AusTraits: a curated plant trait database for the Australian flora

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 > 300 distinct sources, describing > 500 plant traits and > 34,000 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, https://github.com/traitecoevo/austraits.build/. Further information on the project is available at the project website austraits.org and in the associated publication (see below). 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 and the Royal Botanic Gardens 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, https://doi.org/10.47486/DP720A) programs; and grants from the Australian Research Council (FT160100113, DE170100208, FT100100910) and Macquarie University, 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-X.X.X.zip: data in plain text format (.csv, .bib, .yml files). Suitable for anyone, including those using Python. austraits-X.X.X.rds: data as compressed R object. Suitable for users of R (see below). austraits-X.X.X-flattened.rds: contains a flattened version of the dataset for direct loading in R; all data tables are joined into a wider format austraits-X.X.X-flattened.parquet: contains a flattened version of the dataset in parquet format; all data tables are joined into a wider format 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 contains a series of relational tables and files. These elements include all the data, contextual information submitted with each contributed datasets, database schema, and trait definitions. The file dictionary.html provides the same information in textual format. Similar information is available at https://traitecoevo.github.io/traits.build-book/. CONTRIBUTING We envision AusTraits as an on-going collaborative community resource that: Increases our collective understanding the Australian flora; 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 https://github.com/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 https://github.com/traitecoevo/austraits.build/.

AusTraits 是一款变革性数据库，收录了澳大利亚植物类群(plant taxa)的性状(trait)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，该数据集已整合超过300个独立来源的数据，涵盖超过500项植物性状以及34000余个植物类群。

为完成多源数据的统一化处理，我们采用可复现工作流，对每个数据源进行所需的各类调整，使其格式适配并纳入AusTraits数据库。此类调整包括重构数据集、重命名变量、转换变量单位以及修正植物类群名称。

本仓库仅包含已完成统一化的数据集，构建该资源所需的原始数据与代码也可在项目的GitHub仓库获取：https://github.com/traitecoevo/austraits.build/。更多项目相关信息可访问项目官网austraits.org，或查阅相关发表论文（详见下文）。

## 贡献者团队
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（完整贡献者名单见前文）。本项目由麦考瑞大学的Rachael Gallagher博士与Ian Wright教授发起。

我们感谢以下机构提供的数据支持：澳大利亚国家植物园、布里斯班雨林保护与信息网络、邱园植物园、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、南澳大利亚州立标本馆、塔斯马尼亚州标本馆、维多利亚州环境、土地、水与规划部以及维多利亚皇家植物园。

AusTraits的研发得到了澳大利亚研究数据共同体(Australian Research Data Commons, ARDC)的“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, https://doi.org/10.47486/DP720A)项目的资助；同时获得了澳大利亚研究委员会(Australian Research Council)的项目基金(FT160100113、DE170100208、FT100100910)以及麦考瑞大学的支持。ARDC由国家协同研究投资战略(National Collaborative Research Investment Strategy, NCRIS)提供支持。

## 数据访问与使用规范
整合完成的AusTraits数据库采用知识共享署名(CC-BY)开源许可协议发布，允许社区成员二次使用。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：面向澳大利亚植物区系的经过curated(curated)整理的植物性状数据库》，*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，用户可重新分发该数据，但需保留原署名信息。

下方提供了四种格式的数据下载包：
1. `austraits-X.X.X.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的开发者。
2. `austraits-X.X.X.rds`：以压缩R对象形式存储的数据，适用于R语言用户（详见下文）。
3. `austraits-X.X.X-flattened.rds`：包含扁平化后的数据集，可直接在R中加载，所有数据表已合并为宽格式。
4. `austraits-X.X.X-flattened.parquet`：以Parquet(parquet)格式存储的扁平化数据集，所有数据表已合并为宽格式。

对于R语言用户，可通过`austraits` R包辅助数据的获取与操作。该包既可用于下载数据，也提供了示例代码与查询函数。

## AusTraits数据库结构
整合完成的AusTraits数据库包含一系列关系型数据表与文件，涵盖所有原始数据、每份提交数据集附带的上下文信息、数据库架构以及性状定义。`file dictionary.html`文件以文本形式提供了相同的信息。类似的信息也可在https://traitecoevo.github.io/traits.build-book/ 查阅。

## 数据贡献指南
我们将AusTraits视为一项持续推进的协作型社区资源，其目标包括：
1. 深化学界对澳大利亚植物区系的集体认知；
2. 推动性状数据的积累与共享；
3. 构建贡献者与使用者之间的社区联结；
4. 追求最高标准的全透明、可复现研究。

作为一项社区资源，我们热忱欢迎各界人士参与贡献。数据库的搭建与管理依托GitHub仓库https://github.com/traitecoevo/austraits.build/ 开展。您可通过以下多种方式参与贡献：
- 报告错误：若您发现AusTraits中存在疑似错误，请在GitHub上提交Issue。
- 完善文档：我们欢迎各类新增与编辑建议，以帮助社区成员更便捷地使用现有数据或提交新数据。
- 贡献新数据：我们欢迎各界向AusTraits提交新的数据贡献。详见https://github.com/traitecoevo/austraits.build/ 中的完整贡献指南。