AusTraits: a curated plant trait database for the Australian flora

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; andFacilitates accumulation and sharing of trait data;Builds a sense of community among contributors and users; andAspires 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.

### 项目简介
AusTraits是一款具有变革性意义的数据库，收录了澳大利亚本土植物类群的性状测量数据，所有数据均从数百个分散的原始来源中完成标准化整合。截至目前，项目团队已从超过250个独立来源中汇编数据，涵盖超过400项植物性状以及26000余个植物类群。

为实现多样化数据源的标准化整合，我们采用可复现工作流，对每个来源的数据执行各类必要调整，使其格式适配AusTraits数据库的收录要求。此类调整包括重构数据集结构、重命名变量、转换变量单位以及修正类群名称。本仓库仅包含标准化后的最终数据，而构建该资源所需的原始数据与代码，亦可在项目GitHub仓库http://traitecoevo.github.io/austraits.build/中获取。

有关本项目的更多信息，可查阅相关发表论文及项目官方网站austraits.org。

Falster、Gallagher等（2021）《AusTraits：澳大利亚植物区系经整理（curated）的植物性状数据库》，《Scientific Data》8: 254, https://doi.org/10.1038/s41597-021-01006-6

### 贡献者名录
本项目由新南威尔士大学悉尼分校的Daniel Falster博士、西悉尼大学的Rachael Gallagher博士、新南威尔士大学悉尼分校的Elizabeth Wenk博士以及悉尼皇家植物园与领地信托基金的Hervé Sauquet博士联合牵头，并有来自100余家机构的300余名贡献者参与（完整名单见前文）。本项目最初由麦考瑞大学的Rachael Gallagher博士与Ian Wright教授发起。

我们谨向以下贡献数据的机构致以谢意：澳大利亚国家植物园、布里斯班雨林保护与信息网络、英国皇家植物园邱园、新南威尔士州国家标本馆、北领地标本馆、昆士兰州标本馆、西澳大利亚州标本馆、南澳大利亚州标本馆、南澳大利亚州州立标本馆、塔斯马尼亚州标本馆以及维多利亚州环境、土地、水与规划部。

AusTraits得到了澳大利亚研究数据共同体（Australian Research Data Commons, ARDC）的资助，其‘变革性数据馆藏’（https://doi.org/10.47486/TD044）与‘数据合作计划’（https://doi.org/10.47486/DP720）项目均提供了支持；同时获得了澳大利亚研究委员会的研究员基金资助：Falster（FT160100113）、Gallagher（DE170100208）与Wright（FT100100910），以及麦考瑞大学为Gallagher提供的专项基金。ARDC由国家协同研究投资战略（National Collaborative Research Investment Strategy, NCRIS）提供支持。

### 数据获取与使用规范
汇编完成的AusTraits数据库采用知识共享署名许可（CC-BY）发布，允许社区自由重复使用。

使用该数据的必要条件是引用AusTraits官方论文，该论文将所有贡献者列为共同作者：

Falster、Gallagher等（2021）《AusTraits：澳大利亚植物区系经整理（curated）的植物性状数据库》，《Scientific Data》8: 254, https://doi.org/10.1038/s41597-021-01006-6

此外，我们鼓励用户尽可能同时引用原始数据来源。

根据许可协议条款，只要保留完整署名信息，数据可被重新分发。

本次提供两种格式的数据下载包：
1. `austraits-3.0.2.zip`：包含纯文本格式数据（.csv、.bib、.yml文件），适用于所有用户，包括使用Python的研究者。
2. `austraits-3.0.2.rds`：压缩的R对象格式数据，适用于R语言用户（详见下文）。

两种下载包均包含完整数据集与相关元数据。

### AusTraits R工具包
对于R语言用户，可通过`austraits` R工具包便捷获取并处理数据。该工具包支持数据一键下载，并提供查询示例与专属处理函数。

### AusTraits数据库结构
汇编完成的AusTraits数据库包含以下核心组成部分：

austraits
├── traits
├── sites
├── contexts
├── methods
├── excluded_data
├── taxonomic_updates
├── taxa
├── definitions
├── contributors
├── sources
└── build_info

上述组件涵盖了每份提交数据集附带的全部数据与上下文信息。

数据库的架构与字段定义详见下载包中的`definitions`文件/组件。`dictionary.html`文件以文本格式提供了相同的信息。各组件与字段的完整细节均包含在定义文档中。相关信息亦可在以下官方页面查阅：http://traitecoevo.github.io/austraits.build/articles/Trait_definitions.html 与 http://traitecoevo.github.io/austraits.build/articles/austraits_database_structure.html。

### 贡献指引
我们将AusTraits视为一项持续推进的协作型社区资源，其核心目标为：
1. 深化学界对澳大利亚植物区系的科学认知；
2. 推动植物性状数据的全球积累与共享；
3. 构建贡献者与使用者之间的紧密社区联结；
4. 追求最高标准的完全透明与可复现研究。

作为一项开放社区资源，我们热切欢迎各界人士参与贡献。数据库的汇编工作在GitHub仓库`traitecoevo/austraits.build`中进行管理。您可以通过以下方式参与贡献：
1. 错误报告：若您发现AusTraits中存在疑似错误，请在GitHub上提交议题。
2. 文档完善：我们欢迎各类补充与编辑，以降低社区使用现有数据或添加新数据的门槛。
3. 数据贡献：我们诚挚欢迎向AusTraits提交新的数据贡献。有关贡献数据的完整指南，请查阅http://traitecoevo.github.io/austraits.build/articles/contributing_data.html。