Using the APD: exploring and extracting trait definitions and metadata

Author

Elizabeth Wenk

The AusTraits Plant Dictionary (APD) is a published vocabulary, documenting explicit definitions for more than 500 plant trait concepts. The full dictionary is available at https://w3id.org/APD/, and each trait (and trait groupings) has its own URI.

To faciliate use of this formal vocabulary by researchers, the content is also output as a pairs of tables, APD_traits.csv and APD_categorical_values, which can be downloaded from github.com/traitecoevo/APD/tree/master/docs or Zenodo at DOI: 10.5281/zenodo.8040789.

The examples below indicate how the definitions and metadata for specific traits or trait clusters can be extracted from these files, allowing searches for traits by trait name, trait cluster, characteristic measured, reference, previously used trait labels, or matches to identical or similar trait concepts in other vocabularies or databases.

library(tidyverse)
library(stringr)
library(kableExtra)

# Todo: update links after branch merged in
APD_traits <- read_csv("https://raw.githubusercontent.com/traitecoevo/APD/master/APD_traits.csv", show_col_types = FALSE)
APD_categorical_values <- read_csv("https://raw.githubusercontent.com/traitecoevo/APD/master/APD_categorical_values.csv", show_col_types = FALSE)

Metadata fields (annotation properties) documented for each trait include:

names(APD_traits)

field
Entity
trait
label
description
comments
trait_type
allowed_values_min
allowed_values_max
units
constraints
trait_groupings
structure_measured
characteristic_measured
keywords
references
reviewers
created
modified
exact_match
close_match
related_match
examples
description_encoded
deprecated_trait_name
identifier
inScheme

Extracting terms based on specific fields

The following examples show how to extract terms based on specific fields in the APD.

Structure measured

To determine the possible values for structure_measured:

structure_measured <- 
  APD_traits %>%
  dplyr::select(structure_measured) %>%
  dplyr::mutate(structure_measured = (stringr::str_split(structure_measured, "; "))) %>%
  tidyr::unnest_longer("structure_measured") %>%
  dplyr::distinct()

structure_measured
leaf [PO_0025034]
stem [PO_0009047]
wood, secondary xylem [PO_0005848]
bark [PO_0004518]
root [PO_0009005]
reproductive shoot system [PO_0025082]
flower [PO_0009046]
fruit [PO_0009001]
seed [PO_0009010]
whole plant [PO_0000003]
bud [PO_0000055]
inflorescence [PO_0009049]

You can then select the subset of traits that relate to a specific structure.

For instance, to extract traits relating to seeds:

seed_traits <- 
  APD_traits %>%
  dplyr::filter(stringr::str_detect(structure_measured, "seed"))

The first 10 traits on this list are:

trait	label	structure_measured
seed_Ca_per_seed_dry_mass	Seed calcium (Ca) content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
seed_K_per_seed_dry_mass	Seed potassium (K) content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
seed_Mg_per_seed_dry_mass	Seed magnesium (Mg) content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
seed_N_per_seed_dry_mass	Seed nitrogen (N) content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
seed_P_per_seed_dry_mass	Seed phosphorus (P) content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
seed_S_per_seed_dry_mass	Seed sulphur (S) content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
seed_protein_per_seed_dry_mass	Seed protein content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
seed_oil_per_seed_dry_mass	Seed oil content per unit seed dry mass	reproductive shoot system [PO_0025082]; seed [PO_0009010]
accessory_cost_fraction	Seed accessory cost fraction	reproductive shoot system [PO_0025082]; flower [PO_0009046]; fruit [PO_0009001]; seed [PO_0009010]
accessory_cost_mass	Seed accessory cost mass	reproductive shoot system [PO_0025082]; flower [PO_0009046]; fruit [PO_0009001]; seed [PO_0009010]

Trait groupings

To extract all traits within one of the defined trait groupings.

