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1June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Towards a Shared Reference Thesaurus for
Studies on History of Zoology,
Archaeozoology and Conservation Biology
1Archéozoologie et archéobotanique, BBEES, Sorbonne Univ., MNHN, CNRS
2I3S lab, CNRS, Univ. Nice Sophia
C. Callou1, F. Michel2, C. Faron-Zucker2, C. Martin1, J. Montagnat2
First International Workshop on Semantic Web for Scientific Heritage
2June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Introduction
Diverse disciplines share common Data Integration needs:
 Gather, combine, make sense of heterogeneous data and material
Zoomathia: study the history and transmission of
zoological knowledge along historical periods
This involves various data sources:
• Ancient Literature and Iconography
• Bioarchaeology
• Conservation Biology
Need for controlled, well adopted semantic references
Reference Thesauri about taxonomical, cultural,
chronological, geographical information...
3June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
I2AF
The important development of rescue archaeology has generated the
production of many reports rich in bioarchaeological data but hardly
accessible for researchers.
It was urgent to collect these data, to benefit from new technologies, to preserve it for a
long time and make it available for different users.
Creation of Archaeozoological and Archaeobotanical Inventories of
France database (I2AF) – since 2004
4June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
I2AF
This work was possible thanks to institutional partners
and particularly through the participation of all specialists in bioarchaeology
© Méniel, CNRS © Tengberg
5June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
I2AF: some figures
 More than 3,200 references, of which 85% belong to « grey » literature
(excavations reports, specialist studies or academic papers)
 4,700 archaeological sites
 46,600 archaeological contexts (pits, well, stratigraphic units etc.),
dating Middle Paleolithic (300,000-30,000 years) until Modern Period
 180,000 data (fauna and flora)
 2,700 animal species (Mammals, Birds, Fish, Amphibians, Reptiles, Marine and Terrestrial
Molluscs, Arthropods, Insects and some Worms and Parasitic Microorganisms)
These species belong to different categories: species still living today in the country, specially
domestic forms, extinct species (eg Reindeer, Mammoth) or exotic species (eg Monkey, or,
Buffalo, living in old menageries)
 1,100 plant species
Data imported from excavation reports into I2AF is aligned on two thesauri :
 A chronological thesaurus (temporal terms with regards to cultural periods)
 A taxonomic thesaurus of zoological and botanical names
TAXREF (TAXonomical REFerence): used as a national reference
6June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
7June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
CD_NOM : Unique identifier of the scientific name
CD_SUP : Identifier of the upper taxon in the classification
CD_REF : Identifier of the reference taxon
HABITAT: type of habitat in which the taxon usually lives (marine, fresh water, terrestrial …)
A set of Biogeographical statuses, one for each geographical region (E for endemic, X for extinct, P for present …)
RANG : taxonomical rank
8June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
From TAXREF to the Semantic Web
How to transition from this representation...
...to a Thesaurus exploitable as a semantic
reference using semantic web technologies?
SKOS: Simple Knowledge Organization System
W3C RDF-based standard to represent controlled vocabularies, taxonomies and thesauri.
Bridge the gap between existing KOS and the Semantic Web and Linked Data.
