AusTraits: a curated plant trait database for the Australian flora

Full description

INTRODUCTION AusTraits is a transformative database, containing measurements on the traits of Australia’s plant taxa, standardised from hundreds of disconnected primary sources. So far, data have been assembled from > 250 distinct sources, describing > 400 plant traits and > 26,000 taxa. To handle the harmonising of diverse data sources, we use a reproducible workflow to implement the various changes required for each source to reformat it suitable for incorporation in AusTraits. Such changes include restructuring datasets, renaming variables, changing variable units, changing taxon names. While this repository contains the harmonised data, the raw data and code used to build the resource are also available on the project’s GitHub repository, http://traitecoevo.github.io/austraits.build/. Further information on the project is available in the associated publication and at the project website austraits.org. Falster, Gallagher et al (2021) AusTraits, a curated plant trait database for the Australian flora. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6 CONTRIBUTORS The project is jointly led by Dr Daniel Falster (UNSW Sydney), Dr Rachael Gallagher (Western Sydney University), Dr Elizabeth Wenk (UNSW Sydney), and Dr Hervé Sauquet (Royal Botanic Gardens and Domain Trust Sydney), with input from > 300 contributors from over > 100 institutions (see full list above). The project was initiated by Dr Rachael Gallagher and Prof Ian Wright while at Macquarie University. We are grateful to the following institutions for contributing data Australian National Botanic Garden, Brisbane Rainforest Action and Information Network, Kew Botanic Gardens, National Herbarium of NSW, Northern Territory Herbarium, Queensland Herbarium, Western Australian Herbarium, South Australian Herbarium, State Herbarium of South Australia, Tasmanian Herbarium, Department of Environment, Land, Water and Planning, Victoria. AusTraits has been supported by investment from the Australian Research Data Commons (ARDC), via their “Transformative data collections” (https://doi.org/10.47486/TD044) and “Data Partnerships” (https://doi.org/10.47486/DP720) programs; fellowship grants from Australian Research Council to Falster (FT160100113), Gallagher (DE170100208) and Wright (FT100100910), a grant from Macquarie University to Gallagher. The ARDC is enabled by National Collaborative Research Investment Strategy (NCRIS). ACCESSING AND USE OF DATA The compiled AusTraits database is released under an open source licence (CC-BY), enabling re-use by the community. A requirement of use is that users cite the AusTraits resource paper, which includes all contributors as co-authors: Falster, Gallagher et al (2021) AusTraits, a curated plant trait database for the Australian flora. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6 In addition, we encourage users you to cite the original data sources, wherever possible. Note that under the license data may be redistributed, provided the attribution is maintained. The downloads below provide the data in two formats: austraits-3.0.2.zip: data in plain text format (.csv, .bib, .yml files). Suitable for anyone, including those using Python. austraits-3.0.2.rds: data as compressed R object. Suitable for users of R (see below). Both objects contain all the data and relevant meta-data. AUSTRAITS R PACKAGE For R users, access and manipulation of data is assisted with the austraits R package. The package can both download data and provides examples and functions for running queries. STRUCTURE OF AUSTRAITS The compiled AusTraits database has the following main components: austraits ├── traits ├── sites ├── contexts ├── methods ├── excluded_data ├── taxanomic_updates ├── taxa ├── definitions ├── contributors ├── sources └── build_info These elements include all the data and contextual information submitted with each contributed datasets. A schema and definitions for the database are given in the file/component definitions, available within the download. The file dictionary.html provides the same information in textual format. Full details on each of these components and columns are contained within the definition. Similar information is available at http://traitecoevo.github.io/austraits.build/articles/Trait_definitions.html and http://traitecoevo.github.io/austraits.build/articles/austraits_database_structure.html. CONTRIBUTING We envision AusTraits as an on-going collaborative community resource that: Increases our collective understanding the Australian flora; and Facilitates accumulation and sharing of trait data; Builds a sense of community among contributors and users; and Aspires to fully transparent and reproducible research of the highest standard. As a community resource, we are very keen for people to contribute. Assembly of the database is managed on GitHub at traitecoevo/austraits.build. Here are some of the ways you can contribute: Reporting Errors: If you notice a possible error in AusTraits, please post an issue on GitHub. Refining documentation: We welcome additions and edits that make using the existing data or adding new data easier for the community. Contributing new data: We gladly accept new data contributions to AusTraits. See full instructions on how to contribute at http://traitecoevo.github.io/austraits.build/articles/contributing_data.html.

