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

RathachaiChawuthairathachai.c@gmail.com

HideakiTakedaProfessor

VilasWuwongseProfessor

UtsugiJinboEntomologist

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 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?