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1Franck MICHEL, I3S
F. Michel1, C. Callou2, C. Faron-Zucker1, O. Gargominy3, C. Martin2, J. Montagnat1, S. Tercerie, M. Tounsi1, F. Vest3
1 Université Côte d’Azur, CNRS, I3S, France, 2 BBEES, Sorbonne Univ., MNHN, CNRS, 3 Service du Patrimoine Naturel, MNHN, CNRS
Référentiel taxonomique pour l’étude de l’histoire
de la zoologie/biologie/archéozoologie
SemWeb.Pro
Paris, 21/11/2016
2Franck MICHEL, I3S
Introduction
The Hunting Dogs
Mosaic, detail of a winged sea-griffin chasing a dolphin. Corinium Museum, Cirencester
Credit: Carole Raddato - https://www.flickr.com/photos/carolemage/16295160644/
3Franck MICHEL, I3S
Introduction
The Hunting Dogs Mosaic,
detail of a winged sea-griffin
chasing a dolphin
4Franck MICHEL, I3S
Introduction
The Hunting Dogs Mosaic,
detail of a winged sea-griffin
chasing a dolphin
Modern zoological reference
Cetacea, Delphinidae,
Dehlphinus…
5Franck MICHEL, I3S
Introduction
The Hunting Dogs Mosaic,
detail of a winged sea-griffin
chasing a dolphin
Archaeological excavation
mentioning remains of dolphin
Modern zoological reference
Cetacea, Delphinidae,
Dehlphinus…
6Franck MICHEL, I3S
Introduction
The Hunting Dogs Mosaic,
detail of a winged sea-griffin
chasing a dolphin
Archaeological excavation
mentioning remains of dolphin
First Natural History Encycloedia, 1485.
Modern zoological reference
Cetacea, Delphinidae,
Dehlphinus…
7Franck MICHEL, I3S
Introduction
The Hunting Dogs Mosaic,
detail of a winged sea-griffin
chasing a dolphin
Archaeological excavation
mentioning remains of dolphin
First Natural History Encycloedia, 1485.
Modern zoological reference
Cetacea, Delphinidae,
Dehlphinus…
Need for
common references:
taxonomic, geographical,
cultural, chronological,
8Franck MICHEL, I3S
First Natural History Encycloedia, 1485.
Introduction
Archaeological excavation
mentioning remains of dolphin
Modern zoological reference
Cetacea, Delphinidae,
Dehlphinus…
TAXREF
The Hunting Dogs Mosaic,
detail of a winged sea-griffin
chasing a dolphin
9Franck MICHEL, I3S
TAXREF
INPN web portal
Used by collectivities, biologists, architects, teachers, citizens…
Archaeozoological and Archaeobotanical Inventories of France
3200+ references to excavations reports, studies, academic papers
4700 archaeological sites
2700 animal species, 1100 plant species
French TAXonomical REFerence for fauna, flora, fungus
509,000+ names including living/extinct/exotic species
Mainland France and overseas
10Franck MICHEL, I3S
11Franck MICHEL, I3S
12Franck MICHEL, I3S
13Franck MICHEL, I3S
14Franck MICHEL, I3S
Enable use by Linked-Data Based Applications
http://inpn.mnhn.fr/taxref/label/60878
<a href= “...”>
15Franck MICHEL, I3S
Enable use by Linked-Data Based Applications
http://inpn.mnhn.fr/taxref/label/60878
skos:closeMatch,
skos:relatedMatch,
owl:sameAs,
rdfs:seeAlso, ...
<a href= “...”>
16Franck MICHEL, I3S
From TAXREF to the Web of Data
Transition from...
...to a thesaurus exploitable
using SW technologies
SKOS: Simple Knowledge Organization System
W3C RDF-based standard to represent controlled vocabularies: glossary, taxonomy, thesaurus...