First, generate a list of trait_grouping terms:

trait_groupings <- 
  APD_traits %>%
  dplyr::select(trait_groupings) %>%
  dplyr::mutate(trait_groupings = (stringr::str_split(trait_groupings, "; "))) %>%
  tidyr::unnest_longer("trait_groupings") %>%
  dplyr::distinct()

Items 20:29 on this list are:

trait_groupings
whole plant phenotype trait [trait_group_0030006]
plant structure morphology trait [trait_group_0011001]
plant embryo morphology trait [trait_group_0010104]
leaf morphology trait [trait_group_0011202]
leaf size trait [trait_group_0011204]
leaf mass trait [trait_group_0011206]
leaf position trait [trait_group_0011402]
portion of plant tissue morphology trait [trait_group_0011502]
plant cell morphology trait [trait_group_0011503]
leaf stomatal complex morphology trait [trait_group_0011602]

Filter the APD for leaf stomatal complex morphology traits:

stomatal_traits <- 
  APD_traits %>%
  dplyr::filter(stringr::str_detect(trait_groupings, "leaf stomatal complex morphology trait"))

trait	label	trait_groupings
leaf_stomatal_density_abaxial	Stomatal density on the lower leaf surface	leaf stomatal complex morphology trait [trait_group_0011602]
leaf_stomatal_density_adaxial	Stomatal density on the upper leaf surface	leaf stomatal complex morphology trait [trait_group_0011602]
leaf_stomatal_density_average	Stomatal density averaged across both leaf surfaces	leaf stomatal complex morphology trait [trait_group_0011602]
leaf_stomatal_distribution	Stomatal distribution	leaf stomatal complex morphology trait [trait_group_0011602]
leaf_stomatal_hairs	Stomatal hairiness	leaf stomatal complex morphology trait [trait_group_0011602]
leaf_guard_cell_length	Guard cell length	leaf stomatal complex morphology trait [trait_group_0011602]

Characteristic measured

The term characteristic_measured documents “what” is being measured - a mass, length, etc.

Multiple terms may be used, for instance to indicate a trait captures volume and is a ratio:

volume_ratio_traits <- 
  APD_traits %>%
  select(trait, label, characteristic_measured) %>%
  filter(
    str_detect(characteristic_measured, "volume") &
    str_detect(characteristic_measured, "ratio") 
    )

trait	label	characteristic_measured
wood_density	Wood density	mass [PATO_0000125]; volume density [PATO_0001353]; ratio; proportion [PATO_0001470]; mass density, density [PATO_0001019]
stem_density	Herbaceous stem density	mass [PATO_0000125]; volume density [PATO_0001353]; ratio; proportion [PATO_0001470]; mass density, density [PATO_0001019]
bark_density	Bark density	mass [PATO_0000125]; volume density [PATO_0001353]; ratio; proportion [PATO_0001470]; mass density, density [PATO_0001019]
root_fine_root_coarse_root_ratio	Fine root volume to coarse root volume ratio	volume [PATO_0000918]; ratio; proportion [PATO_0001470]
root_wood_density	Root wood density	mass [PATO_0000125]; volume density [PATO_0001353]; ratio; proportion [PATO_0001470]; mass density, density [PATO_0001019]
bulk_modulus_of_elasticity	Bulk modulus of elasticity (e)	pressure [PATO_0001025]; force [PATO_0001035]; volume [PATO_0000918]; ratio; proportion [PATO_0001470]; model parameter [STATO_0000034]
fire_fuel_bed_bulk_density	Fuel bed bulk density	mass [PATO_0000125]; mass fraction [ECSO_00000619]; ratio; proportion [PATO_0001470]; volume density [PATO_0001353]; mass density, density [PATO_0001019]

Or all terms that measure a force:

force_traits <-
  APD_traits %>%
  select(trait, label, characteristic_measured) %>%
  filter(
    str_detect(characteristic_measured, "force") 
    )

