TAXREF-LD is the Linked Data knowledge graph representing TAXREF, the French national taxonomical register for fauna, flora and fungus, that covers mainland France and overseas territories.
TAXREF-LD is a joint initiative of the UMS Patrinat of the National Museum of Natural History, and the I3S laboratory of University Côte d'Azur, CNRS and Inria.
The main modelling choices in TAXREF-LD are as follows:
- each taxon is represented as an OWL class, in the sense of the set of biological individuals that belong to that taxonomic group. A taxon is related to a reference scientific name (a.k.a. valid or accepted name), and any number of synonym names.
- each scientific name is modelled as a SKOS concept (an instance of the skos:Concept class) as well as an instance of the TDWG ontology's TaxonName class.
Additional information is provided for each taxon such as its taxonomic rank, parent taxon, vernacular names, habitat and biogeographical statuses. This RDF modeling is detailed are provided in [1].
Beyond strictly taxonomic information, additional data are provided: species interactions, legal statuses (conventions, directives, regulations, protections), conservation statuses (international/european/national/regional red lists), location and bibliographical sources for vernacular names, cross-references to other datasources by means of external IDs and webpages, media (photos of taxa).
The modelling is exemplified in dataset/examples.
TAXREF-LD namespace is http://taxref.mnhn.fr/lod/, registered as prefix taxref on prefix.cc. All URIs are dereferenceable.
The dataset itslef is identified by URI http://taxref.mnhn.fr/lod/taxref-ld. It comes with descriptions in DCAT, VOID and SPARQL SD vocabularies.
Taxa are assigned URIs in http://taxref.mnhn.fr/lod/taxon/, while scientific names are assigned URIs in http://taxref.mnhn.fr/lod/name/.
TAXREF-LD is linked with multiple third-party biodiversity data sources by means of external IDs and webpages, including in particular AlgaeBase, Fauna Europaea, FishBase, GBIF, IPNI, Index Fungorum, The Plant List, TROPICOS, WoRMS.
TAXREF-LD is also interlinked with third-party Linked Data taxonomic registries: NCBI Organismal Classification, AGROVOC and World Register of Marine Species (WORMS).
A new version of TAXREF is released yearly. TAXREF-LD bears the same major version number (e.g. 13.0, 15.0...), and intermediate versions may be realeased with a minor revision number (e.g. 15.1).
The dataset is downloadable as a set of RDF dumps (in Turtle syntax). As of version 15, the dumps are available from Zenodo. Previous versions are still aviable on this Github repo:
| Version | Download link |
|---|---|
| 17.0 |  |
| 15.2 |  |
| 15.1 |  |
| 13.0 | https://github.com/frmichel/taxref-ld/tree/13.0/dataset |
| 12.0 | https://github.com/frmichel/taxref-ld/tree/12.0/dataset |
| 10.0 | https://github.com/frmichel/taxref-ld/tree/10.0/dataset |
The dataset metadata (in DCAT, VOID and SPARQL SD) as well as the definition of vocabulary terms (classes, concepts, properties) used to represent taxonomic data are provided in dataset/Taxrefld_static*.ttl. Whenever possible, these terms are aligned with their counterparts in thrid-party ontologies.
TAXREF-LD can also be queried through our public Virtuoso OS SPARQL endpoint https://taxref.mnhn.fr/sparql.
You may use the Faceted Browser to look up text or URIs. As an example, you can look up taxon http://taxref.mnhn.fr/lod/taxon/60878.
The following named graphs can be queried from our SPARQL endpoint:
| Named graph | Description |
|---|---|
http://taxref.mnhn.fr/lod/graph/metadata |
DCAT, VOID and SPARQL SD dataset descriptions + definition of various classes, concepts, properties (content of files dataset/Taxrefld_static*.ttl) |
http://taxref.mnhn.fr/lod/graph/biblio |
bibliographic resources |
http://taxref.mnhn.fr/lod/graph/locations |
regions, departements, territories etc. |
http://taxref.mnhn.fr/lod/graph/media |
media (photos) linked to taxa |
http://taxref.mnhn.fr/lod/graph/statuscodes |
description of the status values of types international convention, european directive, protection and regulation. These are represented as instances of the class bibo:DocumentPart (e.g. http://taxref.mnhn.fr/lod/status/BONN/IBOAC) and related to the bibliographic source describing the document with property dct:isPartOf (content of files statusCodes.ttl and statusBiblio.ttl) |
http://taxref.mnhn.fr/lod/graph/classes |
description of taxa as OWL classes |
http://taxref.mnhn.fr/lod/graph/concepts |
description of scientific names as SKOS concepts |
http://taxref.mnhn.fr/lod/graph/interactions |
species interactions |
http://taxref.mnhn.fr/lod/graph/statuses |
all taxa statuses (legal, biogeographical, red list) |
http://taxref.mnhn.fr/lod/graph/vernacular |
taxa vernacular names (direct and as SKOS-XL labels) |
http://taxref.mnhn.fr/lod/graph/dbxref |
cross-references to identifiers of third-party data sources such as GBIF, WoRMS, the Plant List etc. |
http://taxref.mnhn.fr/lod/graph/webpages |
foaf:page links to webpages |
http://taxref.mnhn.fr/lod/graph/links-* |
interllinking to equivalent URIs from NCBI, Agrovoc, WoRMS |
This dataset is made available under the terms of the Creative Commons Attribution 3.0 France (CC BY 3.0 FR) license.
The code used to produce the dataset, provided in folder src, is licensed under the Apache License, Version 2.0.
When mentioning TAXREF-LD in a publication or when redistributing it, please cite this way:
TAXREF-LD: Knowledge Graph of the French taxonomic registery. Franck Michel, Catherine FARON, Sandrine TERCERIE, Olivier GARGOMINY. 2017-2022. DOI: 10.5281/zenodo.6940891
[1] Michel F., Gargominy O., Tercerie S. & Faron-Zucker C. (2017). A Model to Represent Nomenclatural and Taxonomic Information as Linked Data. Application to the French Taxonomic Register, TAXREF. In Proceedings of the 2nd International Workshop on Semantics for Biodiversity (S4BioDiv) co-located with ISWC 2017. CEUR vol. 1933. Vienna, Austria.