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Databases: every backbone, enrichment, and trait

Source: vignettes/articles/databases.Rmd
databases.Rmd

taxify resolves names against local taxonomic backbones and joins external enrichment datasets that carry traits. This page lists all three, straight from the manifest this version ships. In an R session, the same content is one call away:

taxify_databases()   # backbones + enrichments in one frame
list_backbones()     # the taxonomic backbones
list_enrichments()   # the trait / status datasets
list_traits()        # the cross-source trait vocabulary add_trait() draws on

Taxonomic backbones

Each is a pre-built .vtr downloaded once and matched locally. Pass several to taxify() and they form a fallback chain.

Backbone Scope Names MB Version
wfo Vascular plants 1,638,552 760 2026.06 source
col All kingdoms 5,302,873 1,869 2026.06 source
gbif All kingdoms 6,404,001 1,769 2026.06 source
itis US focus, freshwater/marine 991,868 195 2026.06 source
ncbi All life 2,739,317 487 2026.05 source
ott All life (synthetic) 3,690,217 693 3.7.3 source
worms Marine/aquatic 1,557,860 330 2026.07 source
euromed European/Mediterranean plants 133,426 29 2026.06 source
fungorum Fungi 315,037 68 2026.06 source
algaebase Algae 172,351 35 2026.06 source
fishbase Fishes 102,703 18 2026.06 source
sealifebase Non-fish marine/aquatic 134,031 28 2026.06 source
reptiledb Reptiles 50,043 9 2026.06 source
lcvp Vascular plants 1,337,891 241 3.0.1 source
wcvp Vascular plants 1,448,984 318 2026.06 source

Enrichment datasets

Each add_<source>() door joins one dataset to a taxify() result on the accepted name. add_trait() gathers a single trait across every source that carries it. Browse a dataset’s columns in R with enrichment_cols("<name>").

Enrichment Version Rows Columns
algae_traits 2026.07 2,949 47 source
alien_first_records 2026.07 79,944 20 source
amniote 2026.07 23,332 34 source
amphibio 2026.07 7,799 35 source
anage 2026.07 5,012 29 source
animaltraits 2026.07 2,219 41 source
arctic_traits 2026.07 455 20 source
arthropod_traits 2026.07 5,339 28 source
austraits 2026.07 34,938 530 source
avonet 2026.07 12,443 36 source
bacdive 2026.07 19,889 8 source
baseflor 2026.07 8,469 55 source
bee_ostwald 2026.07 2,052 14 source
bet 2026.07 2,025 97 source
beukhof 2026.07 1,793 37 source
bien 2026.07 117,645 52 source
birdbase 2026.07 13,067 95 source
blanchard 2026.07 333 19 source
brot 2026.07 2,882 44 source
chelonians 2026.07 362 79 source
combine 2026.07 6,791 57 source
common_names 2026.07 704,521 3 source
coral_traits 2026.07 1,813 107 source
diaz_traits 2026.07 52,037 29 source
disperse 2026.07 462 12 source
ecoflora 2026.07 3,077 18 source
edwards_phyto 2026.07 169 33 source
eive 2026.07 16,737 18 source
elton_traits 2026.07 17,556 48 source
eupolltrait 2026.07 3,275 39 source
eurobat 2026.07 52 62 source
fishbase 2026.07 37,805 239 source
fishmorph 2026.07 9,043 15 source
floraweb 2026.07 5,594 59 source
freshwater_insects_conus 2026.07 1,030 14 source
frugivoria 2026.07 1,932 60 source
fungal_traits 2026.07 11,061 24 source
fungalroot 2026.07 4,188 18 source
funguild 2026.07 16,094 9 source
gift 2026.07 279,943 109 source
globi 2026.07 544,015 3 source
globtherm 2026.07 2,366 42 source
glonaf 2026.07 10,071 9 source
griis 2026.07 110,378 15 source
groot 2026.07 7,307 38 source
gwdd 2026.07 18,430 15 source
homerange 2026.07 1,051 35 source
hosts 2010.1 19,090 2 source
huang_amph 2026.07 4,776 85 source
italic 2026.07 3,677 4 source
iucn 2026.07 185,874 1 source
kew_sid 2026.07 50,146 7 source
leda 2026.07 14,191 25 source
leptraits 2026.07 13,590 40 source
madin 2026.07 16,746 76 source
nesttrait 2026.07 12,615 34 source
nztd 2026.07 314 18 source
octocoral 2026.07 3,629 127 source
odonata 2026.07 1,486 36 source
pantheria 2026.07 5,957 53 source
parravicini 2026.07 6,910 34 source
pelagic 2026.07 590 57 source
phylacine 2026.07 6,380 23 source
pottier 2026.07 667 77 source
quimbayo 2026.07 2,293 60 source
ramond 2026.07 1,212 32 source
repttraits 2026.07 12,196 47 source
rimet_phyto 2026.07 1,413 62 source
saproxylic 2026.07 1,266 57 source
sealifebase 2026.07 111,710 250 source
sharkipedia 2026.07 179 52 source
sheld 2026.07 313 105 source
spider_traits 2026.07 9,346 11 source
tetradensity 2026.07 1,915 16 source
thermofresh 2026.07 741 5 source
tree_of_sex 2026.07 39,825 68 source
usda_fungus_host 2021.1 73,546 2 source
useful_plants 2026.07 42,217 11 source
wcvp 2026.07 2,096,648 29 source
zanne 2026.07 53,737 2 source
zooplankton 2026.07 4,216 86 source