trait	label	characteristic_measured
leaf_work_to_punch	Leaf work to punch	work [PATO_0001026]; force [PATO_0001035]
leaf_work_to_punch_adjusted	Leaf specific work to punch	work [PATO_0001026]; force [PATO_0001035]; ratio; proportion [PATO_0001470]; thickness [PATO_0000915]
leaf_work_to_shear	Leaf work to shear	work [PATO_0001026]; force [PATO_0001035]
leaf_work_to_shear_adjusted	Leaf specific work to shear (fracture toughness)	work [PATO_0001026]; force [PATO_0001035]; ratio; proportion [PATO_0001470]; thickness [PATO_0000915]
leaf_work_to_tear	Leaf work to tear	work [PATO_0001026]; force [PATO_0001035]
leaf_work_to_tear_adjusted	Leaf specific work to tear	work [PATO_0001026]; force [PATO_0001035]; ratio; proportion [PATO_0001470]; thickness [PATO_0000915]
bark_modulus_of_elasticity	Bark modulus of elasticity	work [PATO_0001026]; force [PATO_0001035]
stem_modulus_of_elasticity	Stem modulus of elasticity	work [PATO_0001026]; force [PATO_0001035]
xylem_modulus_of_elasticity	Xylem modulus of elasticity	work [PATO_0001026]; force [PATO_0001035]
modulus_of_rupture	Modulus of rupture	pressure [PATO_0001025]; force [PATO_0001035]; strength [PATO_0001230]
sapwood_specific_hydraulic_conductivity	Sapwood specific hydraulic conductivity (Ks)	conductivity [PATO_0001585]; per unit length [EnvThes:22004]; ratio; proportion [PATO_0001470]; rate [PATO_0000161]; force [PATO_0001035]; efficiency [PATO_0001029]
sapwood_specific_hydraulic_conductivity_theoretical	Theoretical sapwood specific hydraulic conductivity (Ks)	conductivity [PATO_0001585]; per unit area [EnvThes:22003]; ratio; proportion [PATO_0001470]; rate [PATO_0000161]; force [PATO_0001035]; efficiency [PATO_0001029]
stem_specific_hydraulic_conductivity	Stem specific hydraulic conductivity (Ks)	conductivity [PATO_0001585]; per unit length [EnvThes:22004]; ratio; proportion [PATO_0001470]; rate [PATO_0000161]; force [PATO_0001035]; efficiency [PATO_0001029]
leaf_specific_hydraulic_conductance	Leaf specific hydraulic conductance (kleaf)	conductivity [PATO_0001585]; per unit area [EnvThes:22003]; ratio; proportion [PATO_0001470]; rate [PATO_0000161]; force [PATO_0001035]; efficiency [PATO_0001029]
leaf_specific_hydraulic_conductivity	Leaf specific hydraulic conductivity (Kl)	conductivity [PATO_0001585]; per unit area [EnvThes:22003]; ratio; proportion [PATO_0001470]; rate [PATO_0000161]; force [PATO_0001035]; efficiency [PATO_0001029]
root_specific_hydraulic_conductivity	Root specific hydraulic conductivity	conductivity [PATO_0001585]; per unit length [EnvThes:22004]; ratio; proportion [PATO_0001470]; rate [PATO_0000161]; force [PATO_0001035]; efficiency [PATO_0001029]
water_potential_predawn	Pre-dawn water potential	tension [PATO_0002284]; force [PATO_0001035]
water_potential_midday	Midday water potential	tension [PATO_0002284]; force [PATO_0001035]
leaf_hydraulic_vulnerability	Leaf xylem pressure, 50% lost conductance (P50)	tension [PATO_0002284]; force [PATO_0001035]
water_potential_12percent_lost_conductivity	Stem xylem pressure, 12% lost conductivity (P12)	tension [PATO_0002284]; force [PATO_0001035]
water_potential_50percent_lost_conductivity	Stem xylem pressure, 50% lost conductivity (P50)	tension [PATO_0002284]; force [PATO_0001035]
water_potential_88percent_lost_conductivity	Stem xylem pressure, 88% lost conductivity (P88)	tension [PATO_0002284]; force [PATO_0001035]
hydraulic_safety_margin_50	Hydraulic safety margin, 50%	tension [PATO_0002284]; force [PATO_0001035]
hydraulic_safety_margin_88	Hydraulic safety margin, 88%	tension [PATO_0002284]; force [PATO_0001035]
leaf_turgor_loss_point	Leaf turgor loss point	tension [PATO_0002284]; force [PATO_0001035]; model parameter [STATO_0000034]
osmotic_potential	Osmotic potential	pressure [PATO_0001025]; force [PATO_0001035]
osmotic_potential_at_full_turgor	Osmotic potential at full tugor	pressure [PATO_0001025]; force [PATO_0001035]; model parameter [STATO_0000034]
bulk_modulus_of_elasticity	Bulk modulus of elasticity (e)	pressure [PATO_0001025]; force [PATO_0001035]; volume [PATO_0000918]; ratio; proportion [PATO_0001470]; model parameter [STATO_0000034]
root_water_potential_50percent_lost_conductivity	Root xylem pressure, 50% lost conductivity (P50)	tension [PATO_0002284]; force [PATO_0001035]
root_water_potential_12percent_lost_conductivity	Root xylem pressure, 12% lost conductivity (P12)	tension [PATO_0002284]; force [PATO_0001035]
root_water_potential_88percent_lost_conductivity	Root xylem pressure, 88% lost conductivity (P88)	tension [PATO_0002284]; force [PATO_0001035]
leaf_water_potential_12percent_lost_conductivity	Leaf xylem pressure, 12% lost conductance (P12)	tension [PATO_0002284]; force [PATO_0001035]
leaf_water_potential_88percent_lost_conductivity	Leaf xylem pressure, 88% lost conductance (P88)	tension [PATO_0002284]; force [PATO_0001035]

Categorical values

The allowed values for categorical traits are output in the second table, APD_categorical_values.

