This article shows how taxify decides which backbone resolves each name, how to name the backbones yourself, how to compare their answers for the same names, and how to download and pin backbone versions. It ends with a list of backbone choices for common kinds of name lists. Installation is covered in Get started.
Match with the default fallback chain, or name
the backbones in backbone.
Compare the backbones’ answers with
mode = "wide" or mode = "agreement".
Check names a backbone does not cover with
lookup_genus() and
taxify_register_coverage().
Download and pin versions with
taxify_download(), and list them with
list_backbones().
A backbone is a published taxonomic database stored as a file on your
disk. taxify supports
19
backbones of taxa, and two of vegetation units described in Matching vegetation units.
list_backbones() reports each one’s scope, version, number
of names and whether it is installed:
bb <- list_backbones(verbose = FALSE)
bb[, c("name", "scope", "version", "n_names", "installed")]
#> name scope version n_names installed
#> 1 wfo Vascular plants 2026.06 1664014 TRUE
#> 2 col All kingdoms 2026.09 5432444 TRUE
#> 3 colxr All kingdoms 2026.09 8479599 TRUE
#> 4 gbif All kingdoms 2023.08 6404001 TRUE
#> 5 itis US focus, freshwater/marine 2026.09 1000552 TRUE
#> 6 ncbi All life 2026.09 2952424 TRUE
#> 7 ott All life (synthetic) 2026.09 3690217 TRUE
#> 8 worms Marine/aquatic 2026.09 1565652 TRUE
#> 9 euromed European/Mediterranean plants 2026.08 146922 TRUE
#> 10 fungorum Fungi 2026.08 315037 TRUE
#> 11 algaebase Algae 2026.09 172351 TRUE
#> 12 fishbase Fishes 2026.08 102703 TRUE
#> 13 sealifebase Non-fish marine/aquatic 2026.08 134031 TRUE
#> 14 reptiledb Reptiles 2026.07 50043 TRUE
#> 15 lcvp Vascular plants 2026.08 1337891 TRUE
#> 16 wcvp Vascular plants 2026.06 1448984 TRUE
#> 17 mdd Mammals 2026.08 61862 TRUE
#> 18 avilist Birds 2026.08 40572 TRUE
#> 19 lpsn Prokaryotes (Bacteria/Archaea) 2026.08 44885 TRUE
#> 20 evc European vegetation units (syntaxa) 4 7542 TRUE
#> 21 vegcz Czech vegetation units (syntaxa) 2026.10 2258 TRUEWithout a backbone argument, taxify() uses
every installed backbone of taxa as a fallback chain: each name is
matched against the first backbone, the names left unmatched go to the
second, and so on. The order is fixed by priority. The Extended Release
of the Catalogue of Life (COL XR) comes first, then the Catalogue of
Life (COL), then the backbones of one group (marine species, plants,
fungi, algae, fishes, reptiles, mammals, birds, prokaryotes), then the
broad compilations GBIF, ITIS, NCBI and OTT. On a new setup
install_backbones() installs COL, GBIF and the Integrated
Taxonomic Information System (ITIS); every backbone downloaded later
joins the chain at its place in that order.
The list below mixes a plant, two animals renamed since their description, a fungus, a fish, a bacterium and a brown alga:
mixed <- c(
"Quercus robur", "Panthera leo", "Amanita muscaria", "Salmo trutta",
"Escherichia coli", "Macropus rufus", "Fucus vesiculosus",
"Parus caeruleus"
)
res <- taxify(mixed, verbose = FALSE)
res[, c("input_name", "accepted_name", "backbone")]
#> input_name accepted_name backbone
#> 1 Quercus robur Quercus robur colxr
#> 2 Panthera leo Panthera leo colxr
#> 3 Amanita muscaria Amanita muscaria colxr
#> 4 Salmo trutta Salmo trutta colxr
#> 5 Escherichia coli Escherichia coli colxr
#> 6 Macropus rufus Osphranter rufus colxr
#> 7 Fucus vesiculosus Fucus vesiculosus colxr
#> 8 Parus caeruleus Cyanistes caeruleus colxr
#> Sources: COLXR 2026.08 | cite() for full citationsAll 19 backbones are installed on the machine that built this page,
so the chain starts with COL XR. It resolves all eight names, and the
other 18 backbones are skipped. The backbone column records
which backbone matched each row, and the line under the table names the
backbones to cite for this result: only those that matched a row.
Macropus rufus and Parus caeruleus are synonyms in COL
XR, and their rows carry its accepted names Osphranter rufus
and Cyanistes caeruleus.
The first backbone that matches a name decides its accepted name. taxify does not take a vote across backbones: several backbones copy their treatment from one another, so a majority can follow the oldest treatment. Comparing backbones shows how to see where they disagree.
options(taxify.backbone_priority = ) changes the order
for a session, and options(taxify.default_backbones = ) the
set install_backbones() installs when called without
arguments.
