A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data
description
Transcript of A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data
![Page 1: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/1.jpg)
A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data
HideakiTakedaProfessor
VilasWuwongseProfessor
UtsugiJinboEntomologist
Montpellier, France S4BIODIV - ESWC 2013 May 27th, 2013
![Page 2: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/2.jpg)
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.
![Page 3: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/3.jpg)
Agenda
Introduction Logical Model Prototype Future works
3
![Page 4: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/4.jpg)
4
Introduction
![Page 5: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/5.jpg)
Background
5
![Page 6: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/6.jpg)
Background
6
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.
![Page 7: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/7.jpg)
Background
7
Papilio xuthus Linnaeus, 1767
Papilio xuthulus Bremer, 1861
Papilio chinensis Neuburger, 1900
Papilio koxinga Fruhstorfer, 1908
![Page 8: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/8.jpg)
Background
8
Papilio xuthus Linnaeus, 1767
Papilio xuthulus Bremer, 1861
Papilio chinensis Neuburger, 1900
Papilio koxinga Fruhstorfer, 1908
![Page 9: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/9.jpg)
9
Northern Oriole These birds are found in the Nearctic in summer, primarily the eastern United States.
Challenge
![Page 10: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/10.jpg)
10
Challenge
Icterus bullockii(Swainson, 1827)
Icterus galbula(Linnaeus, 1758)“Baltimore Oriole”
“Bullock’s Oriole”
![Page 11: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/11.jpg)
11
1758 1827
I. bullockii
I. galbula
![Page 12: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/12.jpg)
12
1758 1827 1964
I. galbula
I. bullockii
I. bullockiiI. galbula
![Page 13: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/13.jpg)
13
1758 1827 1964
I. galbula
I. bullockii
MergedInto I. galbula
![Page 14: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/14.jpg)
14
1758 1827 1964 1995
I. galbula
I. bullockii
MergedInto I. galbula
I. bullockii
I. galbula
![Page 15: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/15.jpg)
15
1758 1827 1964 1995
I. galbula
I. bullockii
MergedInto I. galbula
I. bullockii
I. galbula SplitInto
![Page 16: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/16.jpg)
16
Goals
Propose a logical model to manage the change of Taxon Concept.
Implement a prototype to ensure the feasibility of the model.
![Page 17: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/17.jpg)
17
LogicalModel
![Page 18: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/18.jpg)
18
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
![Page 19: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/19.jpg)
19
Change of Taxon Concept
ltk:TaxonMerger ltk:TaxonSplitter
![Page 20: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/20.jpg)
20
Change of Taxon Conceptcka:ConceptEvolution
rdfs:subClassOf rdfs:subClassOf
ltk:TaxonMerger ltk:TaxonSplitter
![Page 21: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/21.jpg)
21
Change of Taxon Conceptcka:ConceptEvolution
rdfs:subClassOf rdfs:subClassOf
ltk:mergedInto ltk:splitInto
cka:linkingProperty
ltk:TaxonMerger ltk:TaxonSplitter
cka:linkingProperty
![Page 22: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/22.jpg)
22
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
![Page 23: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/23.jpg)
23
Scenario
The change of the genera of Snowy OwlNyctea + Bubo = Bubo ?
![Page 24: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/24.jpg)
24
Scene 1
ltk:TaxonMerger
Merging of genus Nyctea and Bubo into Bubo
![Page 25: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/25.jpg)
25
Scene 1
ltk:TaxonMerger
Merging of genus Nyctea and Bubo into Bubo
ex:merge1
rdf:type
![Page 26: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/26.jpg)
26
Scene 1
ltk:TaxonMerger
Merging of genus Nyctea and Bubo into Bubo
ex:merge1
rdf:type
genus:Bubo
genus:Nycteacka:conceptBefore
cka:conceptBefore
![Page 27: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/27.jpg)
27
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
![Page 28: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/28.jpg)
28
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
![Page 29: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/29.jpg)
29
Scene 1Merging of genus Nyctea and Bubo into Bubo
genus:Bubo_1999
genus:Bubo
genus:Nyctea
ltk:majorMergedInto
ltk:mergedInto
![Page 30: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/30.jpg)
30
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
![Page 31: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/31.jpg)
31
Scene 2
ltk:TaxonReplacement
Renaming of Nyctea scandica
ex:replace1
rdf:type
![Page 32: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/32.jpg)
32
Scene 2
ltk:TaxonReplacement
Renaming of Nyctea scandica
ex:replace1
rdf:type
species:Bubo_scandiacus
cka:conceptAfter
species:Nyctea_scandiaca
cka:conceptBefore
![Page 33: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/33.jpg)
33
Scene 2Renaming of Nyctea Scandica
species:Bubo_scandiacus
species:Nyctea_scandiaca
ltk:replacedTo
![Page 34: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/34.jpg)
34
Scene 2Renaming of Nyctea Scandica
species:Bubo_scandiacus
species:Nyctea_scandiaca
ltk:replacedToltk:synonym
skos:exactMatchspecies:hasSynonym
![Page 35: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/35.jpg)
35
Scene 3Changing the higher taxon of Bubo virginianus
species:Bubo_virginianus
genus:Bubo
Before 1999
ltk:higherTaxon
Objective:
![Page 36: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/36.jpg)
36
Scene 3Changing the higher taxon of Bubo virginianus
genus:Bubo
Objective:
species:Bubo_virginianus
genus:Bubo_1999
Since 1999
ltk:higherTaxon
![Page 37: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/37.jpg)
37
Scene 3
ltk:HigherTaxonChange
Changing the higher taxon of Bubo virginianus
skos:broaderTransitive
cka:RelationshipEvolution
rdfs:subClassOf
rdfs:subPropertyOf
ltk:higherTaxoncka:relation
![Page 38: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/38.jpg)
38
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
![Page 39: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/39.jpg)
39
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
![Page 40: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/40.jpg)
40
Scene 5 Associating all changes
ex:change
1999
ex:merge1
ex:replace1 ex:reclass1
![Page 41: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/41.jpg)
41
Scene 5 Associating all changes
ex:change
1999
ex:merge1
ex:replace1 ex:reclass1
cka:assures
cka:
assu
res
cka:assu
res
![Page 42: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/42.jpg)
42
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
![Page 43: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/43.jpg)
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 )
![Page 44: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/44.jpg)
44
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
![Page 45: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/45.jpg)
45
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
![Page 46: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/46.jpg)
46
Prototype
![Page 47: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/47.jpg)
47
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
![Page 48: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/48.jpg)
48
Add a new change 1
![Page 49: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/49.jpg)
49
Add a new change 2
The timestamp suffix is default by the system. However, users can change it.
![Page 50: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/50.jpg)
50
Add a new change 3
![Page 51: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/51.jpg)
51
Add a new change 4
![Page 52: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/52.jpg)
52
Add a new change 5
![Page 53: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/53.jpg)
53
View a Taxon Concept 1
Evolutionary Relationship (from Rules)
Temporal Information (from SPARQL)
![Page 54: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/54.jpg)
54
View a Taxon Concept 2
![Page 55: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/55.jpg)
55
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
![Page 56: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/56.jpg)
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
![Page 57: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/57.jpg)
Final scene
57http://ltk.cs.ait.ac.th/openrdf-sesame/
![Page 58: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/58.jpg)
58
FutureWorks
![Page 59: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/59.jpg)
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.
59
![Page 60: A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data](https://reader036.fdocuments.us/reader036/viewer/2022062501/568166b1550346895ddaad65/html5/thumbnails/60.jpg)
60
Any idea for improvement?