You can first extract all metadata fields for the trait from APD_traits, then merge in the allowed categorical trait values. Researchers might use this information either when merging together disparate datasets or databases, or to acquire a list of trait values to use when scoring study plants.

For life_history:

life_history_values <-
  APD_categorical_values %>%
    filter(trait == "life_history") %>%
    select(-trait, -categorical_trait_identifier, -categorical_trait_synonyms) %>%
    mutate(
      term = "allowed_values_levels",
      value = paste0(allowed_values_levels, ": ", categorical_trait_description)
      ) %>%
    select(term, value)

life_history <- 
  APD_traits %>% 
    filter(trait == "life_history") %>%
    mutate(across(c(1:ncol(APD_traits)), ~ as.character(.x))) %>%
    pivot_longer(cols = 1:ncol(APD_traits)) %>%
    rename(term = name) %>%
    bind_rows(life_history_values) %>%
    filter(!is.na(value))

term	value
Entity	https://w3id.org/APD/traits/trait_0030012
trait	life_history
label	Life history
description	Categorical description of the duration of a plant’s lifespan, from germination to death.
comments	Studies will differ in the subset of terms they use to describe a plant’s life history, such that some researchers will distinguish between ephemeral and annual species, and other researchers will group these life history categories together under `annual`. In addition, only a subset of studies will use the term `short-lived perennial`; the majority will score all perennial plants as `perennial`. Rangeland studies and post-fire studies are those most likely to score species as `ephemeral` or `short-lived perennial`, as these are environments where perennial species’ lifespans are often divided into those that are short-lived due to environmental conditions and those that are able to persist through the environmentally unfavourable period.
trait_type	categorical variable [STATO_0000252]
constraints	none
trait_groupings	whole plant phenotype trait [trait_group_0030006]
structure_measured	whole plant [PO_0000003]
characteristic_measured	organismal quality [PATO_0001995]; duration [PATO_0001309]; time [PATO_0000165]
keywords	death [GO_0016265]; longevity [NCIT_C153298]
references	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; LEDA Data Standards 2005 [https://uol.de/en/landeco/research/leda/standards]
reviewers	Elizabeth Wenk [https://orcid.org/0000-0001-5640-5910]; Hervé Sauquet [https://orcid.org/0000-0001-8305-3236]; Russell Barrett [https://orcid.org/0000-0003-0360-8321]; Ian J. Wright [https://orcid.org/0000-0001-8338-9143]; Peter Vesk [https://orcid.org/0000-0003-2008-7062]; Gregory J. Jordan [https://orcid.org/0000-0002-6033-2766]; Andy Leigh [https://orcid.org/0000-0003-3568-2606]; Patricia Lu-Irving [https://orcid.org/0000-0003-1116-9402]; Lily Dun [https://orcid.org/0000-0002-0712-5143]; David Coleman [https://orcid.org/0000-0002-1773-6597]
created	14/07/2021
modified	05/02/2024
exact_match	life cycle habit [http://purl.obolibrary.org/obo/TO_0002725]
examples	exact match: Plant lifespan (longevity) [TRY:59] (https://www.try-db.org/de/de.php); exact match: lifecycle [GIFT:2.1.1] (https://gift.uni-goettingen.de); related match: Growth form [BROT:1] (http://doi.org/10.1038/sdata.2018.135) (http://doi.org/10.1038/sdata.2018.135); close match: plant lifespan and age of first flowering [LEDA:1.3] (https://uol.de/en/landeco/research/leda/standards)
description_encoded	Categorical description of the duration [PATO:0001309] of a plant’s lifespan (longevity [NCIT:C153298]), from seed germination [GO:0009845] to death [GO:0016265].
identifier	trait_0030012
inScheme	https://w3id.org/APD
allowed_values_levels	ephemeral: A very short-lived plant, generally with a lifespan of only a few months and the exact length of lifespan quite variable and determined by environmental conditions.
allowed_values_levels	annual: A plant that lives for up to one year after germinating, completing its life cycle in a single growing season.
allowed_values_levels	biennial: A plant that lives for up to two years after germinating, requiring two growing seasons to complete its life cycle and dying following the second growing season.
allowed_values_levels	perennial: A plant that lives for three or more growing seasons, with an exact lifespan that is indeterminate.
allowed_values_levels	short_lived_perennial: A perennial whose lifespan is less than approximately five years, with the exact lifespan generally dependent on environmental conditions.

