Multiple graphical views for automatically generating SQL for the MycoDiversity DB; making fungal biodiversity studies accessible

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.真菌（Fungi）是一类高度多样的真核生物，生存环境覆盖范围极广。当前，学界在探究驱动真菌生物多样性的环境因子的同时，也愈发重视观测不同空间尺度下生物多样性的变化规律。元条形码测序（Metabarcoding）作为一种高通量DNA测序技术，已成为环境真菌群落观测的有效手段。尽管元条形码测序研究产生的DNA测序数据已存入公共档案库，但这类宝贵的数据资源无法直接用于真菌生物多样性研究。加之数据存储分散且分布广泛，无法通过单一用户界面直接获取。为此，我们开发了真菌多样性数据库用户界面（MycoDiversity DataBase User Interface，https://mycodiversity.liacs.nl），以实现对公共领域中此前难以获取的真菌数据的直接访问与检索。该界面提供多种数据组分可视化视图，用于解析真菌生物多样性特征。这些数据组分包括可靠的地理位置信息、真菌物种对应的参考分类学学名，以及描述其生存环境的标准特征参数。用户可通过交互式操作拓扑地图与动态层级树视图生成SQL搜索查询，直接检索与真菌相关的公共DNA测序数据。搜索结果将以可自定义配置的数据表格视图展示，用户可下载数据用于后续研究。借助该真菌多样性数据库用户界面，我们实现了真菌生物多样性数据的可及性，助力科研人员及其他相关方利用元条形码测序研究开展真菌生物多样性评估工作。