BF Workbench is a restricted scientific system. Records are available only to registered, authorised accounts.

Taxonomy

Browsing, adding, synonyms, retiring and moving taxa.

How-to

The taxonomy registry is the tree of names a record's identification can be linked to, from phylum down through class, order, family, subfamily, tribe, genus, species and subspecies. A record's taxonomy fields are a link to one taxon in this tree, from which its whole lineage follows. You maintain the tree from Platform Management → Controlled Terms → Taxonomy. Curation is an administrator-only capability: other users meet the taxonomy through the specimen forms, search and the record detail, but cannot change it.

How it works

Each taxon has a canonical scientific name, a rank, a parent (except top-level taxa, which sit under a division, or kingdom), an authority and year, free-text sources, a status of active or defunct, and any number of synonyms. The rank order is fixed: a taxon can only be created under a parent whose rank is allowed to have children of that rank, and a child always sits below its parent in the hierarchy.

The page opens on the top-level taxa with statistics for names, specimens, species and barcodes. Expand a taxon to see its children, or search by the start of a name (% is a wildcard). Each result shows its lineage, so homonyms in different phyla can be told apart. Selecting a taxon shows its lineage, metadata, synonyms and counts.

How uploads are resolved

Batch specimen uploads are matched against a copy of the registry that the record store exports each night. Names are compared ignoring case.

  1. If the record has an identification, the taxa with that name are found and narrowed by each rank the record supplies (phylum, class and so on). If exactly that lineage exists, the record is linked to it.
  2. Otherwise the lowest rank the record supplies is looked up, and the match is accepted only when the parent ranks the record supplies agree with the registry's lineage for that taxon. A phylum on its own resolves directly.
  3. If nothing matches, the link is dropped and the record loads with the text it carried in each rank field. A rank value that is not in the registry at all is removed from the record, which still loads.

The same lookup drives the stop-codon check on sequence uploads: the record's taxon names the translation table for its genome, and a sequence whose taxonomy cannot be resolved is reported as unresolved rather than flagged. See The two ingest jobs.

Add a taxon

Select the parent and choose Add taxon (or the top-level button to add a phylum, which also needs a Division). Give the canonical name and rank; authority, year and sources are optional. The rank must be a valid direct child of the parent's rank, and the parent must be active. A name that is already the canonical name of an active taxon is refused: if the name belongs to an existing taxon, add it there as a synonym instead.

Edit Metadata changes the canonical name, authority, year and sources. Records link to the taxon rather than storing its text, so a corrected spelling carries through to every record that references it.

Synonyms

Add Synonym attaches an alternative name to a taxon, with its own authority. The synonym cannot equal the canonical name and is refused if the taxon already has it. Synonyms show in the detail pane and are found by the page's search, so you can check whether a name is already known under another spelling. Remove a synonym from the same panel.

Good to know: Synonyms are not consulted when uploads are resolved. A spreadsheet must use the canonical name to be linked; a synonym in a rank field is treated as an unknown name.

Retire, reinstate and move

Retire marks a taxon defunct without deleting it. It is refused while records reference the taxon or while it has active child taxa; retire the children first, or re-identify the records. Reinstate makes a retired taxon active again; a retired taxon cannot be given new children until then.

Move re-parents a taxon. The new parent must be active, strictly higher in the rank order, and not one of the taxon's own descendants. A reason is required, and the page warns when the jump in rank is unusually large. Records keep their link to the moved taxon, so their lineage follows the new parent.

Effect on existing records

No action here rewrites a record. Editing a name changes what linked records display; moving a taxon changes the lineage they report; retiring is blocked while records depend on the taxon.

Good to know

  • The reason entered for a move is not kept, and no change history is recorded for the taxonomy registry. Note significant changes elsewhere if your procedures require it.
  • The specimen, species and barcode counts, and the record count that blocks a retire, come from a statistics table and are not live. They are platform-wide, not filtered by project access.
  • Changes reach batch uploads after the next nightly export; the specimen form's autocomplete sees them immediately.