3 Verify taxa

In this chapter we verify taxonomic information returned by the GBIF Backbone Taxonomy. We do this because we want to use the backbone information to unify taxa that can be considered the same within or across checklists. This is straightforward for (accepted) taxa with the same backbone key (bb_key), but requires verification for taxa the backbone does not recognize (no backbone match) or will lump under another name (synonyms). See 3.2.

3.1 Read taxa

Read taxa from data/interim/taxa_with_verification.csv.

3.2 Read verification information

Verification information consists of a manually assigned verificationKey for taxa the backbone does not recognize (no backbone match) or will lump under another name (synonyms). Those checklist/backbone/accepted taxon combinations are stored in references/verification.tsv, which was created/updated in previous runs of this chapter and then manually annoted with a verificationKey.

3.3 Run and save verification

  1. Use the existing verification information to verify taxa with the function trias::verify_taxa:

Note: to start a verification from scratch, use trias::verify_taxa(taxa).

  1. Save taxa with populated verificationKey back to data/interim/taxa_with_verification.csv.

  2. Save updated verification back to references/verification.tsv (sorted on scientificName)

3.4 Show verification status

3.4.1 Unmatched taxa

Status Number of taxa
Verified 1
Unverified 81
New in this run 0
No longer used 6

Unmatched taxa are those for which the automatic backbone matching on the scientific name failed (have BACKBONE_MATCH_NONE in issues), either because the scientific name could not be parsed or because it is not listed in the backbone.

Verification (see 3.2) involves setting the verificationKey to a manually found bb_key. One could even set multiple bb_keys, e.g. to split a hybrid formula into its hybrid parents.

3.4.2 Synonyms

Status Number of taxa
Previously verified 196
Unverified 229
New in this run 0
No longer used 92

Synonyms are taxa that the backbone will lump under an accepted taxon (taxonomicStatus = SYNONYM or similar). This lumping is often correct, but should be verified.

Verification (see 3.2) involves setting the verifiedKey to one of the following:

  • accepted bb_key suggested by GBIF: backbone synonymy is accepted and taxon will be lumped.
  • another accepted bb_key: backbone synonymy is rejected, but taxon will be lumped under another name.
  • bb_key of taxon itself: backbone synonymy is rejected, taxon will be considered as separate taxon.

3.4.3 Accepted taxa

Status Number of taxa
Verified (automatic) 2869
Unverified 0

Accepted taxa are those the backbone considers own entities (taxonomicStatus = ACCEPTED or DOUBTFUL) that won’t be lumped.

No verification is required for these: verificationKey is automatically set to their bb_key.

3.4.4 Erroneous verificationKeys

Provided verification keys that are not found in the GBIF backbone:

3.4.5 Additional information

Additional information regarding the verification information that is of no further consequence.

  • Duplicate taxa (having same bb_key and bb_acceptedKey) that are quick wins to verify:
  • Previously listed synonyms for which the scientific name was updated in the backbone:
  • Previously listed synonyms for which the accepted scientific name was updated in the backbone: