Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Björn Quast (b.quast@leibniz-lib.de)
Received: 10 Aug 2022 | Published: 23 Aug 2022
© 2022 Christian Bräunig, Björn Quast, Peter Grobe
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Bräunig C, Quast B, Grobe P (2022) Bridging a Gap in Metabarcoding Research: The ASV Table Registry. Biodiversity Information Science and Standards 6: e91504. https://doi.org/10.3897/biss.6.91504
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Metabarcoding is a tool to routinely identify species in environmental mass-samples and thereby analyze their species composition. Using metabarcoding techniques outperforms the traditional species identification by human experts in amount, speed and quality when well curated reference data are available.
Therefore, metabarcoding can be seen as the future standard method for all biological research areas where species occurrence and distribution is in question, e.g., ecological research or monitoring projects (
A common outcome of metabarcoding research are Amplicon Sequence Variant tables (ASV,
The number and precision of taxon assignments will increase with the growth of available sequences and quality of identifications in reference databases over time (
Projects with the aim of building up species inventories on a large scale (GBOL) or monitoring programs, like the Automated Multisensor Stations for Monitoring of BioDiversity (
Currently, most ASV tables are stored as supplements to publications or in private repositories. This makes analysis across multiple research projects difficult and error prone as sequences and their taxon assignments are often not accessible. Efforts, like the European Bioinformatics Institute metagenomics with Mgnify serve the needs for uploading and annotating environmental DNA samples (
To fill this gap, we develop an ASV Table Registry as part of the German Barcode of Life III - Dark Taxa project. This allows users to:
register ASV tables and sequences
upload and manage ASV tables with versioning
publish ASV tables with DOIs
search by sequences, taxa, and occurrence data
retrieve API-based data
assign taxonomic names with various tools and reference databases
keep track of the applied search methods and parameters
The data life cycle of the uploaded ASV tables consists of several draft versions (each re-annotation with the identification pipeline creates a new draft version) and eventually a published version with a DOI. New draft versions can be created from the published version, then re-annotated and published again. The tracking of former taxon assignments allows researchers to re-evaluate data of former studies, compare them, and add new results. The ASV Table Registry developed here aims to make ASV tables FAIR (Findable, Accessible, Interoperable, and Reusable) and to foster the shared use in research projects.
Future development focuses on the incorporation of the MIxS standard (
The ASV data portal is accessible at: https://bolgermany.de/metabarcoding; the source code at: https://gitlab.leibniz-lib.de/GBOL/asv-table-registry.
taxon annotation, environmental research, biodiversity monitoring, barcode reference databases, DNA barcodes, FAIR principles
Christian Bräunig
TDWG 2022
The ASV Table Registry is developed within the BMBF funded Project GBOL III - Dark Taxa, German Federal Ministry of Education and Research (BMBF, grant ID: 01LI1901)