Cross-source traits

Name one trait; add_trait() finds and harmonizes it from the sources below.

Trait Label Kind Unit Sources From
activity_time Diel activity time categorical NA 6 repttraits, chelonians, quimbayo, combine, pantheria, spider_traits
age_at_first_reproduction Age at first reproduction numeric yr 1 combine
age_at_maturity Age at female maturity numeric yr 6 anage, amniote, amphibio, chelonians, beukhof, sheld
air_breathing Air breathing (fish) categorical NA 1 fishbase
algal_life_cycle Life-cycle ploidy phase (algae) categorical NA 1 algae_traits
algal_substrate Attachment substrate (algae) categorical NA 1 algae_traits
antenna_length Antenna length numeric mm 1 saproxylic
aspect_ratio Caudal fin aspect ratio numeric index 2 beukhof, quimbayo
beak_depth Beak depth numeric mm 1 avonet
beak_length Beak length (culmen) numeric mm 1 avonet
beak_width Beak width numeric mm 1 avonet
bioluminescence Bioluminescence (zooplankton) categorical NA 1 zooplankton
bioturbation Bioturbation mode (benthic invertebrate) categorical NA 2 arctic_traits, nztd
body_elongation Body elongation (fish) numeric index 1 fishmorph
body_lateral_shape Body lateral shape (fish) numeric index 1 fishmorph
body_length Body length numeric mm 11 combine, amniote, repttraits, amphibio, fishbase, sealifebase, huang_amph, pottier, spider_traits, zooplankton, sheld
body_mass Body mass numeric g 14 combine, amniote, pantheria, elton_traits, avonet, anage, phylacine, repttraits, fishbase, sealifebase, frugivoria, pottier, animaltraits, homerange
body_shape Body shape (fish) categorical NA 3 beukhof, quimbayo, pelagic
brain_mass Brain mass numeric g 2 combine, animaltraits
calcification Calcification (algae) categorical NA 1 algae_traits
carapace_length Carapace length (turtle) numeric mm 1 chelonians
caudal_fin_shape Caudal fin shape (fish) categorical NA 2 beukhof, quimbayo
caudal_peduncle_throttling Caudal peduncle throttling (fish) numeric index 1 fishmorph
cell_biovolume Cell biovolume (microalgae) numeric um3 1 rimet_phyto
cell_length Cell length numeric um 2 rimet_phyto, bacdive
cell_shape Cell shape (prokaryote) categorical NA 2 madin, bacdive
cell_surface_area Cell surface area (microalgae) numeric um2 1 rimet_phyto
cell_thickness Cell thickness (microalgae) numeric um 1 rimet_phyto
cell_width Cell width numeric um 2 rimet_phyto, bacdive
clutch_litter_size Clutch or litter size numeric offspring per clutch/litter 8 amniote, combine, pantheria, anage, repttraits, amphibio, chelonians, birdbase
coloniality Coloniality categorical NA 2 coral_traits, octocoral
colony_diameter Colony maximum diameter (coral) numeric cm 1 coral_traits
colony_growth_form Colony growth form (octocoral) categorical NA 1 octocoral
colour_lightness Body colour lightness (beetle) numeric index 1 saproxylic
conservation_status IUCN Red List status categorical NA 6 conservation_status, birdbase, phylacine, quimbayo, pelagic, pottier
corallite_width Corallite width (coral) numeric mm 1 coral_traits
deciduousness Leaf deciduousness categorical NA 2 gift, austraits
depth_max Maximum depth numeric m 6 fishbase, sealifebase, quimbayo, pelagic, coral_traits, octocoral
depth_min Minimum depth numeric m 6 fishbase, sealifebase, quimbayo, pelagic, coral_traits, octocoral
diel_vertical_migration Diel vertical migration (zooplankton) categorical NA 1 zooplankton