9June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
skosxl:altLabel
SKOS Modelling
Taxon
skos:Concept
Reference name
skosxl:Label
Synonym
skosxl:Label
skosxl:prefLabel
Habitat
skos:Concept
taxref:habitat
Biogeo. status
skos:Concept
Taxonomical Rank
skos:Concept
"Linnaeus, 1758”
nt:has_rank
“Delphinus delphis”
skos:broader
<http://inpn.mnhn.fr/taxref/v8/taxon/60878>
txn:authority
“Van Bree, 1971”
“Delphinus tropicalis”
<http://inpn.mnhn.fr/espece/cd_nom/60881>
txn:authority
skosxl:literalForm
"Short-beaked
common dolphin"@en
taxref:
vernacularName
skosxl:literalForm
<http://inpn.mnhn.fr/espece/cd_nom/60878>
taxref:bioGeoStatusIn
10June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Alignments with domain ontologies
 Static alignments (at mapping design time)
• Used predicates
• Reference values: habitats, taxonomical ranks
 TaxonConcept Ontology:
• properties habitat and authority, taxonomic ranks
 NCBI Organismal Classification:
• property has_rank, taxonomic ranks
 GeoSpecies Knowledge Base:
• taxonomic ranks
 ENVO Environment Ontology:
• habitats
 Geonames:
• mainland France and overseas dpts/territories
11June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Operationalization: xR2RML
 Flexible language to describe mappings from most
common types of database to RDF
 Prototype implementation: Morph-xR2RML
• Support of RDBs (MySQL, PostgreSQL)
• Support of a NoSQL document store: MongoDB
• Data materialization approach
Open source prototype, examples and test databases
https://github.com/frmichel/morph-xr2rml/
12June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
xR2RML in practice
Morph-xR2RML
xR2RML mapping
description
MongoQL
Domain
ontologies
refers to
uses
TAXREF/JSON
13June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Alignments with domain ontologies
 Alignments of taxa and names done afterwards
 Automate search of matches within other taxonomical references
• DBpedia
• NCBI Organismal Classification
• Agrovoc
• Vertebrate Taxonomy Ontology (PaleoDB)
 Difficulties
• Spelling differences
• Disagreements: reference vs. synonym, taxonomical rank
• owl:sameAs, rdfs:seeAlso, skos:exactMatch, skos:closeMatch ?...
 Ongoing work...
14June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Conclusion
 Studies on transmission of zoological knowledge require
integration of heterogeneous data and material:
• Ancient literature, iconographic and archaeozoological resources
 Need for controlled semantic references
 TAXREF: Taxonomical Reference for
• Conservation Biology, Bioarchaeology, teachers, public
collectivitites...
 Ongoing work on the construction of a TAXREF-based
SKOS thesaurus
15June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Perspectives
 Need to extend TAXREF wrt.
• Geographical scope: Mediterranean areas (Greece, Italy)
• Cultural, chronological and philological information
 Enable use by linked-data based applications
• Publish of the SKOS thesaurus
• Improve links with Linked Open Data
• Automatic discovery of links with well-adopted open data sets
• General public sources or domain-specific taxonomies
16June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Thank you!
17June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Backup slides
18June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
TAXREF JSON representation
{ "codeTaxon":60878, "codeReference":60878, "codeParent":191591,
"nomComplet ":"Delphinus delphis",
"libelleAuteur":"Linnaeus, 1758",
"nomVernaculaire":"Dauphin commun à bec court",
"nomVernaculaireAnglais":"Short-beaked common dolphin",
"habitat":1,
"rang":"ES",
"fr":"P", "gua":"P", "reu":"B", (...)
}
{ "codeTaxon":60881, "codeReference":60878, "codeParent":191591,
"nomComplet":"Delphinus tropicalis",
"libelleAuteur":"Van Bree, 1971",
"nomVernaculaire":"Dauphin commun d'Arabie",
"nomVernaculaireAnglais":"Arabian common dolphin",
"habitat":1,
"rang":"ES",
"fr":"P", "gua":"P", "reu":"B", (...)
}
19June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Equivalent SKOS representation
<http://inpn.mnhn.fr/taxref/v8/taxon/60878> a skos:Concept;
skosxl:prefLabel <http://inpn.mnhn.fr/espece/cd_nom/60878>.
skosxl:altLabel <http://inpn.mnhn.fr/espece/cd_nom/60881>;
skos:broader <http://inpn.mnhn.fr/taxref/v8/taxon/191591>;
taxref:hasHabitat <http://inpn.mnhn.fr/taxref/habitat#Marine>;
nt:has_rank <http://inpn.mnhn.fr/taxref/taxrank#Species>;
taxref:bioGeoStatusIn [
taxref:bioGeoStatus <http://inpn.mnhn.fr/taxref/bioGeoStat#P>;
gn:locatedIn <http://sws.geonames.org/3017382/> ];
taxref:bioGeoStatusIn [
taxref:bioGeoStatus <http://inpn.mnhn.fr/taxref/bioGeoStat#P>;
gn:locatedIn <http://sws.geonames.org/3579143/> ];
taxref:bioGeoStatusIn [
taxref:bioGeoStatus <http://inpn.mnhn.fr/taxref/bioGeoStat#B>;
gn:locatedIn <http://sws.geonames.org/935317/> ].
