Downloading species taxonomy from GBIF

Warning: make sure you back up your database before proceeding with the functionality described below as it can be used to batch update large parts of your data without an option to reverse the changes.

Scenario: you have a long list of species names, you need to have higher classification available in the database, and you need to check the validity of the species names.

Assuming you have the list of species names already in EarthCape database (if not, you can load it from a spreadsheet file).

Under Tools toolbar there is “Update taxonomy from GBIF” command that would run selected record names through GBIF‘s species/match service and download data from GBIF Taxonomic Backbone.

What happens next is that “GBIF key”, “GBIF Status”, “GBIF Valid TaxonomicName” columns of TaxonomicName record will be populated from the service. Additionally, All higher taxonomic names for phylum, kingdom, class, order, family, and genus will be created and linked to target species name record (warning: existing links will be overwritten). I addition, in case of a record that is marked as a SYNONYM in GBIF, it would download a valid name and create record for it including higher taxonomy.

What you can do after that is to make sure that when viewing Unit (specimen/observation records) you can tell which names are valid and which are not according to GBIF backbone taxonomy. To do that, you need to open column customization dialog and bring in extra fields linked through TaxonomicName field:

Now those columns are visible and can be used for filtering and searching:

Although higher taxonomic names are stored as a hierarchy (screenshot also includes a user defined customization that highlights taxonomic name records that do not have Unit records directly linked to them), they can also be represented as flat columns in both TaxonomicName and Unit list views (tables) as see in screenshots above.

Limitations

  • currently this function will only download data for species names
  • may download wrong hierarchy if the same name exists in different taxonomic groups
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