diet_breadth Diet breadth numeric count 3 combine, pantheria, birdbase
diet_guild Diet guild categorical NA 7 avonet, elton_traits, repttraits, chelonians, blanchard, parravicini, zooplankton
dispersal_syndrome Dispersal syndrome categorical NA 5 gift, austraits, leda, baseflor, brot
egg_length Egg length numeric mm 3 amniote, repttraits, chelonians
egg_mass Egg mass numeric g 1 amniote
egg_width Egg width numeric mm 3 amniote, repttraits, chelonians
eive_light EIVE light (L) numeric 0-10 (EIVE) 1 eive
eive_moisture EIVE moisture (M) numeric 0-10 (EIVE) 1 eive
eive_nutrients EIVE nutrients (N) numeric 0-10 (EIVE) 1 eive
eive_reaction EIVE reaction (R) numeric 0-10 (EIVE) 1 eive
eive_temperature EIVE temperature (T) numeric 0-10 (EIVE) 1 eive
elevation_max Maximum elevation numeric m 3 birdbase, repttraits, globtherm
elevation_min Minimum elevation numeric m 3 birdbase, repttraits, globtherm
ellenberg_light Ellenberg light (L) numeric 1-9 (classic) 3 floraweb, ecoflora, bet
ellenberg_moisture Ellenberg moisture (F) numeric 1-12 (classic) 3 floraweb, ecoflora, bet
ellenberg_nitrogen Ellenberg nutrients / nitrogen (N) numeric 1-9 (classic) 3 floraweb, ecoflora, bet
ellenberg_reaction Ellenberg reaction (R) numeric 1-9 (classic) 3 floraweb, ecoflora, bet
ellenberg_salt Ellenberg salt (S) numeric 0-9 (classic) 3 floraweb, ecoflora, baseflor
ellenberg_temperature Ellenberg temperature (T) numeric 1-9 (classic) 2 floraweb, bet
elytra_length Elytra length numeric mm 1 saproxylic
feeding_guild Feeding guild (benthic invertebrate) categorical NA 2 arctic_traits, nztd
feeding_mode Feeding mode (fish) categorical NA 1 beukhof
flight_mode Flight mode (odonate) categorical NA 1 odonata
flightless Flightlessness (bird) categorical NA 1 birdbase
flower_colour Flower colour categorical NA 3 gift, baseflor, bien
flowering_end Flowering end (month) numeric month (1-12) 2 baseflor, ecoflora
flowering_start Flowering start (month) numeric month (1-12) 2 baseflor, ecoflora
foraging_mode Foraging mode categorical NA 2 repttraits, chelonians
forelimb_length Forelimb length numeric mm 1 huang_amph
freshwater Freshwater habitat categorical NA 3 sealifebase, combine, phylacine
fruit_type Fruit type categorical NA 3 gift, baseflor, austraits
fungal_trophic_mode Fungal trophic mode categorical NA 2 funguild, fungal_traits
gamete_type Gamete type (algae) categorical NA 1 algae_traits
gc_content Genome GC content (prokaryote) numeric % 1 madin
generation_length Generation length numeric yr 3 bet, frugivoria, combine
genome_size Genome size (prokaryote) numeric bp 1 madin
gestation_incubation Gestation or incubation length numeric days 4 anage, combine, pantheria, amniote
gram_stain Gram stain (prokaryote) categorical NA 2 madin, bacdive
growth_form Growth form categorical NA 4 gift, austraits, bien, brot
habitat_breadth Habitat breadth numeric count 4 birdbase, combine, frugivoria, pantheria
hand_wing_index Hand-wing index numeric index 1 avonet
head_length Head length numeric mm 2 huang_amph, saproxylic
head_width Head width numeric mm 2 huang_amph, saproxylic
hindlimb_length Hindlimb length numeric mm 1 huang_amph
home_range Home range numeric km2 3 combine, homerange, pantheria
hunting_guild Hunting guild (spider) categorical NA 1 spider_traits
incubation_period Egg incubation period numeric days 2 amniote, chelonians
