PDF(Pubmed)
Abstract：
Fungi is a highly diverse group of eukaryotic organisms that live under an extremely wide range of environmental conditions. Nowadays, there is a fundamental focus on observing how biodiversity varies on different spatial scales, in addition to understanding the environmental factors which drive fungal biodiversity. Metabarcoding is a high-throughput DNA sequencing technology that has positively contributed to observing fungal communities in environments. While the DNA sequencing data generated from metabarcoding studies are available in public archives, this valuable data resource is not directly usable for fungal biodiversity investigation. Additionally, due to its fragmented storage and distributed nature, it is not immediately accessible through a single user interface. We developed the MycoDiversity DataBase User Interface (https://mycodiversity.liacs.nl) to provide direct access and retrieval of fungal data that was previously inaccessible in the public domain. The user interface provides multiple graphical views of the data components used to reveal fungal biodiversity. These components include reliable geo-location terms, the reference taxonomic scientific names associated with fungal species and the standard features describing the environment where they occur. Direct observation of the public DNA sequencing data in association with fungi is accessible through SQL search queries created by interactively manipulating topological maps and dynamic hierarchical tree views. The search results are presented in configurable data table views that can be downloaded for further use. With the MycoDiversity DataBase User Interface, we make fungal biodiversity data accessible, assisting researchers and other stakeholders in using metabarcoding studies for assessing fungal biodiversity.
摘要：
真菌是一类高度多样化的真核生物，它们生活在极其广泛的环境条件下。如今,基本的重点是观察生物多样性在不同空间尺度上的变化，除了了解驱动真菌生物多样性的环境因素。Metabarcoding是一种高通量DNA测序技术，为观察环境中的真菌群落做出了积极贡献。虽然从代谢编码研究中产生的DNA测序数据可以在公共档案中获得，这种宝贵的数据资源不能直接用于真菌生物多样性调查。此外,由于其分散的存储和分布式的性质，它不能通过单个用户界面立即访问。我们开发了Mycodiversity数据库用户界面（https://mycodiversity。liacs.nl），以提供对以前在公共领域无法访问的真菌数据的直接访问和检索。用户界面提供了用于揭示真菌生物多样性的数据组件的多个图形视图。这些组件包括可靠的地理位置术语，与真菌物种相关的参考分类学名和描述它们发生的环境的标准特征。通过交互式操作拓扑图和动态分层树视图创建的SQL搜索查询，可以直接观察与真菌相关的公共DNA测序数据。搜索结果以可配置的数据表视图显示，可下载以供进一步使用。借助MycodiversityDataBase用户界面，我们提供真菌生物多样性数据，协助研究人员和其他利益相关者使用代谢编码研究来评估真菌生物多样性。