20June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Equivalent SKOS representation
<http://inpn.mnhn.fr/espece/cd_nom/60878> a skosxl:Label;
skosxl:literalForm "Delphinus delphis";
tc:authority "Linnaeus, 1758";
taxref:vernacularName "Dauphin commun à bec court"@fr;
taxref:vernacularName "Short-beaked common dolphin"@en.
taxref:isPrefLabelOf <http://inpn.mnhn.fr/taxref/v8/taxon/60878>.
<http://inpn.mnhn.fr/espece/cd_nom/60881> a skosxl:Label;
skosxl:literalForm "Delphinus tropicalis".
tc:authority "Van Bree, 1971";
taxref:vernacularName "Dauphin commun d’Arabie"@fr;
taxref:vernacularName "Arabian common dolphin"@en;
taxref:isAltLabelOf <http://inpn.mnhn.fr/taxref/v8/taxon/60878>.
21June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Alternative SKOS modelling
Taxon
skos:Concept
Synonym Taxon
skos:Concept
skos:prefLabel
Habitat
skos:Concepttaxref:habitat
Biogeo. status
skos:Concept
Taxonomical Rank
skos:Concept
txn:authority
"Linnaeus, 1758”
nt:has_rank
skos:broader
(taxon supérieur)
“Delphinus delphis”
taxref:bioGeoStatusIn
taxref:hasSynonym
22June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
Alignments with domain ontologies
Taxon
skos:Concept
Habitat Taxonomical Rank
TaxonConcept
Ontology
NCBI Org.
Classification
ENVO
Envir. Ontology
GeoSpecies
Knowledge Base
Biogeo. status
GeoNames
taxref:habitat nt:has_rank
txn:authority
taxref:
vernacularName

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Towards a Shared Reference Thesaurus for Studies on History of Zoology, Archaeozoology and Conservation Biology

  • 1. 1June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Towards a Shared Reference Thesaurus for Studies on History of Zoology, Archaeozoology and Conservation Biology 1Archéozoologie et archéobotanique, BBEES, Sorbonne Univ., MNHN, CNRS 2I3S lab, CNRS, Univ. Nice Sophia C. Callou1, F. Michel2, C. Faron-Zucker2, C. Martin1, J. Montagnat2 First International Workshop on Semantic Web for Scientific Heritage
  • 2. 2June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Introduction Diverse disciplines share common Data Integration needs:  Gather, combine, make sense of heterogeneous data and material Zoomathia: study the history and transmission of zoological knowledge along historical periods This involves various data sources: • Ancient Literature and Iconography • Bioarchaeology • Conservation Biology Need for controlled, well adopted semantic references Reference Thesauri about taxonomical, cultural, chronological, geographical information...
