jaxinewolfe
commented
3 years ago Workflow Notes
Taxonomic functions:
- resolveTaxa(): Resolves misspellings using a Global Name Resolver (taxize). Documentation of misspellings is retained in the database. This will be a curation function going forward so that misspellings can be nipped in the bud.
In Question:
- classifyTaxa(): this function would automate the classification of taxonomic level for any given taxa (i.e. code_type in our database). The drawback is that taxize::classification() is not always reliable to pull the correct classification (depending on the database you choose) so we might be better off continuing to manually classify code_type.
- Habitat and code_type are manually classified for each species_code in this table. I'd like to merge this with the database table so that we can stick to one species lookup table for post-processing. This will be especially informative for the assignment of core-level habitat. Should the addition of habitat and code_type to the species table be a curation or post-processing step?
HolmquistJ
Create a taxonomic database from the existent species table. Once established, a post-processing workflow will be created to recognize when new taxa have been added to the synthesized species table and update the database.