1. Taxonomic registers are important tools for biodiversity data but linking them as linked open data can be challenging. 2. This document presents TAXREF-LD, a model for representing the French taxonomic register TAXREF as linked data in a way that distinguishes nomenclatural and taxonomic information and can accommodate taxonomic changes. 3. TAXREF-LD was developed to be biologically relevant, compatible with semantic web standards, and able to link to other datasets. It represents TAXREF names and taxa as SKOS concepts and OWL classes with extensive external linking.

1. 1Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
F. Michel1, C. Faron-Zucker1, S. Tercerie2, O. Gargominy2
1Université Côte d’Azur, CNRS, Inria, I3S, France. 2Service du Patrimoine Naturel, MNHN, CNRS, France.
A Model to Represent Nomenclatural and
Taxonomic Information as Linked Data
Application to the French Taxonomic Register, TAXREF
2nd International Workshop on
Semantics for Biodiversity
October 22nd, 2017, Vienna, Austria

2. 2Franck 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

3. 3Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
Different models to represent taxonomic registers as LOD
rank
rank
Delphinus Genus
Species
Delphinus
delphis
owl:Classrdfs:subClassOf
aa
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:Conceptskos:broader
aa
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

4. 4Franck 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
Biological perspective: all equally valid
SW perspective: slightly different state of mind

5. 5Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
Challenge 1: Accommodate taxonomic changes
Delphinus capensis Gray, 1828Delphinus 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.

6. 6Franck 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.

7. 7Franck 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).

8. 8Franck 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

9. 9Franck 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

10. 10Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
TAXREF-LD model overview
Nomenclatural
information
Taxonomic
information
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
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

11. 11Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
Interlinking more flexible but still raises questions
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/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
owl:equivalentClass
skos:exatMatch
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
http://taxref.mnhn.fr/lod/name/60878
Nomenclatural
information
Taxonomic
information
skos:closeMatch
skos:relatedMatch

12. 12Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
Interlinking more flexible but still raises questions
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
owl:equivalentClass
skos:exatMatch
txrfp:isReferenceNameOf
txrfp:hasReferenceName
NBCI Org. Classification
VTO
GeoSpecies
TaxonConcept
urn:lsid:marinespecies.org:taxname:137094
http://aims.fao.org/aos/agrovoc/c_48963
Nomenclatural
information
Taxonomic
information
Taxon "Delphinus delphis"
Scientific name "Delphinus delphis"
AGROVOC

13. 13Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
Check it out!
Entry point:
http://taxref.mnhn.fr/lod/Dataset/10.0/
Delphinus delphis example:
http://taxref.mnhn.fr/lod/taxon/60878/10.0
http://taxref.mnhn.fr/lod/name/60878
Free text and faceted search

14. 14Franck 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:
For scientific/vernacular names, ranks, habitats, geographical locations…
Sources:
TDWG Ontologies, Darwin Core,
ENVO, Relations Ontology (RO), Geonames
TaxonConcept, NCBI Org. Classification, VTO, GeoSpecies,

15. 15Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
TAXREF-LD is an enabler to...
• Advertize: Datahub.io, AgroPortal
• Foster data integration scenarios
• Leverage the WoD to discover information,
infer knowledge, answer scientific questions,
• etc…

16. 16Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France
Let’s talk!
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 2nd International Workshop on Semantics for Biodiversity (S4BioDiv), Vienne, Austria.
CEUR Vol. 1933 (2017).