on the Web of Linked Data TDWG 2017 Biodiversity Information - - PowerPoint PPT Presentation

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on the Web of Linked Data TDWG 2017 Biodiversity Information - - PowerPoint PPT Presentation

Feb 13, 2024 382 likes •561 views

TAXREF-LD: A Reference Thesaurus for Biodiversity on the Web of Linked Data TDWG 2017 Biodiversity Information Standards 1-6 October 2017, Ottawa, Canada F. Michel 1 , C. Faron-Zucker 1 , S. Tercerie 2 , O. Gargominy 2 1 Universit Cte

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1 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

  • F. Michel1, C. Faron-Zucker 1, S. Tercerie2, O. Gargominy2
1Université Côte d’Azur, CNRS, Inria, I3S, France. 2Service du Patrimoine Naturel, MNHN, CNRS, France.

TAXREF-LD: A Reference Thesaurus for Biodiversity

  • n the Web of Linked Data

TDWG 2017

Biodiversity Information Standards 1-6 October 2017, Ottawa, Canada

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3 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Taxonomic registers are biodiversity key tools

Linking Open Data cloud diagram 2017, by Andrejs Abele, John P. McCrae, Paul Buitelaar, Anja Jentzsch and Richard Cyganiak. http://lod-cloud.net/

Backbone of thematic DBs and apps Enable data integration across biological domains, regions, epochs “Natural” candidates for publication in the Web of Data as Linked Data

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4 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Different models to represent taxonomic registers as LOD

rank rank Delphinus Genus Species Delphinus delphis

  • wl:Class

rdfs:subClassOf

a a a a

(a) NCBI Org. Classification, VTO a a Delphinus Genus Species Delphinus delphis genus (d) GeoSpecies, DBpedia, BBC WO rank rank Delphinus Genus Species Delphinus delphis

skos:Concept

skos:broader

a a a a

(b) Agrovoc multiling. agricultural thesaurus

dwc:taxonRank

Delphinus "genus" Delphinus delphis

dwc:Taxon

dwc:parent NameUsageID

a a

"species"

dwc:taxonRank

(c) EOL a Species Delphinus delphis genus "Delphinus" (e) TaxonConcept

OWL: Web Ontology Language SKOS: Simple Knowledge Organization System

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5 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Different models to account for the same reality

Taxonomic Information Nomenclatural information OWL/RDFS Classes SKOS concepts Class instances NCBI VTO AGROVOC EOL, TaxonConcept, GeoSpecies, DBpedia, BBC WO

All equally valid from the biological perspective, yet slightly different from the SW perspective.

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6 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Challenge 1: accommodate taxonomic changes

Delphinus capensis Gray, 1828 Delphinus delphis Linnaeus, 1758 Considered as distinct species until 2015. Since then, Delphinus delphis Linnaeus, 1758 is retained as the taxon’s reference name, while Delphinus capensis Gray, 1828 is a synonym.

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7 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Challenge 1: accommodate taxonomic changes

How to accommodate changes if nomenclatural & taxonomic information are intertwined? Tracking/describing changes require that names & taxa be distinct resources [1].

Taxonomic Information Nomenclatural information OWL/RDFS Classes NCBI VTO AGROVOC EOL, TaxonConcept, GeoSpecies, DBpedia, BBC WO SKOS concepts Class instances

[1] R. Chawuthai, H. Takeda, V. Wuwongse, U. Jinbo. Presenting and Preserving the Change in Taxonomic Knowledge for Linked Data. Semantic Web. 7 (2016) 589–616.

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8 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Challenge 2: interlinking data sets not always possible

How to align classes and class instances?

  • owl:sameAs, skos:exactMatch, owl:equivalentClass: discouraged by DL best practices [2]
  • rdfs:seeAlso: weak semantics

Taxonomic Information Nomenclatural information OWL/RDFS Classes NCBI VTO AGROVOC EOL, TaxonConcept, GeoSpecies, DBpedia, BBC WO SKOS concepts Class instances

[2] F. Baader, D. Calvanese, D.L. McGuinness, D. Nardi, P.F. Patel-Schneider. The Description Logic Handbook: Theory, Implementation, and Applications. Cambridge University Press, New York, NY, USA (2003).

