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 annotated with a verificationKey
.
3.3 Run and save verification
- 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)
.
Save taxa with populated
verificationKey
back todata/interim/taxa_with_verification.csv
.Save updated verification back to
references/verification.tsv
(sorted onscientificName
)
3.4 Show verification status
3.4.1 Unmatched taxa
Status | Number of taxa |
---|---|
Verified | 75 |
Unverified | 16 |
New in this run | 1 |
No longer used | 20 |
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_key
s, e.g. to split a hybrid formula into its hybrid parents.
3.4.2 Synonyms
Status | Number of taxa |
---|---|
Previously verified | 783 |
Unverified | 0 |
New in this run | 0 |
No longer used | 211 |
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) | 5258 |
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
andbb_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: