The AusTraits Plant Dictionary (APD)

The AusTraits Plant Dictionary (APD) includes the trait definitions used by AusTraits, a database of Australian plant traits. Upon its release in 2023, the APD will include definitions for nearly 500 traits pertaining to plant functional ecology and plant morphology. Each trait definition has been reviewed by multiple people and includes references and links to identical/similar traits in other trait databases whenever possible. The APD includes machine-readable formats and endpoints, allowing the traits to be readily re-used by other databases.

The APD is described in the following citation:

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. Scientific Data (in press) (preprint: 10.1101/2023.06.16.545047]).

This repository

This repository is the original source for the APD. It includes

• data files
• code for building machine-readable representations of the APD
• code for generating human-readable access points to the APD
• website files for the APD website

Data files and format

11 files are stored in data/ and are used to generate the APD. These files are:

• APD_traits_input.csv: The core table of trait definitions.
• APD_trait_hierarchy.csv: Table documenting a trait hierarchy into which traits in the APD are mapped.
• APD_categorical_values_input.csv: Table of allowable categorical trait values for categorical traits within the APD.
• APD_glossary.csv: Table of technical vocabulary used for APD trait definitions and keywords which were not located in previously published vocabularies and ontologies.
• APD_references.csv: Table of references used in the APD, including dois and complete reference details.
• APD_reviewers.csv: Table of people who have reviewed trait definitions for the APD, identified by their ORCIDs.
• APD_units.csv: Table of units used in the APD, including links in the Units of Measurement ontology.
• APD_annotation_properties.csv: Table of annotation properties that come from a published ontology and are used in the APD.
• APD_namespace_declaration.csv: Table of all ontologies used within APD. These may be ontologies with annotation properties used by the APD (and listed in annotation_properties.csv) or with terms (classes) used by the APD (and listed in ontology_links.csv) .
• APD_resource.csv: Information about the two APD resources, APD/traits and APD/glossary
• published_classes.csv: List of published terms referenced as keywords (or similar) within the APD.

Each trait includes the following fields:

• trait name (label)
• trait ID
• expected units (for numeric traits; all units aligned to UCUM standards)
• allowable range (for numeric traits)
• allowable trait values (for categorical traits; all trait values are themselves defined)
• trait definition (A definition with technical terms linked to published ontologies as well as, when applicable, longer definitions and comments
• keywords
• structure measured (what plant part is measured, referencing a specific tissue, organ, or the whole plant)
• characteristic measured, such as whether the trait records mass, shape, length, etc.
• a trait hierarchy
• references
• names/ORCIDs of people who have reviewed the trait definition
• links to identical/similar/related traits in other plant trait databases
• dates the trait was first added, most recently modified, and reviewed

Instructions for building the APD

The code in build.qmd builds the APD from the data files in data/, including:

• generated machine-readable representations of the APD, including
  • RDF Turtle: APD.ttl,
  • N-Quad: APD.nq,
  • N-Triple: APD.nt,
  • JSON Linked Data format: APD.json
• create the APD website, saved in docs/
  • hosting via Github pages at https://traitecoevo.github.io/APD/
  • created from files index.qmd and configured with _quarto.yml
  • uses the quarto package for R, with instructions on formatting from <https://quarto.org/docs/reference/projects/websites.html
  • we were inspired by https://i-adopt.github.io with code from https://github.com/i-adopt/i-adopt.github.io

The APD is accessible via https://w3id.org/APD/, https://w3id.org/APD/traits/, and https://w3id.org/APD/glossary/. These links redirect to the site generated here. To enable the links, we sent a pull request to the w3id.org repo, like this example from https://github.com/perma-id/w3id.org/blob/master/iadopt/.

Redirect syntax can be tested at https://htaccess.madewithlove.com.

Testing w3id.org access

To test the redirects via <w3id.org/APD> try the following

curl -sH "Accept: text/turtle" -L https://w3id.org/APD > temp.ttl
curl -sH "Accept: text/turtle" -L https://w3id.org/APD/traits > temp2.ttl
curl -sH "Accept: text/turtle" -L https://w3id.org/APD/traits\#trait_0001 > temp3.ttl

curl -sH "Accept: application/n-triples" -L https://w3id.org/APD > temp.nt
curl -sH "Accept: application/n-triples" -L https://w3id.org/APD/traits > temp2.nt
curl -sH "Accept: application/n-triples" -L https://w3id.org/APD/traits\#trait_0001 > temp3.nt

curl -sH "Accept: text/html" -L https://w3id.org/APD > temp.html
curl -sH "Accept: text/html" -L https://w3id.org/APD/traits > temp2.html
curl -sH "Accept: text/html" -L https://w3id.org/APD/traits\#trait_0001 > temp3.html

Acknowledgements

We are grateful to S Cox, J Smillie, K Levett, M Barlow, and C Brady for useful conversations. The AusTraits project received investment (https://doi.org/10.47486/TD044, https://doi.org/10.47486/DP720) from the Australian Research Data Commons (ARDC). The ARDC is funded by the National Collaborative Research Infrastructure Strategy (NCRIS).