ibge-bim-species (archived)

Validation of species list of Brussels Environment Departement. This project has been closed and the repository archived.

Appendix 1. Test connectivity

Test connection to database by following documentation in test connectivity script (Appendix 1). Please, be aware that connection to ibge_dev database is restricted and login credentials are needed.

Improve parent ID

Workflow

The steps followed during validation are divided in a series of scripts:

1. Get taxa from table biodiv.taxon.
2. Flag used taxa, i.e. taxa mentioned in higher taxonomy or in use in linked tables.
3. Correct taxonomic information by reading a reference file. See Appendix 2 to know how this file has been created.
4. Match to GBIF Taxonomy Backbone.
5. Assign parent IDs based on parent relationships in GBIF Backbone

Appendix 2. Build reference file correcting taxonomic information

We build a reference file to correct taxonomic informations in order to improve match and provide description of the problems while matchin to GBIF Taxonomy Backbone. This is performed in a two-step procedure:

1. Add kingdom: add kingdom by following internal parent IDs where possible
2. Match taxa to GBIF Taxonomy Backbone: try to match taxa to GBIF Taxonomy Backbone in three matching attempts with decreasing restrictions. A reference file with no exact matches is saved for check by experts.

Contributors

List of contributors

License

MIT License for the code and documentation in this repository.