Matches to other databases and vocabularies

Informal matches to traits included in databases and unpublished dictionaries are mapped in as examples, while matches to published vocabularies and ontologies and mapped using the formal terms, exact_match, close_match, and related_match`

To identify all traits that are also in the TRY trait database:

matches_to_TRY <- 
  APD_traits %>%
  select(trait, examples) %>%
  filter(!is.na(examples)) %>%
  mutate(examples = stringr::str_split(examples, "; ")) %>%
  unnest_longer(examples) %>%
  filter(stringr::str_detect(examples, "\\[TRY"))

The first 20 of many trait matches:

trait	examples
leaf_Al_per_dry_mass	exact match: Leaf aluminium (Al) content per leaf dry mass [TRY:249] (https://www.try-db.org/de/de.php)
leaf_B_per_dry_mass	exact match: Leaf boron (B) content per leaf dry mass [TRY:250] (https://www.try-db.org/de/de.php)
leaf_C_per_dry_mass	exact match: Leaf carbon (C) content per leaf dry mass [TRY:13] (https://www.try-db.org/de/de.php)
leaf_Ca_per_dry_mass	exact match: Leaf calcium (Ca) content per leaf dry mass [TRY:252] (https://www.try-db.org/de/de.php)
leaf_Cl_per_dry_mass	exact match: Leaf chlorine (Cl) content per leaf dry mass [TRY:539] (https://www.try-db.org/de/de.php)
leaf_Cr_per_dry_mass	exact match: Leaf chromium (Cr) content per leaf dry mass [TRY:254] (https://www.try-db.org/de/de.php)
leaf_Co_per_dry_mass	exact match: Leaf cobalt (Co) content per leaf dry mass [TRY:253] (https://www.try-db.org/de/de.php)
leaf_Cu_per_dry_mass	exact match: Leaf copper (Cu) content per leaf dry mass [TRY:255] (https://www.try-db.org/de/de.php)
leaf_Fe_per_dry_mass	exact match: Leaf iron (Fe) content per leaf dry mass [TRY:256] (https://www.try-db.org/de/de.php)
leaf_K_per_area	exact match: Leaf potassium (K) content per leaf area [TRY:52] (https://www.try-db.org/de/de.php)
leaf_K_per_dry_mass	exact match: Leaf potassium (K) content per leaf dry mass [TRY:44] (https://www.try-db.org/de/de.php)
leaf_Mg_per_dry_mass	exact match: Leaf magnesium (Mg) content per leaf dry mass [TRY:257] (https://www.try-db.org/de/de.php)
leaf_Mn_per_dry_mass	exact match: Leaf manganese (Mn) content per leaf dry mass [TRY:258] (https://www.try-db.org/de/de.php)
leaf_Mo_per_dry_mass	exact match: Leaf molybdenum (Mo) content per leaf dry mass [TRY:259] (https://www.try-db.org/de/de.php)
leaf_N_per_area	exact match: Leaf nitrogen (N) content per leaf area [TRY:50] (https://www.try-db.org/de/de.php)
leaf_N_per_dry_mass	exact match: Leaf nitrogen (N) content per leaf dry mass [TRY:14] (https://www.try-db.org/de/de.php)
leaf_Na_per_dry_mass	exact match: Leaf sodium (Na) content per leaf dry mass [TRY:260] (https://www.try-db.org/de/de.php)
leaf_Ni_per_dry_mass	exact match: Leaf nickel (Ni) content per leaf dry mass [TRY:261] (https://www.try-db.org/de/de.php)
leaf_P_per_area	exact match: Leaf phosphorus (P) content per leaf area [TRY:51] (https://www.try-db.org/de/de.php)
leaf_P_per_dry_mass	exact match: Leaf phosphorus (P) content per leaf dry mass [TRY:15] (https://www.try-db.org/de/de.php)

