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) 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). 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，项目已整合超过300个独立数据源，涵盖500余个植物性状与34000余个植物类群。 为实现多源异构数据的统一协调，我们采用可复现的工作流，对每个数据源实施所需的各类调整，使其格式适配并纳入AusTraits数据库。此类调整包括重构数据集结构、重命名变量、转换变量单位以及修正植物类群名称。 本仓库包含标准化后的整合数据，而构建该资源所需的原始数据与代码，也可在项目的GitHub仓库https://github.com/traitecoevo/austraits.build/ 中获取。更多项目相关信息可访问项目官网austraits.org，或查阅关联发表论文（详见下文）。 ### 项目团队与致谢 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，得到了来自100余家机构的300余名贡献者的支持（完整名单见前文）。本项目由时任麦考瑞大学的Rachael Gallagher博士与Ian Wright教授发起。我们谨向以下提供数据支持的机构致以谢意：澳大利亚国家植物园、布里斯班雨林行动与信息网络、邱园（Kew）植物园、新南威尔士国家标本馆、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、南澳州立标本馆、塔斯马尼亚标本馆、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 得到了澳大利亚研究数据共同体（Australian Research Data Commons, ARDC）通过其「变革性数据收藏」（https://doi.org/10.47486/TD044）与「数据合作计划」（https://doi.org/10.47486/DP720）项目的资助，同时获得澳大利亚研究理事会（Australian Research Council, 项目编号FT160100113、DE170100208、FT100100910）以及麦考瑞大学的研究经费支持。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 整合后的AusTraits数据库以知识共享署名许可（Creative Commons Attribution, 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资源论文，该论文将所有贡献者列为共同作者：Falster、Gallagher等人（2021）《AusTraits：一款经过整理（curated）的澳大利亚植物区系性状数据库》，*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，在保留原署名的前提下，数据可被重新分发。 下方提供了两种格式的数据下载包： 1. `austraits-X.X.X.zip`：包含纯文本格式的数据（.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`：为压缩的R对象格式数据，适用于R语言用户（详见下文）。 针对R语言用户，可通过`austraits` R包辅助数据的获取与操作。该包既支持数据下载，也提供查询示例与相关函数。 ### 数据库结构 整合后的AusTraits数据库包含一系列关系型数据表与文件。这些元素涵盖全部数据、每份贡献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`以文本格式提供了相同信息。类似信息可在https://traitecoevo.github.io/traits.build-book/ 查阅。 ### 贡献指南 我们将AusTraits视为一项持续推进的社区协作资源，其目标包括： 1. 增进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. 追求最高标准的完全透明且可复现的研究。 作为一项社区资源，我们热切欢迎各界人士参与贡献。数据库的组装工作在GitHub仓库https://github.com/traitecoevo/austraits.build/ 上进行管理。您可以通过以下多种方式参与贡献： - 报告错误：若您发现AusTraits中存在潜在错误，请在GitHub上提交Issue。 - 优化文档：我们欢迎各类新增与编辑内容，以帮助社区更便捷地使用现有数据或添加新数据。 - 贡献新数据：我们诚挚欢迎向AusTraits提交新的数据贡献。有关贡献的详细指南可参阅https://github.com/traitecoevo/austraits.build/。