17Franck MICHEL, I3S
TAXREF SKOS Modelling
Taxon
skos:Concept
Reference name
skosxl:Label
Synonym
skosxl:Label
skosxl:prefLabel
Habitat
skos:Concept
taxprop:habitat
Biogeo. status
skos:Concept
Taxonomical Rank
skos:Concept
"Linnaeus, 1758”
nt:has_rank
“Delphinus delphis”
skos:broader
txn:authority
“Van Bree, 1971”
“Delphinus tropicalis”
http://inpn.mnhn.fr/taxref/label/60881
txn:authority
skosxl:literalForm
"Short-beaked
common dolphin"@en
taxprop:
vernacularName
skosxl:literalForm
http://inpn.mnhn.fr/taxref/label/60878
taxprop:bioGeoStatusIn
skosxl:altLabel
http://inpn.mnhn.fr/taxref/9.0/taxon/60878
18Franck MICHEL, I3S
Taxon => SKOS Concept
Names => SKOS Labels
Vernacular names
Taxonomical Rank
Habitat
Biogeographical status
From TAXREF to the Web of Data
SKOS Model
TAXREF-SKOS
19Franck MICHEL, I3S
Taxon => SKOS Concept
Names => SKOS Labels
Vernacular names
Taxonomical Rank
Habitat
Biogeographical status
From TAXREF to the Web of Data
SKOS Model
TAXREF-SKOS
Taxonomical ranks, habitats,
geographical locations…
Geonames
TaxonConcept Ontology: habitat/authority, tax. ranks
NCBI Organismal Classification: has_rank, tax. ranks
GeoSpecies Knowledge Base: tax. ranks
ENVO Environment Ontology: habitats
Darwin Core Terms: occurenceStatus, locationID
…
20Franck MICHEL, I3S
From TAXREF to the Web of Data
SKOS Model
TAXREF-SKOS
Automatic discovery of
links with well-adopted
open data sets
AGROVOC
Vertebrate Tax. Ontology
NCBI Organismal Classification
Taxon => SKOS Concept
Names => SKOS Labels
Vernacular names
Taxonomical Rank
Habitat
Biogeographical status
ER issues: spelling,
disagreements,
RDFS vs. SKOS
21Franck MICHEL, I3S
Towards sustainable, dereferencable URIs
http://inpn.mnhn.fr/taxref/label/60878
skos:closeMatch,
skos:relatedMatch,
owl:sameAs,
rdfs:seeAlso, ...
SPARQL
Corese-KGRAM
Triple Store
SPARQL 1.1 Endpoint
SPARQL Templates
Linked Data Platform
22Franck MICHEL, I3S
Perspectives and on-going works
Extend TAXREF
• Cultural, chronological and philological information
• Geographical scope: Mediterranean areas
• Red list: vulnerable/endangered species
• …
TAXREF-SKOS is just an enabler to...
• Expose (existing) TAXREF-based datasets as Linked Data
• Develop/extend TAXREF-based applications to enable searching
through the Linked Open Data
23Franck MICHEL, I3S
Thank you

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Construction d’un référentiel taxonomique commun pour des études sur l’histoire de la zoologie, l’archéozoologie et la biologie

  • 1. 1Franck MICHEL, I3S F. Michel1, C. Callou2, C. Faron-Zucker1, O. Gargominy3, C. Martin2, J. Montagnat1, S. Tercerie, M. Tounsi1, F. Vest3 1 Université Côte d’Azur, CNRS, I3S, France, 2 BBEES, Sorbonne Univ., MNHN, CNRS, 3 Service du Patrimoine Naturel, MNHN, CNRS Référentiel taxonomique pour l’étude de l’histoire de la zoologie/biologie/archéozoologie SemWeb.Pro Paris, 21/11/2016
  • 2. 2Franck MICHEL, I3S Introduction The Hunting Dogs Mosaic, detail of a winged sea-griffin chasing a dolphin. Corinium Museum, Cirencester Credit: Carole Raddato - https://www.flickr.com/photos/carolemage/16295160644/
  • 3. 3Franck MICHEL, I3S Introduction The Hunting Dogs Mosaic, detail of a winged sea-griffin chasing a dolphin
  • 4. 4Franck MICHEL, I3S Introduction The Hunting Dogs Mosaic, detail of a winged sea-griffin chasing a dolphin Modern zoological reference Cetacea, Delphinidae, Dehlphinus…
  • 5. 5Franck MICHEL, I3S Introduction The Hunting Dogs Mosaic, detail of a winged sea-griffin chasing a dolphin Archaeological excavation mentioning remains of dolphin Modern zoological reference Cetacea, Delphinidae, Dehlphinus…
  • 6. 6Franck MICHEL, I3S Introduction The Hunting Dogs Mosaic, detail of a winged sea-griffin chasing a dolphin Archaeological excavation mentioning remains of dolphin First Natural History Encycloedia, 1485. Modern zoological reference Cetacea, Delphinidae, Dehlphinus…