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9 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Use case

TAXREF

French TAXonomic REFerence for fauna, flora, fungus maintained by the Muséum National d’Histoire Naturelle. 509,000+ scientific names (living/extinct/exotic) Mainland France and overseas, from Paleolithic up to now Web site, Web service, downloadable text file

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10 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

TAXREF-LD: bring TAXREF to the WoD

3 objectives

  • Relevant to biologists (nomenclature vs. taxonomy),

compliant with the ethos of Semantic Web standards

  • Accommodate taxonomic changes
  • Enable maximum interlinking with 3rd party data sets
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11 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

TAXREF-LD model overview

Nomenclatural information Taxonomic information

txrf: <http://taxref.mnhn.fr/lod/> txrfrk: <http://taxref.mnhn.fr/lod/taxrank#> txrfh: <http://taxref.mnhn.fr/lod/habitat#> txrfp: <http://taxref.mnhn.fr/lod/property#>

txrfp:hasRank

txrfrk:Species

txrfp:hasRank skos:broader skos:broader

txrf:name/191591 "Delphinus "

skos:prefLabel

"Gray, 1828" "Delphinus capensis"

skos:prefLabel

txrf:name/361079

txrfp:hasAuthority

"Linnaeus, 1758"

txrfp:hasAuthority skos:prefLabel

txrf:name/60878 "Delphinus delphis"

txrfp:hasReferenceName rdfs:subClassOf txrfp:hasSynonym txrfp:hasRank

txrf:taxon/191591/10.0

txrfp:habitat txrfp:bioGeoStatusIn

…

txrfh:Marine "Short-beaked common dolphin"@en

txrfp:vernacularName

txrf:taxon/60878/10.0

SKOS concept OWL class

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12 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Interlinking more flexible but still raises questions

Nomenclatural information Taxonomic information

txrf: <http://taxref.mnhn.fr/lod/> txrfrk: <http://taxref.mnhn.fr/lod/taxrank#> txrfh: <http://taxref.mnhn.fr/lod/habitat#> txrfp: <http://taxref.mnhn.fr/lod/property#>

SKOS concept OWL class

http://taxref.mnhn.fr/lod/name/60878 http://taxref.mnhn.fr/lod/taxon/60878/10.0 http://lod.geospecies.org/ses/enwsi

http://lod.taxonconcept.org/ses/enwsi.html#Species http://purl.obolibrary.org/obo/NCBITaxon_9728

http://purl.obolibrary.org/obo/VTO_0011448

  • wl:equivalentClass

skos:exatMatch skos:closeMatch skos:closeMatch skos:relatedMatch txrfp:hasReferenceName NBCI Org. Classification VTO GeoSpecies TaxonConcept

Taxon "Delphinus delphis" Scientific name "Delphinus delphis"

urn:lsid:marinespecies.org:taxname:137094 http://aims.fao.org/aos/agrovoc/c_48963

AGROVOC

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13 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Interlinking more flexible but still raises questions

Nomenclatural information Taxonomic information

txrf: <http://taxref.mnhn.fr/lod/> txrfrk: <http://taxref.mnhn.fr/lod/taxrank#> txrfh: <http://taxref.mnhn.fr/lod/habitat#> txrfp: <http://taxref.mnhn.fr/lod/property#>

SKOS concept OWL class

http://taxref.mnhn.fr/lod/name/60878 http://taxref.mnhn.fr/lod/taxon/60878/10.0 http://lod.geospecies.org/ses/enwsi

http://lod.taxonconcept.org/ses/enwsi.html#Species http://purl.obolibrary.org/obo/NCBITaxon_9728

http://purl.obolibrary.org/obo/VTO_0011448

  • wl:equivalentClass

skos:exatMatch txrfp:isReferenceNameOf txrfp:hasReferenceName NBCI Org. Classification VTO GeoSpecies TaxonConcept

Taxon "Delphinus delphis" Scientific name "Delphinus delphis"

urn:lsid:marinespecies.org:taxname:137094 http://aims.fao.org/aos/agrovoc/c_48963

AGROVOC

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14 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Check it out!

Delphinus delphis example: http://taxref.mnhn.fr/lod/taxon/60878/10.0 Entry point: http://taxref.mnhn.fr/lod/Dataset/10.0/ Free text search: http://erebe-vm2.i3s.unice.fr:8890/fct/

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15 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

TAXREF-LD massively linked with 3rd party data sets

TAXREF-LD species/genus automatically aligned with:

267K resources from 6 reference RDF data sets 992K Web pages from 100 scientific databases (foaf:page)

Manual alignment of TAXREF-LD classes & properties:

What for: scientific/vernacular names, ranks, habitats, geographical locations… Sources: DwC, Geonames, TaxonConcept, NCBI Org. Classification, GeoSpecies, ENVO, Relations Ontology, VTO

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16 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

TAXREF-LD is an enabler to...

  • Foster data integration scenarios,
  • Leverage the WoD to discover information, infer

knowledge, answer scientific questions,

  • Meet citizen’s needs
  • etc…
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17 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

Let’s talk!

Read more:

  • F. Michel, O. Gargominy, S. Tercerie and C. Faron-Zucker. A Model to Represent

Nomenclatural and Taxonomic Information as Linked Data. Application to the French Taxonomic Register, TAXREF. In Proc. of the S4BioDiv international workshop, Vienne, Austria. CEUR 1933 (2017). http://ceur-ws.org/Vol-1933/