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BiodiversiteQuebec / bdqc_taxa

`BIOQC-taxa` is a python package that interface with *Biodiversité Québec*'s database to query reference taxa sources, parse their return and generate records.
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Synonymes match de différents clades #10

Closed vincent-beauregard-ielab closed 11 months ago

vincent-beauregard-ielab commented 1 year ago

Exemple de Salix, match avec des animaux et avec des Plantes.

vincent-beauregard-ielab commented 11 months ago

Fixed with optional arguments in method TaxaRef.from_all_sources() :

From updated README.md :

Conflicts

Certain scientific names corresponds to different organism within two entirely different branches of the tree of life. For example, the scientific name Salix corresponds to the genus of willows in the plant kingdom and to a genus of tunicates in the animal kingdom. To avoid matching for such case, the user can specify a parent taxa name to restrict the results to the branch containing the parent taxa. For example, the user can specify the parent taxa name Plantae to restrict the results to the plant kingdom.

The parent_taxa argument is optional. If not specified, the module will return all results for the given scientific name.

from bdqc_taxa.taxa_ref import TaxaRef

results = TaxaRef.from_all_sources('Salix', parent_taxa='Plantae')

Next steps will be to update atlas-db and coleo-db ressources to allow the usage of this optionnal parameter.

https://github.com/ReseauBiodiversiteQuebec/atlas-db/issues/105 https://github.com/ReseauBiodiversiteQuebec/Coleo_DB/issues/127

vcameron1 commented 11 months ago

Final step will be to add parent_taxa_name to all taxa names that match with multiple organisms