interbirth_interval Interbirth or inter-litter interval numeric yr 4 pantheria, combine, amniote, anage
itd Inter-tegular distance (bee body size) numeric mm 2 bee_ostwald, eupolltrait
kipps_distance Kipp’s distance numeric mm 1 avonet
larval_nutrition Larval nutrition (bee) categorical NA 1 eupolltrait
ldmc Leaf dry matter content numeric mg/g 4 leda, gift, brot, diaz_traits
leaf_area Leaf area numeric mm2 3 austraits, bien, brot
leaf_length Leaf length numeric mm 1 austraits
leaf_lifespan Leaf lifespan numeric months 3 austraits, brot, bien
leaf_n Leaf nitrogen per dry mass numeric mg/g 2 austraits, bien
leaf_p Leaf phosphorus per dry mass numeric mg/g 2 austraits, bien
leaf_thickness Leaf thickness numeric mm 2 bien, gift
leaf_type Leaf type categorical NA 2 austraits, diaz_traits
leaf_width Leaf width numeric mm 1 austraits
lecty Pollen host breadth (bee lecty) categorical NA 1 eupolltrait
lichen_growth_form Lichen growth form (thallus) categorical NA 1 italic
life_form Raunkiaer life form categorical NA 3 gift, ecoflora, floraweb
life_history Life history categorical NA 2 gift, austraits
living_habit Living habit (benthic invertebrate) categorical NA 2 arctic_traits, nztd
longevity Maximum longevity numeric yr 9 anage, amniote, combine, pantheria, repttraits, chelonians, amphibio, beukhof, sheld
male_maturity Age at male maturity numeric yr 3 anage, amniote, combine
marine Marine habitat categorical NA 3 sealifebase, combine, phylacine
mate_guarding Mate guarding (odonate) categorical NA 1 odonata
metabolic_rate Metabolic rate numeric W 2 anage, animaltraits
migration Migratory behaviour (bird) categorical NA 1 avonet
motility Motility (prokaryote) categorical NA 2 madin, bacdive
mouth_position Mouth position (fish) categorical NA 1 quimbayo
mycorrhizal_type Mycorrhizal type categorical NA 1 fungalroot
neonate_mass Neonate body mass numeric g 4 amniote, combine, pantheria, anage
nest_attachment Nest attachment (birds) categorical NA 1 nesttrait
nest_site Nest site (birds) categorical NA 1 nesttrait
nest_structure Nest structure (birds) categorical NA 1 nesttrait
nesting_strategy Nesting strategy (bee) categorical NA 1 eupolltrait
optimal_growth_ph Optimal growth pH (prokaryote) numeric pH 2 madin, bacdive
optimal_growth_temperature Optimal growth temperature (prokaryote) numeric deg C 2 madin, bacdive
oral_gape_position Oral gape position (fish) numeric index 1 fishmorph
oxygen_metabolism Oxygen metabolism (prokaryote) categorical NA 2 madin, bacdive
parental_care Parental care (fish) categorical NA 1 beukhof
pectoral_fin_position Pectoral fin position (fish) numeric index 1 fishmorph
pectoral_fin_size Pectoral fin size (fish) numeric index 1 fishmorph
photobiont Lichen photobiont categorical NA 1 italic
photosynthetic_pathway Photosynthetic pathway categorical NA 3 gift, austraits, ecoflora
plant_height Plant height numeric m 5 gift, diaz, austraits, bien, brot
plant_lifespan Whole-plant lifespan numeric yr 3 bien, gift, austraits
pollination_vector Pollination vector categorical NA 4 baseflor, ecoflora, floraweb, austraits
population_density Population density numeric individuals/km2 3 pantheria, combine, tetradensity
pronotum_length Pronotum length numeric mm 1 saproxylic
range_size Geographic range size numeric km2 3 avonet, chelonians, coral_traits
