Goal of this project

The aim of this repository is to propose an up-to-date correspondance between latin and vernacular french names for as many taxa as possible. This is used for the french version of the Lifemap Explorer of the tree of Life

Dataset produced

Using the three data sources listed below (GBIF, INPN and wikidata), and the dedicated code extract-taxo.py we recover vernacular names for 140 538 distinct taxa.

The resulting tab-delimited file, TAXONOMIC-VERNACULAR-FR.txt, contains one vernacular name per taxa, so that taxa with multiple vernacular names are present multiple times. This file contains 209 313 rows.

Data sources and retrieval strategies

For now, three sources of data are used. Here is the Venn diagram representing the content of each data source (in terms of the number of taxa with vernacular names in French) and their overlap.

In total, we recover vernacular names for 140 538 distinct taxa.

1. Wikidata

Wikidata is a great resource for species names translation. The following code (Sparkle) can be used to retrieve the common names of taxons in french, using the online service https://query.wikidata.org.

SELECT DISTINCT ?sci ?comm WHERE {
  ?taxon wdt:P31 wd:Q16521;
    wdt:P225 ?sci;
    wdt:P1843 ?comm.
  FILTER(LANGMATCHES(LANG(?comm), "fr"))
  SERVICE wikibase:label { bd:serviceParam wikibase:language "fr". }
} 

The downloaded result (tsv format) is called query.tsv

Vernacular names for 18 955 taxa (April 20th, 2020)

• data was modified as follows:
  • Duplicates with other databases were removed. The version with more uppercase letters was always prefered.

2. GBIF

GBIF contains vernacular names for many species in many languages. A single zip file can be downloaded here : http://rs.gbif.org/datasets/backbone/backbone-current.zip

The important files here are VernacularName.tsv and Taxon.tsv

Vernacular names for 33 359 taxa (April 20th, 2020)

• data was modified as follows:
  • Duplicates with other databases were removed. The version with more uppercase letters was always prefered.

3. INPN

The INPN is a great resource for species names of species living in France (but not the others). The complete data can be downloaded from https://inpn.mnhn.fr/docs-web/docs/download/301786

The important file here is TAXREFvXX.txt where XX is the current version.

Vernacular names for 114 193 taxa (April 20th, 2020; TAXREFv13)

• data was modified as follows:
  • Articles (Le, La, L') were removed
  • Duplicates with other databases were removed. The version with more uppercase letters was always prefered.

Ambiguities

Of course, nothing is always simple, and some ambiguities exist because some taxa that are at distant in the tree of life have the same name. The most famous example is a genera of inscects that is called... Bacteria.

Other example :

• Arenaria : genus of birds (Family: Scolopacidae) and genus of flower (Family: Caryophylaceae). The latter is called "Sablines" in french.

Contributions

If you think that some important data sources should be added, please open an issue indicating the resource you have in mind, and I will try to integrate it.

If you identify errors in the french names, please open an issue.

Please note the GBIF ans INPN are already combining data from a variety of sources.

For questions, remarks, or if you want to help and contribute, please send me an email or open an issue.

Citation

If you use this dataset, please cite the paper presenting Lifemap: