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

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 Université Côte d’Azur, CNRS, Inria, I3S, France. 2 Service du Patrimoine Naturel, MNHN, CNRS, France. Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 1

Taxonomic registers are biodiversity key tools 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 Linking Open Data cloud diagram 2017, by Andrejs Abele, John P. McCrae, Paul Buitelaar, Anja Jentzsch and Richard Cyganiak. http://lod-cloud.net/ Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 3

Different models to represent taxonomic registers as LOD dwc:taxonRank Delphinus Genus Delphinus "genus" Delphinus Genus rank rank a a a a a dwc:parent skos:broader dwc:Taxon skos:Concept rdfs:subClassOf NameUsageID owl:Class a a a a a Delphinus Delphinus Delphinus Species "species" Species rank delphis delphis rank delphis dwc:taxonRank (b) Agrovoc multiling. (a) NCBI Org. Classification, VTO (c) EOL agricultural thesaurus "Delphinus" Delphinus Genus a genus genus Delphinus Delphinus Species Species a a delphis delphis (d) GeoSpecies, DBpedia, BBC WO (e) TaxonConcept OWL: Web Ontology Language Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France SKOS: Simple Knowledge Organization System 4

Different models to account for the same reality Taxonomic Information EOL, TaxonConcept, NCBI GeoSpecies, AGROVOC VTO DBpedia, BBC WO Nomenclatural information OWL/RDFS SKOS concepts Class instances Classes All equally valid from the biological perspective, yet slightly different from the SW perspective. Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 5

Challenge 1: accommodate taxonomic changes Delphinus delphis Linnaeus, 1758 Delphinus capensis Gray, 1828 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. Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 6

Challenge 1: accommodate taxonomic changes Taxonomic Information EOL, TaxonConcept, NCBI GeoSpecies, AGROVOC VTO DBpedia, BBC WO Nomenclatural information OWL/RDFS SKOS concepts Class instances Classes Tracking/describing changes How to accommodate changes require that names & taxa be if nomenclatural & taxonomic distinct resources [1]. information are intertwined? [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. Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 7

Challenge 2: interlinking data sets not always possible Taxonomic Information EOL, TaxonConcept, NCBI GeoSpecies, AGROVOC VTO DBpedia, BBC WO Nomenclatural information OWL/RDFS SKOS concepts Class instances Classes How to align classes and class instances?  owl:sameAs, skos:exactMatch, owl:equivalentClass : discouraged by DL best practices [2]  rdfs:seeAlso : weak semantics [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). Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 8

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

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 3 rd party data sets Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 10

TAXREF-LD model overview txrf:taxon/191591/10.0 … Taxonomic information txrfp:bioGeoStatusIn rdfs:subClassOf txrfh:Marine txrf:taxon/60878/10.0 txrfp:habitat txrfp:vernacularName "Short-beaked common dolphin"@en txrfp:hasRank txrfp:hasReferenceName txrfp:hasSynonym txrfrk:Species Nomenclatural information txrfp:hasRank txrfp:hasRank txrf:name/361079 txrf:name/60878 skos:broader skos:broader skos:prefLabel skos:prefLabel txrf:name/191591 txrfp:hasAuthority txrfp:hasAuthority skos:prefLabel "Delphinus delphis" "Delphinus capensis" "Gray, 1828" "Linnaeus, 1758" "Delphinus " txrf: <http://taxref.mnhn.fr/lod/> SKOS concept txrfrk: <http://taxref.mnhn.fr/lod/taxrank#> txrfh: <http://taxref.mnhn.fr/lod/habitat#> OWL class Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 11 txrfp: <http://taxref.mnhn.fr/lod/property#>

Interlinking more flexible but still raises questions VTO http://purl.obolibrary.org/obo/VTO_0011448 NBCI Org. Classification Taxonomic information http://purl.obolibrary.org/obo/NCBITaxon_9728 owl:equivalentClass http://taxref.mnhn.fr/lod/taxon/60878/10.0 Taxon "Delphinus delphis" txrfp:hasReferenceName Nomenclatural http://taxref.mnhn.fr/lod/name/60878 Scientific name "Delphinus delphis" information skos:exatMatch skos:closeMatch skos:closeMatch skos:relatedMatch urn:lsid:marinespecies.org:taxname:137094 GeoSpecies http://lod.geospecies.org/ses/enwsi AGROVOC http://aims.fao.org/aos/agrovoc/c_48963 TaxonConcept http://lod.taxonconcept.org/ses/enwsi.html#Species txrf: <http://taxref.mnhn.fr/lod/> SKOS concept txrfrk: <http://taxref.mnhn.fr/lod/taxrank#> txrfh: <http://taxref.mnhn.fr/lod/habitat#> OWL class Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 12 txrfp: <http://taxref.mnhn.fr/lod/property#>

Interlinking more flexible but still raises questions VTO http://purl.obolibrary.org/obo/VTO_0011448 NBCI Org. Classification Taxonomic information http://purl.obolibrary.org/obo/NCBITaxon_9728 owl:equivalentClass http://taxref.mnhn.fr/lod/taxon/60878/10.0 Taxon "Delphinus delphis" txrfp:hasReferenceName Nomenclatural http://taxref.mnhn.fr/lod/name/60878 Scientific name "Delphinus delphis" information skos:exatMatch txrfp:isReferenceNameOf urn:lsid:marinespecies.org:taxname:137094 GeoSpecies http://lod.geospecies.org/ses/enwsi AGROVOC http://aims.fao.org/aos/agrovoc/c_48963 TaxonConcept http://lod.taxonconcept.org/ses/enwsi.html#Species txrf: <http://taxref.mnhn.fr/lod/> SKOS concept txrfrk: <http://taxref.mnhn.fr/lod/taxrank#> txrfh: <http://taxref.mnhn.fr/lod/habitat#> OWL class Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 13 txrfp: <http://taxref.mnhn.fr/lod/property#>

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

TAXREF-LD massively linked with 3 rd 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 Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 15

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

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/ Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France 17