datasets

This is a collection of scripts which compiles a list of marine datasets in GBIF. A file containing taxon lists for all datasets is required, but not incuded in this repository. Species profiles are retrieved from the GBIF API and checked for a WoRMS or IRMNG marine flag.

How-to

gbif_export/gbif_occurrence_table.sql

This creates a table occurrence for the name_export.txt file provided by GBIF.

gbif_export/gbif_occurrence_copy.sql

This copies the name_export.txt file to database.

gbif_names.sql

This creates a names table from the occurrence table.

gbif_profiles.py

This queries the GBIF API for species profiles. The names table gets populated with WoRMS and IRMNG marine flags.

id_mapping.sqlandid_mapping_copy.sql

This creates a table and copies the id_mapping.csv file to database.

gbif_datasets.sql

This creates a datasets table from the occurrence and names tables. Only datasets with marine taxa are included.

gbif_datasets.py

This queries the GBIF API for dataset information.

totalrecords.sql

This adds the total number of records to the datasets.

gbif_organizations.sql and gbif_organizations.py

This creates a organizations table from the datasets table and queries the GBIF API for publishing organization information.

gbif_nodes.sql and gbif_nodes.py

This creates a nodes table from the organizations table and queries the GBIF API for node information.

gbif_installations.sql and gbif_installations.py

This creates a installations table from the datasets table and queries the GBIF API for installation information.

obis.py

This marks OBIS datasets.

output_datasets.sql

This outputs the datasets.csv and datasets_sample.csv tables.