A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data
HideakiTakedaProfessor
VilasWuwongseProfessor
UtsugiJinboEntomologist
Montpellier, France S4BIODIV - ESWC 2013 May 27th, 2013
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Overview
Millions of species throughout the world have
been classified and named by different
perspectives among taxonomists. For example,
the Northern Orioles named Icterus galbula
and Icterus bullockii have 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.
Agenda
Introduction Logical Model Prototype Future works
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4
Introduction
Background
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Background
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Chinese Yellow Swallowtail ButterflyPapilio 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.
Background
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Papilio xuthus Linnaeus, 1767
Papilio xuthulus Bremer, 1861
Papilio chinensis Neuburger, 1900
Papilio koxinga Fruhstorfer, 1908
Background
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Papilio xuthus Linnaeus, 1767
Papilio xuthulus Bremer, 1861
Papilio chinensis Neuburger, 1900
Papilio koxinga Fruhstorfer, 1908
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Northern Oriole These birds are found in the Nearctic in summer, primarily the eastern United States.
Challenge
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Challenge
Icterus bullockii(Swainson, 1827)
Icterus galbula(Linnaeus, 1758)“Baltimore Oriole”
“Bullock’s Oriole”
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1758 1827
I. bullockii
I. galbula
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1758 1827 1964
I. galbula
I. bullockii
I. bullockiiI. galbula
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1758 1827 1964
I. galbula
I. bullockii
MergedInto I. galbula
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1758 1827 1964 1995
I. galbula
I. bullockii
MergedInto I. galbula
I. bullockii
I. galbula
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1758 1827 1964 1995
I. galbula
I. bullockii
MergedInto I. galbula
I. bullockii
I. galbula SplitInto
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Goals
Propose a logical model to manage the change of Taxon Concept.
Implement a prototype to ensure the feasibility of the model.
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LogicalModel
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Change of Taxon ConceptCh
ange
s of T
axon
Con
cept
Name
RenameNew name
Spelling sequence
Synonym
Junior Synonym
Senior Synonym
Common Name
HomonymJunior Homonym
Senior Homonym
Classification
RemodelMerging
Splitting
Hierarchy Change
Promoting
Demoting
Changing higher taxon
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Change of Taxon Concept
ltk:TaxonMerger ltk:TaxonSplitter
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Change of Taxon Conceptcka:ConceptEvolution
rdfs:subClassOf rdfs:subClassOf
ltk:TaxonMerger ltk:TaxonSplitter
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Change of Taxon Conceptcka:ConceptEvolution
rdfs:subClassOf rdfs:subClassOf
ltk:mergedInto ltk:splitInto
cka:linkingProperty
ltk:TaxonMerger ltk:TaxonSplitter
cka:linkingProperty
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Change of Taxon Conceptcka:ConceptEvolution
rdfs:subClassOf rdfs:subClassOf
rdfs:subPropertyOf rdfs:subPropertyOf
skos:relatedMatch
ltk:mergedInto ltk:splitInto
ltk:TaxonMerger ltk:TaxonSplitter
cka:linkingProperty cka:linkingProperty
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Scenario
The change of the genera of Snowy OwlNyctea + Bubo = Bubo ?
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Scene 1
ltk:TaxonMerger
Merging of genus Nyctea and Bubo into Bubo
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Scene 1
ltk:TaxonMerger
Merging of genus Nyctea and Bubo into Bubo
ex:merge1
rdf:type
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Scene 1
ltk:TaxonMerger
Merging of genus Nyctea and Bubo into Bubo
ex:merge1
rdf:type
genus:Bubo
genus:Nycteacka:conceptBefore
cka:conceptBefore
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Scene 1Merging of genus Nyctea and Bubo into Bubo
genus:Bubo
cka:conceptAfter
ltk:TaxonMerger
ex:merge1
rdf:type
genus:Bubo
genus:Nycteacka:conceptBefore
cka:conceptBefore
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Scene 1Merging of genus Nyctea and Bubo into Bubo
genus:Bubo
cka:conceptAfter
ltk:TaxonMerger
ex:merge1
rdf:type
genus:Bubo
genus:Nycteacka:conceptBefore
cka:conceptBeforecka:majorConceptBefore
genus:Bubo_1999
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Scene 1Merging of genus Nyctea and Bubo into Bubo
genus:Bubo_1999
genus:Bubo
genus:Nyctea
ltk:majorMergedInto
ltk:mergedInto
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Scene 1Merging of genus Nyctea and Bubo into Bubo
genus:Bubo_1999
genus:Bubo
genus:Nyctea
ltk:majorMergedInto
ltk:mergedInto
ltk:mergedInto
skos:closeMatch
skos:relatedMatch
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Scene 2
