Obtaining GBIF's Current CoL Backbone Version

Taxonomy
1

Hello all,

I’m in the process of migrating my code for a project to better align with the Catalogue of Life update. I’m excited for this change!

An issue I’ve run into is that the current Catalogue of Life Extended Release doesn’t seem to align with the taxonomy that GBIF is using at the moment. For instance, GBIF is currently referencing Tapinoma with taxonID “7SPC”. When viewing this taxon in Catalogue of Life, it is listed as removed as of more than a month ago. The new proper ID is “P8H66”, which GBIF identifies as “provisionally accepted” — observations are not currently resolved to this taxon.

As a result, when trying to align GBIF observations with the current CoL backbone, Tapinoma observations end up orphaned.

Is there any way to access GBIF’s current CoL backbone version? If this is simply a discrepancy between CoL’s release times and GBIF backbone update schedule, that would be an easy solution. As it is, I only see a reference to CoL’s current version, which isn’t aligned with GBIF’s.

Any thoughts?

Thank you!

COL XR needs to be referenced via dataset identifier, not just `taxonID`
3

While the solution in this thread seems correct (use GBIF’s API to track down the DOI of the in-use backbone → use that DOI to retrieve the key for the dataset on ChecklistBank → download the associated backbone) the problem I described persists.

This makes it seem like GBIF and CoL are out of sync in a way that GBIF isn’t making clear. The referenced taxonID (7SPC) doesn’t appear in the version of the backbone that is referenced using GBIF’s API.

Scratch all that! The solution in the other thread works. I was referencing the wrong result.

To be clear, my solution is currently to:

  1. Use the GBIF API to retrieve the current DOI for the in-use backbone
  2. Use the ChecklistBank API to retrieve the associated key for the dataset associated with that DOI
  3. Use this format — https://api.checklistbank.org/dataset/{DATABASE_KEY}/export.zip?extended=true&format=DwCA — to retrieve the correct backbone from the archive.