To obtain matches to other informally published trait matches in dictionary and ontologies, use the following patterns with str_detect:

Vocabulary / Database	string to match to
TRY Plant Trait Database	\\[TRY
TOP Thesaurus	\\[TOP
BIEN	\\[BIEN
GIFT	\\[GIFT
LEDA	\\[LEDA
BROT Database	\\[BROT
Palm Traits Database	\\[Palm

Slightly different code is required to extract lists of formally published trait definitions for which there are matches:

matches_to_WoodyPlants <- 
  APD_traits %>%
  select(trait, exact_match, close_match, related_match) %>%
  pivot_longer(cols = 2:4) %>%
  filter(!is.na(value)) %>%
  mutate(value = stringr::str_split(value, "; ")) %>%
  unnest_longer(value) %>%
  filter(stringr::str_detect(value, "CO_357"))

The first 20 matches to the Woody Plants Ontology are:

trait	name	value
leaf_C_per_dry_mass	exact_match	Leaf carbon content [https://cropontology.org/rdf/CO_357:0000086]
leaf_N_per_area	exact_match	Leaf nitrogen content [https://cropontology.org/rdf/CO_357:0000159]
leaf_N_per_dry_mass	exact_match	Leaf nitrogen content [https://cropontology.org/rdf/CO_357:0000159]
leaf_CN_ratio	exact_match	Ratio leaf nitrogen to leaf carbon [https://cropontology.org/rdf/CO_357:0000287]
leaf_CN_ratio	exact_match	C/N [https://cropontology.org/rdf/CO_357:0000512]
leaf_soluble_protein_per_area	exact_match	Leaf soluble protein content [https://cropontology.org/rdf/CO_357:0000281]
leaf_chlorophyll_per_area	exact_match	Leaf chlorophyll content [https://cropontology.org/rdf/CO_357:0000249]
leaf_chlorophyll_per_dry_mass	exact_match	Leaf chlorophyll content [https://cropontology.org/rdf/CO_357:0000250]
leaf_chlorophyll_A_per_area	close_match	Chlorophyll a [https://cropontology.org/rdf/CO_357:0000514]
leaf_chlorophyll_A_per_dry_mass	exact_match	Chlorophyll a [https://cropontology.org/rdf/CO_357:0000514]
leaf_chlorophyll_B_per_area	close_match	Chlorophyll b [https://cropontology.org/rdf/CO_357:0000515]
leaf_chlorophyll_B_per_dry_mass	exact_match	Chlorophyll b [https://cropontology.org/rdf/CO_357:0000515]
leaf_chlorophyll_A_B_ratio	exact_match	Chlorophyll a to b ratio [https://cropontology.org/rdf/CO_357:0000516]
leaf_rubisco_per_leaf_dry_mass	exact_match	Leaf rubisco content [https://cropontology.org/rdf/CO_357:0000273]
leaf_delta13C	exact_match	Delta C13 [https://cropontology.org/rdf/CO_357:0000085]
wood_delta13C	exact_match	Wood Carbon content [https://cropontology.org/rdf/CO_357:0000113]
leaf_delta15N	exact_match	Delta 15N [https://cropontology.org/rdf/CO_357:0000513]
plant_width	close_match	Crown size [https://cropontology.org/rdf/CO_357:0000101]
plant_height	exact_match	Tree height [https://cropontology.org/rdf/CO_357:0000111]
plant_height	exact_match	Tree height [https://cropontology.org/rdf/CO_357:0000048]

To obtain matches to other formally published trait in ontologies, use the following patterns with str_detect:

Vocabulary / Database	string to match to
Woody Plants Ontology	CO_357
Plant Trait Ontology (TO)	obo\\/TO_
Flora Phenotype Ontology (FLOPO)	obo\\/FLOPO_
EnvThes	EnvThes

References

As appropriate, references are listed for each trait concept, under references.

fluorescence <- 
  APD_traits %>%
  select(trait, label, references) %>%
  filter(str_detect(trait, "fluorescence"))

trait	label	references
leaf_fluorescence_fv_over_fm	Leaf maximum quantum yield (Fv/Fm)	Maxwell & Johnson 2000 [https://doi.org/10.1093/jexbot/51.345.659]; Long 1993 [https://doi.org/10.1007/BF00195081]
leaf_fluorescence_quantum_yield	Leaf ambient quantum yield	Maxwell & Johnson 2000 [https://doi.org/10.1093/jexbot/51.345.659]; Long 1993 [https://doi.org/10.1007/BF00195081]

Alternatively, if you know the doi for a reference andyou can search for traits that reference it.