ltk:TaxonReplacement
Renaming of Nyctea scandica
ex:replace1
rdf:type
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Scene 2
ltk:TaxonReplacement
Renaming of Nyctea scandica
ex:replace1
rdf:type
species:Bubo_scandiacus
cka:conceptAfter
species:Nyctea_scandiaca
cka:conceptBefore
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Scene 2Renaming of Nyctea Scandica
species:Bubo_scandiacus
species:Nyctea_scandiaca
ltk:replacedTo
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Scene 2Renaming of Nyctea Scandica
species:Bubo_scandiacus
species:Nyctea_scandiaca
ltk:replacedToltk:synonym
skos:exactMatchspecies:hasSynonym
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Scene 3Changing the higher taxon of Bubo virginianus
species:Bubo_virginianus
genus:Bubo
Before 1999
ltk:higherTaxon
Objective:
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Scene 3Changing the higher taxon of Bubo virginianus
genus:Bubo
Objective:
species:Bubo_virginianus
genus:Bubo_1999
Since 1999
ltk:higherTaxon
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Scene 3
ltk:HigherTaxonChange
Changing the higher taxon of Bubo virginianus
skos:broaderTransitive
cka:RelationshipEvolution
rdfs:subClassOf
rdfs:subPropertyOf
ltk:higherTaxoncka:relation
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Scene 3
ltk:HigherTaxonChange
Changing the higher taxon of Bubo virginianus
ex:reclass1
rdf:type
species:Bubo_virginianus
genus:Bubo
genus:Bubo_1999
cka:child
cka:parentBeforecka:parentAfter
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Scene 4Giving reference data
cka:interval
ex:change
1999
1999
tl:beginAtDateTime
pp:Wing
pp:Heidrich
http://www.uni-heidelberg.de/
institute/fak14/ipmb/phazb/pdf-files/
2000%20Pdf.Pubwink/26.%202000.pdf
bibo:performer
bibo:performer
dcterms:source
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Scene 5 Associating all changes
ex:change
1999
ex:merge1
ex:replace1 ex:reclass1
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Scene 5 Associating all changes
ex:change
1999
ex:merge1
ex:replace1 ex:reclass1
cka:assures
cka:
assu
res
cka:assu
res
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Scene 5 Associating all changes
ex:change
1999
ex:merge1
ex:replace1 ex:reclass1
cka:assures
cka:
assu
res
cka:assu
res
cka:cause cka:cause
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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 )
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Using Jena Rule:
[ConceptChange:( ?com cka:assures?link )( ?link rdf:typecka:ConceptEvolution )( ?link cka:conceptBefore ?before)( ?link cka:conceptAfter ?
after )( ?link rdf:type
?class)( ?class cka: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)
To Link Evolutionary Relationship
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Using SPARQL:
SELECT {?subject ?property ?object }WHERE {
?uck cka:ensures ?relEv .?relEv cka:subject
species:Bubo_virginianus.?uck cka:interval ?intv .?intv tl:beginAtDateTime ?begin .
?relEv rdf:type?class .
?relEv cka:subject ?subject .
?class cka:relation ?property .
?relEv cka: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.
Query the information of Bubo virginianus at year 2013
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Prototype
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System Architecture
RDF Store(Open RDF)Knowledge
Engine(J2EE)
Web Client(PHP)
Ontology(OWL)
Rules(Jena)
- Define and execute the change of taxon concepts.- Present temporal information of a taxon concept
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Add a new change 1
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Add a new change 2
The timestamp suffix is default by the system. However, users can change it.
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Add a new change 3
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Add a new change 4
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Add a new change 5
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View a Taxon Concept 1
Evolutionary Relationship (from Rules)
Temporal Information (from SPARQL)
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View a Taxon Concept 2
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Demo
1) http://ltk.cs.ait.ac.th/taxon/concept.php?concept=http://lod.ac/genus/Icterus
2) http://ltk.cs.ait.ac.th/taxon/concept.php?concept=http://lod.ac/genus/Bubo
Demonstrate temporal information of a taxon concept
Conclusion Introduce the change of taxon concept in
RDF Define semantics web rules to transform
dynamic RDF to linked taxon concepts Implement a prototype• Define and execute the change of taxon
concepts• Present temporal information of a taxon
concept56
Final scene
57http://ltk.cs.ait.ac.th/openrdf-sesame/
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FutureWorks
Future Works
Algorithm to move precise attributes from the old taxon concept to the new taxon concept.
Algorithm to move sub-taxon concepts to a new higher taxon concept.
Computing with billion temporal data.
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Any idea for improvement?