towards a shared reference thesaurus for studies on history of zoology, archaeozoology and...

1 June 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


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...


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


I2AF

This work was possible thanks to institutional partners

and particularly through the participation of all specialists in bioarchaeology

© Méniel, CNRS © Tengberg

http://www.inrap.fr/archeologie-preventive/p-7-Accueil


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


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


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.


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


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


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/

https://github.com/frmichel/morph-xr2rml/




xR2RML in practice

Morph-xR2RML xR2RML mapping

description

MongoQL

Domain ontologies

refers to

uses

TAXREF/JSON



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...


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


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


Thank you!


Backup slides


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", (...)

}


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/> ].


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>.


Alternative SKOS modelling

Taxon skos:Concept

Synonym Taxon skos:Concept

skos:prefLabel

Habitat skos:Concept taxref: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



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

towards a shared reference thesaurus for studies on history of zoology, archaeozoology and...

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