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Download a species occurrence cube from GBIF.org

Suggestion citation:

Desmet P (2024). Download a species occurrence cube from GBIF.org. https://docs.b-cubed.eu/tutorials/download-a-cube-from-gbif/

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 during or after 2000:

    occurrence search screenshot

  4. Go to the Download tab and select Cube:

    occurrence download

  5. In the window that appears, 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 to completely customize your query:

    cube sql

  7. Click the Download button at the bottom of the window and your cube will be generated:

    cube processing

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

  9. 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

  10. 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  familycount  genuscount  occurrences  mintemporaluncertainty  mincoordinateuncertaintyinmeters
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Brachionidae  3880  Brachionus  1000593  Brachionus calyciflorus  4984102  2012-06  1kmE4880N3502  1  1  1  86400  1000.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Brachionidae  3880  Brachionus  1000593  Brachionus angularis  4984131  2011-05  1kmE4900N3354  1  1  1  86400  1000.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Brachionidae  3880  Brachionus  1000593  Brachionus calyciflorus  4984102  2005-05  1kmE4941N3511  2  1  1  86400  1000.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Bdelloidea  1234  Philodinidae  8058  Rotaria  1000832  Rotaria neptunia  1000873  2011-05  1kmE4741N3096  4  4  3  2678400  10.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Bdelloidea  1234  Philodinidae  8058  Rotaria  1000832  Rotaria rotatoria  1000850  2011-05  1kmE4741N3096  4  4  1  2678400  10.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Trichocercidae  8115  Trichocerca  1001946  Trichocerca similis  1002086  2011-08  1kmE4955N3318  1  1  1  2678400  10.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Brachionidae  3880  Kellicottia  1002568  Kellicottia longispina  1002569  2012-05  1kmE4692N3116  1  1  1  86400  1000.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Brachionidae  3880  Keratella  1002582  Keratella quadrata  1002648  2010-08  1kmE4909N3535  1  1  1  86400  1000.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Brachionidae  3880  Keratella  1002582  Keratella quadrata  1002648  2004-04  1kmE4944N3524  1  1  1  86400  1000.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Synchaetidae  3887  Synchaeta  1003145  Synchaeta fennica  1003148  2008-08  1kmE4765N3590  1  1  1  86400  1000.0
    Animalia  1  Rotifera  91  Eurotatoria  307  Ploima  1235  Synchaetidae  3887  Synchaeta  1003145  Synchaeta pectinata  1003169  2011-05  1kmE4920N3191  2  1  1  2678400  10.0
    Animalia  1  Arthropoda  54  Ostracoda  353  Podocopida  1438  Cyprididae  9259  Eucypris  1029198  Eucypris virens  1029200  2001-06  1kmE4813N3271  9  9  9  86400  1000.0
    Animalia  1  Arthropoda  54  Insecta  216  Mecoptera  1000  Panorpidae  7925  Panorpa  1031814  Panorpa communis  5742495  2023-06  1kmE4976N3237  2  2  2  1  7.0
    Animalia  1  Arthropoda  54  Insecta  216  Mecoptera  1000  Panorpidae  7925  Panorpa  1031814  Panorpa communis  5742495  2021-05  1kmE5148N3216  1  1  1  60  15.0
    Animalia  1  Arthropoda  54  Insecta  216  Mecoptera  1000  Panorpidae  7925  Panorpa  1031814  Panorpa communis  5742495  2023-07  1kmE5193N3200  1  1  1  1  27.0
    Animalia  1  Arthropoda  54  Insecta  216  Psocodea  7612838  Pediculidae  7930  Pediculus  1031922  Pediculus humanus  4987991  2022-06  1kmE5240N3179  1  1  1  60  1534.0
    Animalia  1  Arthropoda  54  Insecta  216  Coleoptera  1470  Hydrochidae  4734  Hydrochus  1033653  Hydrochus elongatus  5745443  2002-06  1kmE5166N3022  1  1  1  86400  1000.0
    Animalia  1  Arthropoda  54  Insecta  216  Coleoptera  1470  Hydrophilidae  7830  Cryptopleurum  1034240  Cryptopleurum minutum  1034242  2012-05  1kmE4984N2979  8  3  3  950400  1000.0
    Animalia  1  Arthropoda  54  Insecta  216  Coleoptera  1470  Hydrophilidae  7830  Cryptopleurum  1034240  Cryptopleurum minutum  1034242  2013-05  1kmE5041N2957  7  1  1  86400  1000.0
    Animalia  1  Arthropoda  54  Insecta  216  Coleoptera  1470  Hydrophilidae  7830  Cercyon  1034418  Cercyon impressus  1034479  2013-05  1kmE5217N2980  1  1  1  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.