When most names of a list belong to one group, that group’s backbone
can come first. A backbone vector replaces the default
chain with your own; here the mixed list is resolved against World Flora
Online (WFO) first, with COL for the rest. Before a name moves on,
taxify checks the genus register, an index of the genera of every
backbone, and does not send a name to a backbone that holds none of its
genus:
res <- taxify(mixed, backbone = c("wfo", "col"))
#> Matching 8 names against 2 backbones: wfo -> col
#> [wfo] Matching 8 names...
#> [col] Matching 6 remaining names...
res[, c("input_name", "accepted_name", "match_type", "backbone")]
#> input_name accepted_name match_type backbone
#> 1 Quercus robur Quercus robur exact wfo
#> 2 Panthera leo Panthera leo exact col
#> 3 Amanita muscaria Amanita muscaria exact col
#> 4 Salmo trutta Salmo trutta exact col
#> 5 Escherichia coli Escherichia coli exact col
#> 6 Macropus rufus Osphranter rufus exact col
#> 7 Fucus vesiculosus <NA> out_of_scope <NA>
#> 8 Parus caeruleus Cyanistes caeruleus exact col
#> Sources: WFO + COL | cite() for full citationsThe progress lines show the chain: WFO matched Quercus robur, and COL received six of the seven remaining names. A name present in both backbones takes the treatment of the one listed first, including its accepted name, family and synonym resolution. Fuzzy matching runs inside each backbone before the name moves on, so a misspelt plant name is compared with WFO’s names before it reaches COL.
Fucus vesiculosus was not sent to COL, because the register
records that neither WFO nor COL holds its genus; the row has
match_type = "out_of_scope". The register is described in
How names are matched. Adding
AlgaeBase, the backbone for algae, resolves it:
res <- taxify(mixed, backbone = c("wfo", "algaebase", "col"),
verbose = FALSE)
res[res$input_name == "Fucus vesiculosus",
c("input_name", "accepted_name", "match_type", "backbone")]
#> input_name accepted_name match_type backbone
#> 7 Fucus vesiculosus Fucus vesiculosus exact algaebase
#> Sources: ALGAEBASE 2026.09 | cite() for full citationsA row that comes back out_of_scope needs a backbone that
holds its genus. lookup_genus() returns the genus
register’s entry for a genus, and
taxify_register_coverage() lists the backbones that hold
it:
lookup_genus("Fucus")[, c("genus", "kingdom", "family", "life_form")]
#> genus kingdom family life_form
#> 176828 Fucus Chromista Fucaceae brown alga
taxify_register_coverage("Fucus")
#> genus backbone version date_added
#> 1 Fucus worms 2026.09 2026-09-14
#> 2 Fucus sealifebase 2026.08 2026-08-27
#> 3 Fucus ott 2026.09 2026-09-14
#> 4 Fucus ncbi 2026.09 2026-09-14
#> 5 Fucus itis 2026.09 2026-09-14
#> 6 Fucus gbif 2023.08 2026-09-22
#> 7 Fucus colxr 2026.08 2026-09-23
#> 8 Fucus algaebase 2026.09 2026-09-14The COL release used here is not among them, while COL XR, which adds
names from further sources, is. An out_of_scope row
therefore points to a backbone to add to the chain, where
match_type = "none" leaves open whether the name is
misspelt or exists in no backbone.
Backbones can treat the same name differently, and the fallback chain
shows only the first one’s answer. mode = "wide" matches
every name against every backbone in backbone and adds one
accepted_<backbone> column per backbone, plus
all_agree:
names3 <- c("Macropus rufus", "Parus caeruleus", "Quercus robur")
wide <- taxify(names3, backbone = c("col", "gbif", "itis"),
mode = "wide", verbose = FALSE)
wide[, c("input_name", "accepted_col", "accepted_gbif", "accepted_itis",
"all_agree")]
#> input_name accepted_col accepted_gbif accepted_itis
#> 1 Macropus rufus Osphranter rufus Macropus rufus Osphranter rufus
#> 2 Parus caeruleus Cyanistes caeruleus Cyanistes caeruleus Cyanistes caeruleus
#> 3 Quercus robur Quercus robur Quercus robur Quercus robur
#> all_agree
#> 1 FALSE
#> 2 TRUE
#> 3 TRUE
#> Sources: COL + GBIF + ITIS | cite() for full citationsCOL and ITIS place the red kangaroo in Osphranter; the GBIF
Backbone Taxonomy keeps it in Macropus.
accepted_name is still the pick of the fallback chain, here
COL’s, so the result passes to the add_*() functions
unchanged.
mode = "agreement" reports the same comparison as
counts:
agr <- taxify(names3, backbone = c("col", "gbif", "itis"),
mode = "agreement", verbose = FALSE)
agr[, c("input_name", "n_backbones_matched", "n_distinct_accepted",
"all_agree")]
#> input_name n_backbones_matched n_distinct_accepted all_agree
#> 1 Macropus rufus 3 2 FALSE
#> 2 Parus caeruleus 3 1 TRUE
#> 3 Quercus robur 3 1 TRUE
#> Sources: COL + GBIF + ITIS | cite() for full citationsall_agree is NA when fewer than two
backbones matched a name.