  • 3. 3June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage I2AF The important development of rescue archaeology has generated the production of many reports rich in bioarchaeological data but hardly accessible for researchers. It was urgent to collect these data, to benefit from new technologies, to preserve it for a long time and make it available for different users. Creation of Archaeozoological and Archaeobotanical Inventories of France database (I2AF) – since 2004
  • 4. 4June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage I2AF This work was possible thanks to institutional partners and particularly through the participation of all specialists in bioarchaeology © Méniel, CNRS © Tengberg
  • 5. 5June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage I2AF: some figures  More than 3,200 references, of which 85% belong to « grey » literature (excavations reports, specialist studies or academic papers)  4,700 archaeological sites  46,600 archaeological contexts (pits, well, stratigraphic units etc.), dating Middle Paleolithic (300,000-30,000 years) until Modern Period  180,000 data (fauna and flora)  2,700 animal species (Mammals, Birds, Fish, Amphibians, Reptiles, Marine and Terrestrial Molluscs, Arthropods, Insects and some Worms and Parasitic Microorganisms) These species belong to different categories: species still living today in the country, specially domestic forms, extinct species (eg Reindeer, Mammoth) or exotic species (eg Monkey, or, Buffalo, living in old menageries)  1,100 plant species Data imported from excavation reports into I2AF is aligned on two thesauri :  A chronological thesaurus (temporal terms with regards to cultural periods)  A taxonomic thesaurus of zoological and botanical names TAXREF (TAXonomical REFerence): used as a national reference
  • 6. 6June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage
  • 7. 7June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage CD_NOM : Unique identifier of the scientific name CD_SUP : Identifier of the upper taxon in the classification CD_REF : Identifier of the reference taxon HABITAT: type of habitat in which the taxon usually lives (marine, fresh water, terrestrial …) A set of Biogeographical statuses, one for each geographical region (E for endemic, X for extinct, P for present …) RANG : taxonomical rank
  • 8. 8June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage From TAXREF to the Semantic Web How to transition from this representation... ...to a Thesaurus exploitable as a semantic reference using semantic web technologies? SKOS: Simple Knowledge Organization System W3C RDF-based standard to represent controlled vocabularies, taxonomies and thesauri. Bridge the gap between existing KOS and the Semantic Web and Linked Data.
  • 9. 9June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage skosxl:altLabel SKOS Modelling Taxon skos:Concept Reference name skosxl:Label Synonym skosxl:Label skosxl:prefLabel Habitat skos:Concept taxref:habitat Biogeo. status skos:Concept Taxonomical Rank skos:Concept "Linnaeus, 1758” nt:has_rank “Delphinus delphis” skos:broader <http://inpn.mnhn.fr/taxref/v8/taxon/60878> txn:authority “Van Bree, 1971” “Delphinus tropicalis” <http://inpn.mnhn.fr/espece/cd_nom/60881> txn:authority skosxl:literalForm "Short-beaked common dolphin"@en taxref: vernacularName skosxl:literalForm <http://inpn.mnhn.fr/espece/cd_nom/60878> taxref:bioGeoStatusIn
  • 10. 10June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Alignments with domain ontologies  Static alignments (at mapping design time) • Used predicates • Reference values: habitats, taxonomical ranks  TaxonConcept Ontology: • properties habitat and authority, taxonomic ranks  NCBI Organismal Classification: • property has_rank, taxonomic ranks  GeoSpecies Knowledge Base: • taxonomic ranks  ENVO Environment Ontology: • habitats  Geonames: • mainland France and overseas dpts/territories
  • 11. 11June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Operationalization: xR2RML  Flexible language to describe mappings from most common types of database to RDF  Prototype implementation: Morph-xR2RML • Support of RDBs (MySQL, PostgreSQL) • Support of a NoSQL document store: MongoDB • Data materialization approach Open source prototype, examples and test databases https://github.com/frmichel/morph-xr2rml/
  • 12. 12June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage xR2RML in practice Morph-xR2RML xR2RML mapping description MongoQL Domain ontologies refers to uses TAXREF/JSON
  • 13. 13June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Alignments with domain ontologies  Alignments of taxa and names done afterwards  Automate search of matches within other taxonomical references • DBpedia • NCBI Organismal Classification • Agrovoc • Vertebrate Taxonomy Ontology (PaleoDB)  Difficulties • Spelling differences • Disagreements: reference vs. synonym, taxonomical rank • owl:sameAs, rdfs:seeAlso, skos:exactMatch, skos:closeMatch ?...  Ongoing work...
  • 14. 14June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Conclusion  Studies on transmission of zoological knowledge require integration of heterogeneous data and material: • Ancient literature, iconographic and archaeozoological resources  Need for controlled semantic references  TAXREF: Taxonomical Reference for • Conservation Biology, Bioarchaeology, teachers, public collectivitites...  Ongoing work on the construction of a TAXREF-based SKOS thesaurus
  • 15. 15June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Perspectives  Need to extend TAXREF wrt. • Geographical scope: Mediterranean areas (Greece, Italy) • Cultural, chronological and philological information  Enable use by linked-data based applications • Publish of the SKOS thesaurus • Improve links with Linked Open Data • Automatic discovery of links with well-adopted open data sets • General public sources or domain-specific taxonomies
  • 16. 16June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Thank you!
