Change log for the AusTraits Plant Dictionary (APD) Ontology

APD Version 2.1.0

Add new traits

  • leaf_lipid_P_per_dry_mass
  • leaf_nucleic_acid_P_per_dry_mass
  • leaf_residual_P_per_dry_mass
  • leaf_inorganic_P_per_dry_mass
  • leaf_metabolite_P_per_dry_mass
  • plant_height_climbing_plant
  • plant_height_reproductive
  • stem_length
  • leaflet_count
  • leaflet_length
  • leaflet_width
  • leaf_surface_colour
  • leaf_surface_reflectivity
  • stem_hairs
  • xylem_to_leaf_area_ratio
  • stem_saturated_water_content_per_dry_mass
  • root_vascular_anatomy
  • storage_organ_length
  • storage_organ_diameter
  • inflorescence_length
  • inflorescence_diameter
  • flower_petal_length
  • fruit_surface_hairs
  • seed_colour
  • leaf_vessel_wall_thickness
  • stem_vessel_wall_thickness
  • leaf_vessel_length
  • stem_vessel_length
  • leaf_critical_temperature_minimum
  • leaf_critical_temperature_maximum
  • leaf_maximum_temperature
  • leaf_ice_nucleation_temperature
  • leaf_cuticular_conductance
  • leaf_conductance_surface_water
  • leaf_foliar_water_uptake_rate
  • leaf_chlorophyll_content_SPAD
  • foliage_time

Rename traits The following traits have had edits to their name (to standardise with similar traits for other plant tissues). The previous names are documented under deprecated names

  • stem_water_potential_12percent_lost_conductivity (previously water_potential_12percent_lost_conductivity)
  • stem_water_potential_50percent_lost_conductivity (previously water_potential_50percent_lost_conductivity)
  • stem_water_potential_88percent_lost_conductivity (previously water_potential_88percent_lost_conductivity)
  • leaf_water_potential_50percent_lost_conductivity (previously leaf_hydraulic_vulnerability)

Change allowable ranges, keywords Minor changes to allowable ranges or keywords have been made to the following traits:

  • leaf_N_per_area
  • leaf_N_per_dry_mass
  • leaf_tannin_per_dry_mass
  • leaf_photosynthetic_rate_per_area_maximum
  • leaf_photosynthetic_rate_per_area_saturated
  • leaf_photosynthetic_rate_per_dry_mass_ambient
  • leaf_photosynthetic_rate_per_dry_mass_maximum
  • leaf_photosynthetic_rate_per_dry_mass_saturated
  • leaf_capacitance

Edit units The following traits have had their units edited. These are all traits where the units are in moles, but didn’t specify “moles of what”, making it impossible to convert between mass and molar units.: - leaf_epidermis_Ca_per_fresh_mass - leaf_hypodermis_Ca_per_fresh_mass - leaf_internal_parenchyma_Ca_per_fresh_mass - leaf_palisade_mesophyll_Ca_per_fresh_mass - leaf_sclerenchyma_Ca_per_fresh_mass - leaf_spongy_mesophyll_Ca_per_fresh_mass - leaf_epidermis_P_per_fresh_mass - leaf_hypodermis_P_per_fresh_mass - leaf_internal_parenchyma_P_per_fresh_mass - leaf_palisade_mesophyll_P_per_fresh_mass - leaf_sclerenchyma_P_per_fresh_mass - leaf_spongy_mesophyll_P_per_fresh_mass - leaf_carotenoid_per_area - leaf_carotenoid_per_dry_mass - leaf_chlorophyll_per_area - leaf_chlorophyll_per_dry_mass - leaf_chlorophyll_A_per_area - leaf_chlorophyll_A_per_dry_mass - leaf_chlorophyll_B_per_area - leaf_chlorophyll_B_per_dry_mass - leaf_chlorophyll_A_B_ratio - leaf_photosynthesis_Jmax_per_area - leaf_photosynthesis_Jmax_per_area_25C - leaf_photosynthesis_Jmax_per_mass - leaf_photosynthesis_Vcmax_per_area - leaf_photosynthesis_Vcmax_per_area_25C - leaf_photosynthesis_Vcmax_per_mass

Minor fixes - fix errors in GIFT trait names (had all trait names uppercase, but turns out GIFT names are a mix of uppercase and lowercase)

  • fix errors in TRY trait names

There were 63 instances of TRY names/trait codes that did not match the current list of TRY names/trait codes. 3 of those were instances where APD had a mismatched name-code for a TRY match and the remainder were where TRY had slightly edited their trait names since our previous matches. We have continued to replace “;” with “,” in TRY trait names, because “;” are a delimiter used in APD.

Also found a few additional matches to TRY traits to add. This is not a comprehensive review of additional trait matches that might exist, but simply adding a few that were apparent

APD Version 2.0.0

Structural changes, resulting from peer review:

  • removing all mapping to OWL classes
  • indicating that matches to databases, thesauruses without actually resolvable identifies are examples not skos:exactMatch, etc.
  • adding all SWEET sub-namespaces to namespace declaration
  • in APD_traits_input.csv, collapsing multiple columns (e.g. measured_structure_1, measured_structure_2, etc.) into a single ;-delimited column; this allows an undefined number of values for each field corresponding changes made to R-scripts to build rdf representations, website from the new csv format

Create using_the_APD.qmd

  • creating a document with sample code to explore/use the APD

Minor changes to traits:

  • adding many additional mapping to Plant Trait Ontology, Crop Ontology, FLOPO, EnvThes
  • adding 3 new traits (bud_length, bud_width, buds_per_inflorescence)
  • edits to plant_growth form and woodiness, based on review of Complete Traits manuscript
  • incorporate suggested changes from @reykt (issue #24, issue #25)

Paper provisionally accepted for publication at Scientific Data.

APD Version 1.1.0

  • APD submitted for publication and preprint:

Wenk EH, Sauquet H, Gallagher RV, Brownlee R, Boettiger C, Coleman D, Yang S, Auld T, Barrett RL, Brodribb T, Choat B, Dun L, Ellsworth D, Gosper C, Guja L, Jordan GJ, Breton T, Leigh A, Irving P, Medlyn B, Nolan R, Ooi M, Sommerville KD, Vesk P, White M, Wright IJ, Falster DS (2024) The AusTraits Plant Dictionary. bioRxiv doi: 10.1101/2023.06.16.545047]).

https://doi.org/10.5281/zenodo.8040789