Notes

External Organisations
University of New South Wales; Macquarie University; National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney; CSIRO; NSW Department of Primary Industries; Centre for Australian National Biodiversity Research; Swinburne University of Technology; Western Sydney University; La Trobe University; School for Field Studies; University of Melbourne; The Australian National University; NSW Department of Planning Industry and Environment; Southern Cross University; University of Vienna; Queensland Herbarium; University of Tasmania; Imperial College; University of Wollongong; Australian Institute of Botanical Science; Max-Planck Institute for Biogeochemistry; James Cook University; Charles Sturt University; Monash University; The University of Melbourne; University of Adelaide; King's College London; University of Western Australia; Department of Agriculture, Australia; Western Australian Herbarium; Federation University; Royal Botanic Gardens, Kew; State Herbarium of South Australia; University of New England; Brooklyn Botanic Garden; The University of Queensland; Northern Territory Herbarium; Australian National Herbarium; Lincoln University; University of Technology Sydney; Environment Department, Alcoa of Australia; Tasmanian Herbarium; University of Liege; Lanzhou University; Guizhou University; University of Canberra; Royal Botanic Gardens and Domain Trust, Sydney; Melbourne Water; Conservation Commission of the Northern Territory; Queensland University of Technology; Universidade Federal do Rio Grande do Norte, Natal, Brazil; Queensland Herbarium, Australia; The University of Sydney; Pathways Bushland and Environment Consultancy; University of California; USDA-ARS, WMSRU; Department of Biodiversity, Conservation and Attractions, Western Australia; Curtin University; Cambridge University; The University of Adelaide; Massachusetts Institute of Technology; CSIRO, Australia; Parks Australia, Department of Agriculture, Water and the Environment; Murdoch University; Berowa NSW; Nanchang Institute of Technology; Universidad Autonoma de Nuevo Leon, Mexico; Australian Wildlife Conservancy; Department of Biodiversity, Conservation and Attractions, WA; NSW Rural Fire Service; Department of Environment, Land, Water and Planning, Victoria; University of Goettingen; University of Canterbury; Université de Montréal; Australian National University; University of Wyoming; Royal Botanic Garden Edinburgh; Fordham University; Universidad Nacional Autónoma de México; University of Otago; University of Waikato; University of Auckland; Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, WA; Manaaki Whenua – Landcare Research, Lincoln, New Zealand; Cumberland Ecology, Australia; CSIRO Land and Water; Linkoping University; Currency Creek Arboretum, Australia; Estonian University of Life Sciences; Leistershire County Council, Leicester, United Kingdom; New College of Florida; Kyoto University; University of Sheffield; Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Western Australia; Istanbul Technical University; University of Aukland; Griffith University; Greening Australia; McGill University; CSIRO Land and Water, Australia; Elizabeth Macarthur Agricultural Institute; University of Helsinki; University Hohenheim; Rider University; University of the Sunshine Coast; Bern University; Academy of Science Czech Republic; Xishuangbanna Tropical Botanic Garden; Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Sydney; Wageningen University; Deakin University; University of Peradeniya; National Herbarium of NSW and Royal Botanic Gardens and Domain Trust; Department of Environment, Land, Water and Planning, Victoria, Australia; University of Miami; Université de Montpellier

