Skip to content
B-Cubed documentation

Download a species occurrence cube from GBIF.org

How to cite

Section titled “How to cite”

Desmet P (2025). Download a species occurrence cube from GBIF.org. https://docs.b-cubed.eu/tutorials/download-a-cube-from-gbif/

Steps

Section titled “Steps”

Here are the steps to create and download a species occurrence cube from GBIF.org:

  1. Go to https://gbif.org.

  2. Log into your GBIF account (you can register for free):

    login screenshot

  3. Go to the occurrence search and look for the data you want to include in your cube. Here we select occurrences of animals from Poland, recorded since 2000:

    occurrence search screenshot

  4. Go to the Download tab, scroll to Occurrence cube and click Configure:

    occurrence download

  5. Choose how the data should be cubed, including its Dimensions, Measures and Data quality aspects. Here we choose 3 dimensions: taxonomic (by species), temporal (by year and month) and spatial (using the EEA reference grid with 1 km grid cells):

    cube options

  6. If you want more advanced options, click Edit as SQL at the bottom to completely customize your query:

    cube sql

  7. Click Continue and agree to the terms.

    cube terms

  8. Click Create download and your cube will be generated:

    cube processing

  9. You will receive an email at the address linked with your GBIF account when the data are ready for download. You can also find all your downloads in your profile.

  10. Click the link to open the unique landing page for your cube. Here you can download the data, see how to cite it using its DOI, get an overview of all the parameters that were used and learn what datasets contributed data to it:

    download page

  11. Download the data and unzip it. It is a tab-delimited text file, where each row represents the requested measures per dimension combination:

    kingdom  kingdomkey  phylum  phylumkey  class  classkey  order  orderkey  family  familykey  genus  genuskey  species  specieskey  yearmonth  eeacellcode  kingdomcount  phylumcount  classcount  ordercount  familycount  genuscount  occurrences  mintemporaluncertainty  mincoordinateuncertaintyinmeters
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea alba  GCHR  2022-01  1kmE4601N3317  2  2  2  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2012-05  1kmE4604N3425  10  10  10  1  1  1  1  60  1235.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea alba  GCHR  2022-10  1kmE4643N3286  15  15  15  2  2  2  2  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2024-08  1kmE4644N3434  4  4  4  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea alba  GCHR  2023-04  1kmE4645N3286  55  55  55  3  3  3  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2023-04  1kmE4645N3286  55  55  55  3  3  3  2  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2023-10  1kmE4658N3323  15  15  15  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea alba  GCHR  2023-12  1kmE4669N3232  22  22  22  4  4  4  2  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2023-12  1kmE4669N3232  22  22  22  4  4  4  2  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea alba  GCHR  2021-05  1kmE4682N3462  10  10  10  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2024-08  1kmE4693N3242  2  2  2  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2022-08  1kmE4744N3323  12  12  12  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2024-07  1kmE4772N3148  4  4  4  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea alba  GCHR  2023-08  1kmE4777N3159  14  14  14  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2022-08  1kmE4777N3297  37  37  37  4  4  4  3  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea alba  GCHR  2022-08  1kmE4777N3297  37  37  37  4  4  4  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2016-05  1kmE4782N3530  14  14  14  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2022-08  1kmE4784N3533  15  15  15  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2021-05  1kmE4791N3266  58  58  58  1  1  1  1  86400  1000.0
    Animalia  N  Chordata  CH2  Aves  V2  Pelecaniformes  3RZ  Ardeidae  6PB  Ardea  32FH  Ardea cinerea  GCHS  2023-12  1kmE4804N3067  16  16  16  2  2  2  2  86400  1000.0

See the software and tutorials on this website for ways to explore and process the data. The steps describe above can also be repeated programmatically, using the GBIF SQL download API.