The AusTraits plant dictionary

Abstract

Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.

Fig. 1

Explicit definitions and value descriptions are needed to reconcile inconsistencies in how researchers align plant phenotypic diversity with particular traits and trait values. (a) For some taxa, for some phenotype observations, all researchers are likely to assign the same observation to the same trait and trait value; (b) For other taxa, the same trait might not be consistently scored, especially without explicit definitions; (c) Some phenotypes will be aligned to different traits or different trait values by different researchers, especially if clear trait and trait value descriptions are not available. Photo credits: Russell Barrett (Corynotheca lateriflora seed); John Cull, iNaturalist (Eucalyptus obliqua leaves); Gillian Kowalick (Eucalyptus croajingolensis cross-section); Dean Nicolle, iNaturalist (Eucalyptus erythronema subsp. erythronema); Elizabeth Wenk (Acacia ulicifolia; Rhaphidophora hayi); Dylan Wishart, iNaturalist (Eucalyptus obliqua fruits); hughberry, iNaturalist (Stylidium lineare).

Fig. 2

A trait dictionary is an essential component of the AusTraits workflow, specifying (i) trait concepts, (ii) standard units, (iii) allowable categorical trait values and (iv) allowable ranges for numeric traits. The structured metadata file that accompanies each dataset explicitly maps data columns to specific trait concepts from the dictionary and includes substitutions to align categorical trait values with those in the dictionary. The four elements of the trait definitions are then used by the traits.build R pipeline to integrate the data source into the AusTraits database.

Fig. 3

There were initially 68 trait values mapped to the semantically messy trait concept ‘plant growth form’ and incomplete trait concepts ‘parasitic’ and ‘stem growth habit’ (left). For the refined trait concepts (right), these were able to be condensed to 53, despite adding more detailed trait values to parasitic, plant succulence and stem growth habit traits. For the APD, the retained trait values were mapped across five traits: plant growth form, plant succulence, plant growth substrate, parasitic and stem growth habit. The mixing of semantic concepts within ‘plant growth form’ had previously resulted in hybrid terms which could now be eliminated, such as “shrub_aquatic”.

Fig. 4

The APD scripts, inputs and output data are stored on the project’s GitHub repository. Versioned releases are archived at Zenodo and the Australian Data Research Common’s Research Vocabulary Australia (RVA) portal. APD has been registered as a namespace within w3id.org, with term URIs redirecting back to an html landing page within the GitHub repository. The APD inputs are also used to generate the traits.yml file required to build the AusTraits trait database.