BT12225 <- 
  APD_traits %>%
  select(trait, label, references) %>%
  filter(str_detect(references, "doi.org/10.1071/BT12225"))

The first 15 traits referencing Pérez-Harguindeguy 2013:

trait	label	references
plant_height	Plant vegetative height	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; Falster 2003a [https://doi.org/10.1016/S0169-5347(03)00061-2]
plant_spinescence	Plant spinescence	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_area	Leaf area	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_length	Leaf length	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_thickness	Leaf thickness	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_dry_mass	Leaf dry mass	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_fresh_mass	Leaf fresh mass	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_mass_per_area	Leaf mass per area	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; Wright 2004 [https://doi.org/10.1038/nature02403]
leaf_lamina_mass_per_area	Leaf lamina mass per area	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_fresh_mass_per_area	Leaf fresh mass per leaf area	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]
leaf_type	Leaf type	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; Burrows 2001 [https://doi.org/10.1086/319579]
fruit_dry_mass	Fruit dry mass	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; Kew Seed Information Database 2022 [https://data.kew.org/sid/sidsearch.html]
fruit_length	Fruit length	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; Kew Seed Information Database 2022 [https://data.kew.org/sid/sidsearch.html]
fruit_width	Fruit width	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; Kew Seed Information Database 2022 [https://data.kew.org/sid/sidsearch.html]
fruit_height	Fruit breadth	Pérez-Harguindeguy 2013 [https://doi.org/10.1071/BT12225]; Kew Seed Information Database 2022 [https://data.kew.org/sid/sidsearch.html]

Deprecated trait names

For AusTraits users, if you have used an old version of AusTraits, previous names used for trait concepts are documented under deprecated_trait_name.

You can extract all trait names that have changed, with 10 of them displayed:

deprecated_trait_names <- 
  APD_traits %>%
  select(trait, label, deprecated_trait_name) %>%
  filter(!is.na(deprecated_trait_name))

trait	label	deprecated_trait_name
leaf_chlorophyll_B_per_area	Leaf chlorophyll B content per unit leaf area	chlorophyll_B_per_area
leaf_chlorophyll_B_per_dry_mass	Leaf chlorophyll B content per unit leaf dry mass	chlorophyll_B_per_dry_mass
leaf_chlorophyll_A_B_ratio	Ratio of leaf chlorophyll A content to leaf chlorophyll B content	chlorophyll_A_B_ratio
leaf_rubisco_per_leaf_dry_mass	Leaf rubisco content per unit leaf dry mass	cell_rubisco_concentration
seed_protein_per_seed_dry_mass	Seed protein content per unit seed dry mass	seed_protein_content
seed_oil_per_seed_dry_mass	Seed oil content per unit seed dry mass	seed_oil_content
leaf_ash_per_dry_mass	Leaf ash content per unit leaf dry mass	leaf_ash_content_per_dry_mass
bark_ash_per_dry_mass	Bark ash content per unit bark dry mass	bark_ash_content_per_dry_mass
plant_diameter_breast_height	Stem diameter at breast height	basal_diameter
stem_count	Stem count	stem_count_categorical
plant_spinescence	Plant spinescence	spinescence

Or look up a specific trait name that is no longer used:

deprecated_fire_traits <- 
  APD_traits %>%
  select(trait, label, deprecated_trait_name) %>%
  filter(str_detect(deprecated_trait_name, "fire"))

trait	label	deprecated_trait_name
resprouting_capacity	Post-fire resprouting capacity	fire_response
resprouting_capacity_proportion_individuals	Post-fire proportion resprouting individuals	fire_response_numeric
resprouting_capacity_juvenile	Post-fire resprouting capacity of juvenile plants	fire_response_juvenile
resprouting_capacity_stem_ratio	Post-fire to pre-fire stem ratio	fire_response_stem_ratio
resprouting_capacity_non_fire_disturbance	Plant vegetative response to disturbances other than fire	regeneration_non_fire_disturbance
post_fire_recruitment	Post-fire recruitment	fire_and_establishing
fire_time_from_fire_to_fruiting	Time from fire to fruiting	time_from_fire_to_fruit