relative_eye_size Relative eye size (fish) numeric index 1 fishmorph
relative_maxillary_length Relative maxillary length (fish) numeric index 1 fishmorph
reproductive_frequency Litters or clutches per year numeric per year 6 amniote, combine, anage, pantheria, repttraits, chelonians
reproductive_mode Reproductive (parity) mode categorical NA 2 repttraits, sharkipedia
reproductive_strategy Reproductive strategy (sexual / asexual) categorical NA 1 italic
root_diameter Root diameter numeric mm 2 groot, austraits
root_dry_matter_content Root dry matter content numeric g/g 2 groot, austraits
root_mass_fraction Root mass fraction numeric g/g 2 groot, austraits
root_mycorrhizal_colonization Root mycorrhizal colonization numeric percent 1 groot
root_n_concentration Root nitrogen concentration numeric mg/g 2 groot, austraits
root_tissue_density Root tissue density numeric g/cm3 1 groot
rooting_depth Rooting depth numeric m 2 groot, brot
secondary1 First-secondary length numeric mm 1 avonet
seed_length Seed length numeric mm 4 austraits, leda, gift, bien
seed_mass Seed mass numeric mg 7 diaz, gift, austraits, bien, brot, ecoflora, kew_sid
sexual_system Sexual system categorical NA 4 tree_of_sex, coral_traits, octocoral, sheld
skeletal_rigidity Skeletal rigidity (octocoral) categorical NA 1 octocoral
sla Specific leaf area numeric mm2/mg 4 leda, gift, bien, brot
sociality Sociality (bee) categorical NA 1 eupolltrait
specific_root_area Specific root area numeric cm2/g 1 groot
specific_root_length Specific root length numeric m/g 2 groot, austraits
sporulation Sporulation (prokaryote) categorical NA 1 madin
substrate Substrate categorical NA 1 italic
tail_length Tail length numeric mm 1 avonet
tarsus_length Tarsus length numeric mm 1 avonet
teat_number Teat or nipple number numeric count 2 pantheria, combine
territoriality Territoriality (odonate) categorical NA 1 odonata
thermal_max Upper thermal limit numeric deg C 2 globtherm, pottier
thermal_min Lower thermal limit numeric deg C 1 globtherm
tongue_length Tongue length (bee) numeric mm 2 bee_ostwald, eupolltrait
trophic_level Trophic level numeric trophic level (~1-5) 6 fishbase, beukhof, quimbayo, pelagic, arctic_traits, sealifebase
venomous Venomous (reptile) categorical NA 1 repttraits
vertical_eye_position Vertical eye position (fish) numeric index 1 fishmorph
voltinism Voltinism (generations per year) numeric per year 2 arthropod_traits, eupolltrait
von_bertalanffy_k Von Bertalanffy growth coefficient (K) numeric per yr 2 beukhof, sharkipedia
von_bertalanffy_linf Von Bertalanffy asymptotic length (Linf) numeric cm 2 beukhof, sharkipedia
vulnerability Vulnerability to fishing numeric 0-100 index 3 fishbase, sealifebase, quimbayo
water_clarity Water clarity preference categorical NA 2 coral_traits, octocoral
wave_exposure Wave exposure preference categorical NA 2 coral_traits, octocoral
weaning_age Weaning age numeric days 3 amniote, anage, pantheria
web_building Web building (spider) categorical NA 1 spider_traits
wing_length Wing length numeric mm 2 avonet, saproxylic
wingspan Wingspan (butterfly) numeric mm 1 leptraits
wood_density Wood density numeric g/cm3 5 gwdd, austraits, bien, gift, leda
woodiness Woodiness categorical NA 4 zanne, gift, austraits, bien
zooxanthellate Zooxanthellate symbiosis (coral) categorical NA 2 coral_traits, octocoral