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

Biodiversity Data Journal, vol. 12, pp. e119660

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.

Authors 7

1. Irene Martorelli corresponding Aachen Leiden Institute of Advanced Computer Science Netherlands Leiden Institute of Advanced Computer Science (LIACS) Naturalis Biodiversity Center Netherlands Naturalis Biodiversity Center Leiden Netherlands

   Leiden University · Naturalis Biodiversity Center

   Affiliation as printed

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands Leiden Institute of Advanced Computer Science (LIACS), Leiden University Leiden Netherlands

   Naturalis Biodiversity Center, Leiden, Netherlands Naturalis Biodiversity Center Leiden Netherlands

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands

   Naturalis Biodiversity Center, Leiden, Netherlands

2. Aram Pooryousefi Aachen Leiden Institute of Advanced Computer Science Netherlands Leiden Institute of Advanced Computer Science (LIACS)

   Leiden University

   Affiliation as printed

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands Leiden Institute of Advanced Computer Science (LIACS), Leiden University Leiden Netherlands

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands

3. Haike van Thiel Aachen Leiden Institute of Advanced Computer Science Netherlands Leiden Institute of Advanced Computer Science (LIACS)

   Leiden University

   Affiliation as printed

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands Leiden Institute of Advanced Computer Science (LIACS), Leiden University Leiden Netherlands

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands

4. Floris Sicking Aachen Leiden Institute of Advanced Computer Science Netherlands Leiden Institute of Advanced Computer Science (LIACS)

   Leiden University

   Affiliation as printed

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands Leiden Institute of Advanced Computer Science (LIACS), Leiden University Leiden Netherlands

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands

5. Guus J. Ramackers Aachen Leiden Institute of Advanced Computer Science Netherlands Leiden Institute of Advanced Computer Science (LIACS)

   Leiden University

   Affiliation as printed

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands Leiden Institute of Advanced Computer Science (LIACS), Leiden University Leiden Netherlands

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands

6. Vincent S. F. T. Merckx Aachen Naturalis Biodiversity Center Netherlands Naturalis Biodiversity Center Leiden Netherlands Leiden Institute of Advanced Computer Science

   Leiden University · Naturalis Biodiversity Center · University of Amsterdam

   Affiliation as printed

   Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam Netherlands

   Naturalis Biodiversity Center, Leiden, Netherlands Naturalis Biodiversity Center Leiden Netherlands

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands

7. Fons J. Verbeek Aachen Leiden Institute of Advanced Computer Science Netherlands Leiden Institute of Advanced Computer Science (LIACS)

   Leiden University

   Affiliation as printed

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands Leiden Institute of Advanced Computer Science (LIACS), Leiden University Leiden Netherlands

   Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, Netherlands