Taxon_id to TAXREF ID

General
1

Yeah :)
I use API for take data on INaturalsit but I don’t no how use taxon_id. I finally need to have TAXREF ID (French taxa reference). Do you know how I can do link into this database ?
Ty

2

not sure exactly why you need to translate iNaturalist’s taxon_id to the ID in TAXREF, but i think i would try one or more of 3 options below:

  1. you might be able to go through through Wikidata. just for example, you can see in the Wikidata page for Trifolium repens (https://www.wikidata.org/wiki/Q148675) that the iNaturalist ID is 55745 and the TAXREF ID is 127454. not every species is going to have an entry (or a complete entry) in Wikidata though. you could use the Wikidata Query Service to return this information systematically: https://query.wikidata.org/.
  2. you could try looking up taxa in TAXREF based on on scientific name and taxon rank (ex. https://taxref.mnhn.fr/api/taxa/search?version=15.0&scientificNames=trifolium%20repens&taxonomicRanks=ES)
  3. you could try translating from iNat taxon id to TAXREF ID via GBIF ID. it looks like the TAXREF API does provide the GBIF ID given a TAXREF ID (https://taxref.mnhn.fr/api/taxa/127454/externalIds). i’m not sure where the iNat-GBIF cross-reference lives, but iNat pushes data to GBIF. so i assume there must be a cross-reference (probably in GBIF?) that defines iNat ID to GBIF ID.
4 Likes
3

I’m also trying to translate iNaturalist species names to TAXREF names and the simplest way so far seems to be to use the rtaxref R package which is a wrapper on the TAXREF API. I know you use R, so that may make things a bit easier than going through the API. You can just send a query for an iNat name to get the reference name used by TAXREF:

library(rtaxref) # on GitHub, not on CRAN yet
x <- rt_taxa_search(sciname = "Acroceras hubbardii")
x[ , c("scientificName", "referenceName")]
### A tibble: 1 x 2
##  scientificName      referenceName                             
##  <chr>               <chr>                                     
##1 Acroceras hubbardii Panicum hubbardii (A.Camus) Renvoize, 2018

In some cases though, there is more than one match and changing author’s name and it is very difficult to completely automate the process…

Eventually, we may get a direct link between TAXREF and the taxize package (which already links to iNat), but it does not seem to be there yet.

1 Like
4

Thank you :)

5

Thank you ;), funny to see you here :smile:

6

Linking from this post, it looks like the ChecklistBank API can be used to go from iNat to TAXREF (or vice versa). Here is a UI and here are the API docs.

7

This topic was automatically closed 60 days after the last reply. New replies are no longer allowed.