The output columns are the same for every backbone. Three functions
add the columns that only one backbone carries, and fill them on the
rows that backbone matched; other rows get NA:
add_wfo_info(): the place of publication, the parent
name and WFO’s higher classification.
add_col_info(): COL’s classification from kingdom to
order, nomenclatural code and status, and whether the species is
extinct, marine, freshwater or terrestrial.
add_gbif_info(): the hybrid type, nomenclatural
status, basionym author and year, and how the name entered the GBIF
backbone.
crab <- taxify(c("Carcinus maenas", "Quercus robur"), backbone = "col",
verbose = FALSE)
crab <- add_col_info(crab)
crab[, c("input_name", "kingdom", "is_marine", "is_terrestrial")]
#> input_name kingdom is_marine is_terrestrial
#> 1 Carcinus maenas Animalia TRUE FALSE
#> 2 Quercus robur Plantae NA NA
#> Sources: COL 2026.09 | cite() for full citationsCOL matched the oak as well but records no habitat for it, so
NA there means not recorded, not unmatched.
The columns hold the same kind of value for every backbone, with these differences:
Identifiers. taxon_id and
accepted_id use each backbone’s own system: WFO IDs, opaque
COL IDs (4R5YN for Quercus robur), GBIF integer
keys, ITIS TSNs, NCBI Taxonomy IDs, WoRMS AphiaIDs.
Authorship. NCBI and OTT record no authors, so
authorship is NA on their rows.
Synonyms. Each source encodes synonyms in its own way.
An ID is meaningful only within its backbone. When a backbone is
built, its synonyms are converted to is_synonym,
accepted_name and accepted_id, and a synonym
that points to another synonym is followed to the accepted name.
The source, licence and citation of each backbone are listed in The backbones and datasets.
Each backbone is downloaded once into taxify_data_dir()
and read from disk after that. install_backbones() and
taxify_download() fetch backbones ahead of time, for a
server or a session without network access. A function that needs a
backbone that is not on disk asks before downloading it in an
interactive session; in a script it stops with an error naming the
install_backbones() call, unless
options(taxify.auto_download = TRUE) or the environment
variable TAXIFY_AUTO_DOWNLOAD allows the download:
The download goes into a latest folder that is replaced
when a newer version is released. taxify compares the local versions
with the published ones once per session, at the first call, and updates
latest then; the version never changes during a session.
The replaced version is deleted. Without network access, or with
options(taxify.offline = TRUE) or the environment variable
TAXIFY_OFFLINE set, it uses the files on disk.
taxify_store() lists the builds on disk with their
sizes. taxify_clean() removes builds taxify no longer reads
and files left by an interrupted download;
taxify_clean("gbif") removes one backbone, and
taxify_clean("all") the whole data directory.
A version string downloads into a folder of its own that is never replaced:
Every row records the backbone version that matched it:
unique(res$backbone_version)
#> [1] "wfo:2026.06 (2026-09-15)" "col:2026.09 (2026-09-14)"
#> [3] "algaebase:2026.09 (2026-09-14)"taxify_lock() writes these versions with a checksum of
each file to a JSON file, and
taxify_restore(install = TRUE) reinstalls the same builds
on another machine, as shown in Get started.
taxify_build() builds a backbone from its source files
instead of downloading it, which needs the taxifydb package.
The first backbone in the vector sets the treatment for most names, and broader backbones after it resolve the rest:
Vascular plants: "wfo", or
c("wfo", "col") for cultivars, names from older floras and
recently moved genera that WFO lacks. The World Checklist of Vascular
Plants ("wcvp") and the Leipzig Catalogue of Vascular
Plants ("lcvp") are alternatives with their own
treatment.
European vegetation data:
c("euromed", "wfo"). Euro+Med PlantBase covers the native
and introduced vascular plants of Europe, the Mediterranean and the
Caucasus, and WFO resolves the names outside it.
Marine and aquatic species:
"worms", the World Register of Marine Species, with
"col" after it for the terrestrial taxa of an estuarine
list.
Fungi: c("fungorum", "col"),
Species Fungorum first.
Algae: c("algaebase", "col").
AlgaeBase is licensed for non-commercial use only (CC BY-NC).
Fishes, reptiles, mammals, birds, prokaryotes:
"fishbase", "reptiledb", "mdd",
"avilist" or "lpsn", each followed by
"col".
Sequence-linked lists (metabarcoding, eDNA):
c("ncbi", "col"). NCBI Taxonomy IDs link to GenBank
records, and NCBI covers bacteria, archaea and viruses.
Phylogenetic work: "ott", the Open
Tree of Life taxonomy, which cross-references NCBI, GBIF, WoRMS and
other sources.
Lists of unknown composition: the default chain,
or c("col", "gbif").
How names are matched: the match stages, the fuzzy threshold and the genus register.
Matching within a region: restricting matches to species present in a region.
Matching large lists: timings and memory for lists of many names.
The backbones and datasets: the source, size and licence of every backbone.