

26. Scene 1 Merging of genus Nyctea and Bubo into Bubo genus:Bubo ltk:TaxonMerger cka:conceptBefore rdf:type genus:Nyctea cka:conceptBefore ex:merge1

27. Scene 1 Merging of genus Nyctea and Bubo into Bubo genus:Bubo ltk:TaxonMerger cka:conceptBefore rdf:type genus:Nyctea cka:conceptBefore ex:merge1 genus:Bubo cka:conceptAfter

28. Scene 1 Merging of genus Nyctea and Bubo into Bubo genus:Bubo ltk:TaxonMerger cka:majorConceptBefore cka:conceptBefore rdf:type genus:Nyctea cka:conceptBefore ex:merge1 genus:Bubo cka:conceptAfter genus:Bubo_1999

29. Scene 1 Merging of genus Nyctea and Bubo into Bubo genus:Bubo ltk:majorMergedInto genus:Bubo_1999 genus:Nyctea ltk:mergedInto

30. Scene 1 Merging of genus Nyctea and Bubo into Bubo skos:closeMatch ltk:mergedInto genus:Bubo ltk:majorMergedInto genus:Bubo_1999 genus:Nyctea ltk:mergedInto skos:relatedMatch

31. Scene 2 Renaming of Nycteascandica ltk:TaxonReplacement rdf:type ex:replace1

32. Scene 2 Renaming of Nycteascandica ltk:TaxonReplacement rdf:type cka:conceptBefore species:Nyctea_scandiaca ex:replace1 species:Bubo_scandiacus cka:conceptAfter

33. Scene 2 Renaming of NycteaScandica species:Bubo_scandiacus species:Nyctea_scandiaca ltk:replacedTo

34. Scene 2 Renaming of NycteaScandica skos:exactMatch species:hasSynonym ltk:synonym species:Bubo_scandiacus species:Nyctea_scandiaca ltk:replacedTo

35. Scene 3 Changing the higher taxon of Bubo virginianus Objective: genus:Bubo ltk:higherTaxon species:Bubo_virginianus Before 1999

36. Scene 3 Changing the higher taxon of Bubo virginianus Objective: genus:Bubo_1999 genus:Bubo ltk:higherTaxon species:Bubo_virginianus Since 1999

37. Scene 3 Changing the higher taxon of Bubo virginianus cka:RelationshipEvolution rdfs:subClassOf ltk:HigherTaxonChange cka:relation ltk:higherTaxon rdfs:subPropertyOf skos:broaderTransitive

38. Scene 3 Changing the higher taxon of Bubo virginianus ltk:HigherTaxonChange species:Bubo_virginianus cka:child rdf:type ex:reclass1 genus:Bubo cka:parentBefore cka:parentAfter genus:Bubo_1999

39. Scene 4 Giving reference data pp:Wing bibo:performer 1999 ex:change1999 bibo:performer tl:beginAtDateTime pp:Heidrich dcterms:source cka:interval http://www.uni-heidelberg.de/institute/fak14/ipmb/phazb/pdf-files/2000%20Pdf.Pubwink/26.%202000.pdf

40. Scene 5 Associating all changes ex:merge1 ex:reclass1 ex:replace1 ex:change1999

41. Scene 5 Associating all changes ex:merge1 ex:reclass1 ex:replace1 cka:assures cka:assures ex:change1999 cka:assures

42. Scene 5 Associating all changes ex:merge1 cka:cause ex:reclass1 cka:cause ex:replace1 cka:assures cka:assures ex:change1999 cka:assures

43. Semantics Web Rules • Transform Dynamic RDF to Static RDF • Dynamic RDF • The change of Taxon Concept(concept_before, concept_after) • Temporal relationship between concepts(parent_before, parent_after) • Static RDF • Linked data ( ?x skos:relatedMatch ?y ) • Triple ( ?subject ?predicate ?object )

44. Using Jena Rule: To Link Evolutionary Relationship [ConceptChange: ( ?com cka:assures ?link ) ( ?link rdf:typecka:ConceptEvolution ) ( ?link cka:conceptBefore ?before ) ( ?linkcka:conceptAfter ?after ) ( ?linkrdf:type ?class) ( ?classcka:linkingProperty?link ) -> ( ?before?link?after) ] Note: The main reason of using Jena is that the system sometime has to create an instance at runtime. (It is a feature of Jena)

45. Using SPARQL: Query the information of Bubo virginianusat year 2013 SELECT {?subject ?property ?object } WHERE { ?uckcka:ensures ?relEv . ?relEvcka:subjectspecies:Bubo_virginianus. ?uckcka:interval ?intv . ?intvtl:beginAtDateTime ?begin . ?relEvrdf:type ?class . ?relEvcka:subject ?subject . ?class cka:relation ?property . ?relEvcka:newObject ?object . FILTER ( xsd:dateTime(?begin) >= “...2013...”) } Note: The input taxon concept can be either subject and object, so the query expression is more complex than the example. Moreover, the input date must be in xsd:dateTime format.

46. Prototype

47. System Architecture Rules (Jena) Ontology (OWL) RDF Store (Open RDF) Knowledge Engine (J2EE) Web Client (PHP) - Define and execute the change of taxon concepts. - Present temporal information of a taxon concept

48. Add a new change 1

49. Add a new change 2 The timestamp suffix is default by the system. However, users can change it.

50. Add a new change 3