  • 17. 17June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Backup slides
  • 18. 18June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage TAXREF JSON representation { "codeTaxon":60878, "codeReference":60878, "codeParent":191591, "nomComplet ":"Delphinus delphis", "libelleAuteur":"Linnaeus, 1758", "nomVernaculaire":"Dauphin commun à bec court", "nomVernaculaireAnglais":"Short-beaked common dolphin", "habitat":1, "rang":"ES", "fr":"P", "gua":"P", "reu":"B", (...) } { "codeTaxon":60881, "codeReference":60878, "codeParent":191591, "nomComplet":"Delphinus tropicalis", "libelleAuteur":"Van Bree, 1971", "nomVernaculaire":"Dauphin commun d'Arabie", "nomVernaculaireAnglais":"Arabian common dolphin", "habitat":1, "rang":"ES", "fr":"P", "gua":"P", "reu":"B", (...) }
  • 19. 19June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Equivalent SKOS representation <http://inpn.mnhn.fr/taxref/v8/taxon/60878> a skos:Concept; skosxl:prefLabel <http://inpn.mnhn.fr/espece/cd_nom/60878>. skosxl:altLabel <http://inpn.mnhn.fr/espece/cd_nom/60881>; skos:broader <http://inpn.mnhn.fr/taxref/v8/taxon/191591>; taxref:hasHabitat <http://inpn.mnhn.fr/taxref/habitat#Marine>; nt:has_rank <http://inpn.mnhn.fr/taxref/taxrank#Species>; taxref:bioGeoStatusIn [ taxref:bioGeoStatus <http://inpn.mnhn.fr/taxref/bioGeoStat#P>; gn:locatedIn <http://sws.geonames.org/3017382/> ]; taxref:bioGeoStatusIn [ taxref:bioGeoStatus <http://inpn.mnhn.fr/taxref/bioGeoStat#P>; gn:locatedIn <http://sws.geonames.org/3579143/> ]; taxref:bioGeoStatusIn [ taxref:bioGeoStatus <http://inpn.mnhn.fr/taxref/bioGeoStat#B>; gn:locatedIn <http://sws.geonames.org/935317/> ].
  • 20. 20June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Equivalent SKOS representation <http://inpn.mnhn.fr/espece/cd_nom/60878> a skosxl:Label; skosxl:literalForm "Delphinus delphis"; tc:authority "Linnaeus, 1758"; taxref:vernacularName "Dauphin commun à bec court"@fr; taxref:vernacularName "Short-beaked common dolphin"@en. taxref:isPrefLabelOf <http://inpn.mnhn.fr/taxref/v8/taxon/60878>. <http://inpn.mnhn.fr/espece/cd_nom/60881> a skosxl:Label; skosxl:literalForm "Delphinus tropicalis". tc:authority "Van Bree, 1971"; taxref:vernacularName "Dauphin commun d’Arabie"@fr; taxref:vernacularName "Arabian common dolphin"@en; taxref:isAltLabelOf <http://inpn.mnhn.fr/taxref/v8/taxon/60878>.
  • 21. 21June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Alternative SKOS modelling Taxon skos:Concept Synonym Taxon skos:Concept skos:prefLabel Habitat skos:Concepttaxref:habitat Biogeo. status skos:Concept Taxonomical Rank skos:Concept txn:authority "Linnaeus, 1758” nt:has_rank skos:broader (taxon supérieur) “Delphinus delphis” taxref:bioGeoStatusIn taxref:hasSynonym
  • 22. 22June 1st. 2015 SW4SH 2015: First International Workshop on Semantic Web for Scientific Heritage Alignments with domain ontologies Taxon skos:Concept Habitat Taxonomical Rank TaxonConcept Ontology NCBI Org. Classification ENVO Envir. Ontology GeoSpecies Knowledge Base Biogeo. status GeoNames taxref:habitat nt:has_rank txn:authority taxref: vernacularName