Taxonomic Curation

This document describes operations implemented by the EukMap platform to propose changes to the taxonomy. All taxonomic operations are available from a toolbar shown at the left side of the taxonomy browser after selecting one or more taxa. The toolbar is shown only if the user has sufficient privileges to propose changes, which requires the user to have at least the contributor role. Additionally, changes must be proposed on special copy of the candidate taxonomy, a darft.

See the User Roles and Workflow documentation for more details.

Create Taxon

The create taxon operation is used to create a single new taxon in the taxonomy.

After selecting a (single) taxon in the taxonomy browser as the new taxon's parent, contributors have the option to create a taxon by selecting the add taxon operation from the taxonomic toolbar. This opens a pop-up that requires the contributor to specify the name of the taxon and allows to provide optional data, such as a publication reference as the naming authority and the taxonomic rank.

See Taxon for a full description of a Taxon and associated data.

Newly created taxa are assigned a numerical identifier, the Taxon#taxon-identifier(UniEuk Taxon ID), automatically.

Update Taxon (Metadata)

The update taxon operation allows to change the (meta)data associated with a taxon, except the taxon's name and identifier.

After selecting a (single) taxon in the taxonomy browser, contributors have the option to update the taxon by selecting the update taxon operation from the taxonomic toolbar or by clicking the edit button in the title of the taxon panel shown at the right side of the taxonomy browser. This opens the taxon details page in edit mode, which allows the contributor to modify the data and save the changes.

Rename Taxon

The rename taxon operation allows to change a taxon's name and naming authority.

After selecting a (single) taxon in the taxonomy browser, contributors have the option to rename the taxon by selecting the rename taxon operation from the taxonomic toolbar. This opens a pop-up that shows the current name and naming authority of the taxon and allows the contributor to change this information. The rename operation does not simply overwrite the previous data but adds a new entry in the taxon's naming history, with the newly added name being the default name of the taxon.

Delete Taxa

The delete taxon operation allows to delete one or more taxa from the taxonomy.

After selecting one or more taxa in the taxonomy browser, contributors have the option to delete all selected taxa by selecting the delete taxa operation from the taxonomic toolbar. This opens a pop-up requesting the contributor to confirm that the selected taxa should actually be deleted. Deleting a taxon will also delete all taxa contained within the subtree defined by the taxon.

Move Taxa

The move taxa operation allows to move one ore more taxa into a taxonomic group (another taxon).

After selecting one or more taxa in the taxonomy browser, contributors have the option to move all selected taxa into a another taxon by selecting the move taxa operation from the taxonomic toolbar. This opens a pop-up asking the contributor to select the taxonomic group into which the selected taxa should be moved (the target). Important: selecting the target currently closes this pop-up and the contributor has to select the move operation from the toolbar again, after selecting the target, to actually move taxa. The second pop-up shows a short summary of the planed operation and asks the contributor to confirm the move operation.

Replace Taxon

The replace taxon operation allows to replace/update a complete subtree of the taxonomy.

After selecting a (single) taxon in the taxonomy browser, contributors have the option to replace/update the selected taxon, and all taxa within the subtree defined by the selected taxon, by selecting the replace taxon operation from taxonomic toolbar. This operation requires the contributor to prepare a file in the EukMap-TSV-Format(EukMap TSV format) that lists taxa in the selected subtree to update. Taxa listed in the replacement file will be created, if they do not exist in the current (candidate) taxonmy. The replace operation requires the contributor to specify how to handle taxa existing in the current taxonomy, that are not listed in the replacement file. Options are:

• report missing taxa as error and abort the operation,
• delete missing taxa as they are considered obsolete,
• ignore missing taxa, neither delete these taxa nor report an error.