How to check scientific name

Data Use
1

Hi, I have about 2000 scientific names of plants to check for correct spelling.
How can I do that ?

2

Hi @VIBI
If you would like to align the scientific names with he GBIF backbone taxonomy (you can read more about what it is here), you could can use the GBIF Species matching tool Species name matching or the species match API Species API :: Technical Documentation. Lear more about the species API here: (Almost) everything you want to know about the GBIF Species API - GBIF Data Blog

3

Hiya VIBI, welcome.

What kind of tools are you familiar with? Are you looking for a R or Python scripted solution? OpenRefine? Something else? :smile:

I’d fall back to the API for this, but you’ll definitely need some human judgement calls at least some of the time.

4

Hi Pieter,

Thanks a lot for your answer.

I installed Python but I’m not a specialist at all. In fact, I am carrying out a botanical inventory and I have Excel spreadsheets with several thousand scientific names of plants that I need to check.

It is not possible to do it name by name.

Also I would like to obtain the geographical origin for each of these plants. I don’t know if this is possible on GBIF. I know it’s possible on POWO, but I don’t know how to go about it either.

Thanks anyway for your help.

Vincent Blondel

Guide naturaliste/MĂ©diateur scientifique et culturel

Naturelles Balades

Boulevard de la Liberté

309 Astarté - le Carthage

83320 Carqueiranne - France.
http://www.naturellebalade.com
Siret : 419 276 407 00030 APE 7990Z

TVA intracommunautaire : FR 6641927640700030
Téléphone : 04.94.58.57.97 - Mobile : 06.85.70.68.81

https://www.facebook.com/NBVincentBlondel

5

@VIBI It sounds like you could be more comfortable using a web interface. You can upload a CSV table containing your names here: Species name matching and download a normalised version of the name (the matches in the GBIF Backbone taxonomy)

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6

Hi,

I will try this.

That’s a lot for your help.

BEsts

Vincent Blondel

Guide naturaliste/MĂ©diateur scientifique et culturel

Naturelles Balades

Boulevard de la Liberté

309 Astarté - le Carthage

83320 Carqueiranne - France.
http://www.naturellebalade.com
Siret : 419 276 407 00030 APE 7990Z

TVA intracommunautaire : FR 6641927640700030
Téléphone : 04.94.58.57.97 - Mobile : 06.85.70.68.81

https://www.facebook.com/NBVincentBlondel

image003.jpg

7

Hi - in the blog post for (Almost) everything you want to know about the GBIF Species API - GBIF Data Blog, most of the links to code are broken (or seem outdated).

  1. During data ingestion, are names normalized using the same process as the species-lookup tool?
  2. Is the code for ingestion and the species-lookup tool public?

Thanks in advance!

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8

OpenRefine is another tool that could help, you could match both gbif and powo (from a local file even). I’m not sure if there is already a tutorial on how to do this somewhere.

9

You can use OpenRefine plugged into Global Names:

Or use gnverifier directly: https://verifier.globalnames.org/

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10

Thanks for linking to gnames @dimus!

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11

Hi @shellyleegaynor sorry I had missed your questions!

  1. Yes the names in the scientificName field for occurrences are normalised using the same process at the spices lookup too (it is a bit different for checklist records).
  2. The code is public but has changed since the blog post was published. I have updated the links in the post.

On a related topic, note that we a Data Use Club recorded webinar on the backbone taxonomy and name matching: Data Use Club Practical Sessions: Name matching and the GBIF Taxonomic Backbone

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