pieterprovoost / occurrence-cube

Workflows for producing species occurrence cubes from GBIF mediated data

Occurrence Cube

Functions for producing species occurrence cubes from GBIF-mediated data.

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This will contain software for running on GBIF and a public cloud (AWS, Azure etc) using a monthly data export.

It is envisaged the workflow will be structured as follows, and initiated through the GBIF API using e.g. rGBIF, pyGBIF or gbif.org:

1. Initial GBIF search filter

2. Filter unwanted data options

3. Apply transformations (phase 2)

   • E.g. reorganise to taxonomy X

4. Define the dimensions. E.g.:

   1. Taxon

      • bucket by family

   2. Temporal

      • bucket on year
      • discard data outside precision

   3. Geography

      • bucket on cell-id (e.g. UTM)
      • randomise using “technique-x”
      • (Or possibly assign to a higher point in the hierarchy.)

   4. Lifestage

      • bucket by vocabulary (nulls default to NOT-SUPPLIED)

5. Select output format(s):

   1. CSV
   2. Parquet
   3. NetCDF
   4. HDF 5
   5. GeoTIFF
   6. ZAAR
   7. Etc

6. Assign DOI (Including links to the source datasets)

7. Select destination (AWS, Azure, GCS, GBIF storage etc)

   1. Stored (also) on GBIF’s systems for a year, or indefinitely if cited

Licence

Occurrence Cube is licensed under the Apache License, Version 2.0 or the MIT license , at your option.

Acknowledgements

This work receives funding from the European Union's Horizon Europe research and innovation programme under grant agreement No. 101059592 (Biodiversity Building Blocks for Policy).

Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Commission. Neither the EU nor the EC can be held responsible for them.