GBIF TaxonID

[Deon de Jager]

Hi team,

I noticed what is potentially an error with the GBIF TaxonID example, but correct me if I'm wrong. The example in the Kobo form v4 is for Juniperus blancoi, with the GBIF TaxonID given as "6NGG2", but it turns out this is actually the Catalogue of Life TaxonID (https://www.catalogueoflife.org/data/taxon/6NGG2). The GBIF ID for J. blancoi appears to be "2684495". If you search for Juniperus blancoi on GBIF, you get to this page (https://www.gbif.org/species/2684495), and if you scroll down to the bottom of the page, it lists all the TaxonIDs from various databases.

I noticed this because I couldn't find the same page for Cape buffalo (Syncerus caffer), as the example given (https://www.gbif.org/species/175148903/verbatim), with "verbatim" view.

Should I go ahead and list the GBIF TaxonID in future ("7261410" for Cape buffalo), or the Catalogue of Life TaxonID (7L4HB, for Cape buffalo)?

Cheers

Deon

[Deon de Jager]

Cape buffalo is Syncerus caffer caffer (I only gave the species name in the first message).

[Alicia Mastretta]

Hi,

This is a mistake on my side. You should include the taxonID from GBIF, I will change the example of J. blancoi in the form.

[Deon de Jager]

Hi Alicia,

Thanks for confirming!

Jessica (da Silva), if you see this, could you please update the GBIF Taxon ID for the Syncerus caffer caffer assessment I just submitted for South Africa? It should change from 7L4HB to 7261410.

[Fumiko ISHIHAMA]

Hi all,

As you might know, if you are a R user, "name_suggest" function of rgbif package is useful to obtain the taxon ID.

library(rgbif)

#for a species, ID only
name_suggest("Syncerus caffer caffer")$key

#the code need to be as follows for older versions (add $data)
#name_suggest("Syncerus caffer caffer")$data$key

#full search results
name_suggest("Syncerus caffer caffer")


#for multiple species
sname <- list("Syncerus caffer caffer","Juniperus blancoi")
sapply(sname, function(x){name_suggest(x)$key})

#it returns multiple IDs for Juniperus blancoi
name_suggest("Juniperus blancoi")

# A tibble: 4 × 3
# key canonicalName rank
# <int> <chr> <chr>
#1 2684495 Juniperus blancoi SPECIES
#2 2684498 Juniperus blancoi huehuentensis VARIETY
#3 2684496 Juniperus blancoi mucronata VARIETY
#4 7071103 Juniperus blancoi blancoi VARIETY

#if you would like a result for "species" level, you can specify as follows
name_suggest("Juniperus blancoi", rank='species')


Best,

Fumiko


________________________________________
差出人: genetic-indic...@googlegroups.com <genetic-indic...@googlegroups.com> が Deon de Jager <deja...@gmail.com> の代理で送信
送信日時: 2022年11月10日 6:45
宛先: Genetic indicators project
件名: Re: GBIF TaxonID

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[Jessica da Silva]

Hi Deon. 

Thanks for noticing this. I will correct it in the manual and in your Kobo submission.

Jess

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[heue...@gmail.com]

Thanks all for this, we have submissions for a few species to correct as well and will do so!

The France team :)

[Alicia Mastretta]

Thanks Fumiko for the nice R tip.

Sorry to everyone I didn't point the J. blancoi example to the right id. This has now been corrected in the form. Commit https://github.com/AliciaMstt/GeneticIndicators/commit/b56357f207e50ce114caf36d9ee217d0e14fbb3f

If anyone else submitted the wrong id, please let us know in which species this happened and we (or someone from your country) can made the corrections in the data.