  • 7. 7Franck MICHEL, I3S Introduction The Hunting Dogs Mosaic, detail of a winged sea-griffin chasing a dolphin Archaeological excavation mentioning remains of dolphin First Natural History Encycloedia, 1485. Modern zoological reference Cetacea, Delphinidae, Dehlphinus… Need for common references: taxonomic, geographical, cultural, chronological,
  • 8. 8Franck MICHEL, I3S First Natural History Encycloedia, 1485. Introduction Archaeological excavation mentioning remains of dolphin Modern zoological reference Cetacea, Delphinidae, Dehlphinus… TAXREF The Hunting Dogs Mosaic, detail of a winged sea-griffin chasing a dolphin
  • 9. 9Franck MICHEL, I3S TAXREF INPN web portal Used by collectivities, biologists, architects, teachers, citizens… Archaeozoological and Archaeobotanical Inventories of France 3200+ references to excavations reports, studies, academic papers 4700 archaeological sites 2700 animal species, 1100 plant species French TAXonomical REFerence for fauna, flora, fungus 509,000+ names including living/extinct/exotic species Mainland France and overseas
  • 14. 14Franck MICHEL, I3S Enable use by Linked-Data Based Applications http://inpn.mnhn.fr/taxref/label/60878 <a href= “...”>
  • 15. 15Franck MICHEL, I3S Enable use by Linked-Data Based Applications http://inpn.mnhn.fr/taxref/label/60878 skos:closeMatch, skos:relatedMatch, owl:sameAs, rdfs:seeAlso, ... <a href= “...”>
  • 16. 16Franck MICHEL, I3S From TAXREF to the Web of Data Transition from... ...to a thesaurus exploitable using SW technologies SKOS: Simple Knowledge Organization System W3C RDF-based standard to represent controlled vocabularies: glossary, taxonomy, thesaurus...
  • 17. 17Franck MICHEL, I3S TAXREF SKOS Modelling Taxon skos:Concept Reference name skosxl:Label Synonym skosxl:Label skosxl:prefLabel Habitat skos:Concept taxprop:habitat Biogeo. status skos:Concept Taxonomical Rank skos:Concept "Linnaeus, 1758” nt:has_rank “Delphinus delphis” skos:broader txn:authority “Van Bree, 1971” “Delphinus tropicalis” http://inpn.mnhn.fr/taxref/label/60881 txn:authority skosxl:literalForm "Short-beaked common dolphin"@en taxprop: vernacularName skosxl:literalForm http://inpn.mnhn.fr/taxref/label/60878 taxprop:bioGeoStatusIn skosxl:altLabel http://inpn.mnhn.fr/taxref/9.0/taxon/60878
  • 18. 18Franck MICHEL, I3S Taxon => SKOS Concept Names => SKOS Labels Vernacular names Taxonomical Rank Habitat Biogeographical status From TAXREF to the Web of Data SKOS Model TAXREF-SKOS
  • 19. 19Franck MICHEL, I3S Taxon => SKOS Concept Names => SKOS Labels Vernacular names Taxonomical Rank Habitat Biogeographical status From TAXREF to the Web of Data SKOS Model TAXREF-SKOS Taxonomical ranks, habitats, geographical locations… Geonames TaxonConcept Ontology: habitat/authority, tax. ranks NCBI Organismal Classification: has_rank, tax. ranks GeoSpecies Knowledge Base: tax. ranks ENVO Environment Ontology: habitats Darwin Core Terms: occurenceStatus, locationID …
  • 20. 20Franck MICHEL, I3S From TAXREF to the Web of Data SKOS Model TAXREF-SKOS Automatic discovery of links with well-adopted open data sets AGROVOC Vertebrate Tax. Ontology NCBI Organismal Classification Taxon => SKOS Concept Names => SKOS Labels Vernacular names Taxonomical Rank Habitat Biogeographical status ER issues: spelling, disagreements, RDFS vs. SKOS
  • 21. 21Franck MICHEL, I3S Towards sustainable, dereferencable URIs http://inpn.mnhn.fr/taxref/label/60878 skos:closeMatch, skos:relatedMatch, owl:sameAs, rdfs:seeAlso, ... SPARQL Corese-KGRAM Triple Store SPARQL 1.1 Endpoint SPARQL Templates Linked Data Platform
  • 22. 22Franck MICHEL, I3S Perspectives and on-going works Extend TAXREF • Cultural, chronological and philological information • Geographical scope: Mediterranean areas • Red list: vulnerable/endangered species • … TAXREF-SKOS is just an enabler to... • Expose (existing) TAXREF-based datasets as Linked Data • Develop/extend TAXREF-based applications to enable searching through the Linked Open Data