Associated Persons
Daniel Falster (Creator); Rachael Gallagher (Creator); Elizabeth Wenk (Creator); Hervé Sauquet (Contributor); Ian J. Wright (Contributor); Dony Indiarto (Contributor); Sam Andrew (Contributor); Caitlan Baxter (Contributor); James Lawson (Contributor); Stuart Allen (Contributor); Anne Fuchs (Contributor); Anna Monro (Contributor); Fonti Kar (Contributor); Mark A Adams (Contributor); Collin W. Ahrens (Contributor); Matthew Alfonzetti (Contributor); Sophia Amini (Contributor); Tara Angevin (Contributor); Deborah M.G. Apgaua (Contributor); Stefan Arndt (Contributor); Julian Ash (Contributor); Owen K. Atkin (Contributor); Joe Atkinson (Contributor); Tony Auld (Contributor); Andrew Baker (Contributor); Maria von Balthazar (Contributor); Anthony Bean (Contributor); Chris J. Blackman (Contributor); Keith Bloomfield (Contributor); Tara Boreham (Contributor); David M. J. S. Bowman (Contributor); Ross Bradstock (Contributor); Jason Bragg (Contributor); Willi A. Brand (Contributor); Amber Briggs (Contributor); John Brock (Contributor); Timothy J. Brodribb (Contributor); Genevieve Buckton (Contributor); Don Butler (Contributor); Elizabeth Caldwell (Contributor); James Camac (Contributor); Raymond Carpenter (Contributor); Jane A. Catford (Contributor); Gregory R. Cawthray (Contributor); Lucas A. Cernusak (Contributor); Gregory Chandler (Contributor); Alex R. Chapman (Contributor); David Cheal (Contributor); Alexander W. Cheesman (Contributor); Si-Chong Chen (Contributor); Robert Chinnock (Contributor); Brendan Choat (Contributor); Peter Clarke (Contributor); Derek Clayton (Contributor); Steven Clemants (Contributor); Harold Trevor Clifford (Contributor); Brook Clinton (Contributor); Peta L. Clode (Contributor); Michelle Cochrane (Contributor); Helen Coleman (Contributor); Bronwyn Collins (Contributor); Alessandro Conti (Contributor); Wendy Cooper (Contributor); William Cooper (Contributor); William K. Cornwell (Contributor); Meredith Cosgrove (Contributor); Ian Cowie (Contributor); Lyn Craven (Contributor); Michael Crisp (Contributor); Erika Cross (Contributor); Kristine Y. Crous (Contributor); Saul Cunningham (Contributor); Timothy Curran (Contributor); Ellen Curtis (Contributor); Ian Davidson (Contributor); Matthew I. Daws (Contributor); Miguel de Salas (Contributor); Félix de Tombeur (Contributor); Jane L. DeGabriel (Contributor); Matthew D. Denton (Contributor); Ning Dong (Contributor); Pengzhen Du (Contributor); Honglang Duan (Contributor); David H. Duncan (Contributor); Richard P. Duncan (Contributor); Marco Duretto (Contributor); John M. Dwyer (Contributor); Derek Eamus (Contributor); Cheryl Edwards (Contributor); Judy Egan (Contributor); Manuel Esperon-Rodriguez (Contributor); John R. Evans (Contributor); Susan E. Everingham (Contributor); Chris Fahey (Contributor); Daniel Falster (Contributor); Claire Farrell (Contributor); Jennifer Firn (Contributor); Carlos Roberto Fonseca (Contributor); Paul Irwin Forster (Contributor); John Foster (Contributor); Ben J. French (Contributor); Tony French (Contributor); Allison Frith (Contributor); Doug Frood (Contributor); Jennifer L. Funk (Contributor); Rachael Gallagher (Contributor); Ronald Gardiner (Contributor); Sonya R. Geange (Contributor); Oula Ghannoum (Contributor); Malcolm Gill (Contributor); Sean M. Gleason (Contributor); Ethel Goble-Garratt (Contributor); Carl R. Gosper (Contributor); Emma Gray (Contributor); Philip K. Groom (Contributor); Saskia Grootemaat (Contributor); Caroline Gross (Contributor); Peter Grubb (Contributor); Greg Guerin (Contributor); Caio Guilherme Pereira (Contributor); Chris Guinane (Contributor); Lydia Guja (Contributor); Amy K. Hahs (Contributor); TJ Hall (Contributor); Monique Hallet (Contributor); Matthew Tom Harrison (Contributor); Tammy Haslehurst (Contributor); Foteini Hassiotou (Contributor); Patrick E. Hayes (Contributor); Martin Henery (Contributor); John Herbohn (Contributor); Dieter Hochuli (Contributor); Peter Hocking (Contributor); Jocelyn Howell (Contributor); Jing Hu (Contributor); Guomin Huang (Contributor); Kate Hughes (Contributor); Lesley Hughes (Contributor); John Huisman (Contributor); Jugoslav Ilic (Contributor); Muhammad Islam (Contributor); Ashika Jagdish (Contributor); Daniel Jin (Contributor); Gregory Jordan (Contributor); Enrique Jurado (Contributor); John Kanowski (Contributor); Sabine Kasel (Contributor); Ian Kealley (Contributor); Greg Keighery (Contributor); Jürgen Kellermann (Contributor); Belinda Kenny (Contributor); James Kirkpatrick (Contributor); Kirsten Knox (Contributor); Michele Kohout (Contributor); Robert M. Kooyman (Contributor); Martyna M. Kotowska (Contributor); Luka Kovac (Contributor); Kaely Kreger (Contributor); John Kuo (Contributor); Hao Ran Lai (Contributor); Etienne Laliberté (Contributor); Hans Lambers (Contributor); Martin Lambert (Contributor); Byron B. Lamont (Contributor); Dana Lanceman (Contributor); Robert Lanfear (Contributor); Daniel C. Laughlin (Contributor); Bree-Anne Laugier-Kitchener (Contributor); Susan Laurance (Contributor); Michael Lawes (Contributor); Claire Laws (Contributor); James Lawson (Contributor); Emma Laxton (Contributor); Caroline E. R. Lehmann (Contributor); Andrea Leigh (Contributor); Michelle R. Leishman (Contributor); Tanja Lenz (Contributor); Brendan Lepschi (Contributor); James D. Lewis (Contributor); Felix Lim (Contributor); Liz Lindsay (Contributor); Udayangani Liu (Contributor); Daniel Montoya Londono (Contributor); Andrea López Martinez (Contributor); Janice Lord (Contributor); Christiane Ludwig (Contributor); Ian Lunt (Contributor); Christopher H. 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