How to get GBIF TaxonKey for checklist dataset

Data Use
1

Hi!

I have a seemingly simple task - get the GBIF taxonKey for a checklist dataset which is also hosted on GBIF. From the front page of the dataset the overlap with the GBIF backbone is shown, so the match between the two datasets has already been made, but I simply can’t figure out how to access it?

So what I want to do is to get the GBIF taxonKey for the Swedish Dyntaxa dataset. What would the recommended approach be here?

Best regards
Lars

2

Hej Lars.

The Dyntaxa checklist has 180K or so records, each with its own identifying key. Are you looking for a way to extract these?

/Daniel

3

Hej Daniel

Thanks for your response :slightly_smiling_face:

I’ll only be using a subset of the Dyntaxa dataset, but still app. 3000 species. But otherwise yes, I’d basically like to add a column with the GBIF taxonkey to the Dyntaxa checklist.

I guess I could write a method in R to hit the API, but I was just wondering if this really is the way to do this?

4

Hi @ldalby yes, you will need to use the species API to access the information.

You can use the search function to filter by:

The corresponding key in the GBIF backbone will be in the field nubKey.

You can use this method for up to 100,000 records. Above that, I suggest to contact helpdesk@gbif.org.

1 Like
5

I guess it depends on which species. Are they all are within a single taxon? If so, doing a search using ´higher_taxon` might be the easiest way, e.g., all accepted species names in Lepidoptera:

Web:
https://www.gbif.org/species/search?rank=SPECIES&dataset_key=de8934f4-a136-481c-a87a-b0b202b80a31&highertaxon_key=159955155&origin=SOURCE&status=ACCEPTED&advanced=1

API:
https://api.gbif.org/v1/species/search?rank=SPECIES&dataset_key=de8934f4-a136-481c-a87a-b0b202b80a31&highertaxon_key=159955155&origin=SOURCE&status=ACCEPTED&advanced=1

In the results, you not only get the taxonKey (field key) but also the matching species in the backbone (nubKey)

If your species of interest are not in a single group, you can also search for them individually by sourceID, e.g.,

https://api.gbif.org/v1/species?datasetkey=de8934f4-a136-481c-a87a-b0b202b80a31&origin=SOURCE&advanced=1&sourceId=urn:lsid:dyntaxa.se:Taxon:214018

In the latter case, a simple script would probably come in handy to retrieve all 3000 species.

If I’m missing your point completely, do let me know :slight_smile:

6

Looks like Marie and I have similar thoughts on the subject :slight_smile:

7

Thank you both for your replies!

OK, I was thinking something along these lines. I guess I better just get to it then :slightly_smiling_face:

8

This topic was automatically closed 30 days after the last reply. New replies are no longer allowed.