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Introduction

Important
 The MDT and this guide is continuously being developed. Even when using the most recent version of the guide, it may be slightly out of sync with the exact appearance of the MDT.

editor idea: move some of the Introduction to a "resources" section

GBIF and DNA

GBIF provides access to extensive biodiversity data, primarily focused on species occurrences, including where and when species have been recorded. These records, gathered from collections, surveys, and citizen science efforts, contain species names, observation dates, locations, and other important details. In addition to traditional biodiversity records, GBIF also supports DNA-associated data, such as DNA metabarcoding datasets. A general guide – Publishing DNA-derived data through biodiversity data platforms – was released in 2021 to assist with these specific data types. However, consultations with the GBIF network and research community in 2022 and 2023 highlighted the need for user-friendly tools to facilitate the formatting and publishing of DNA metabarcoding data in particular.

The Metabarcoding Data Toolkit (MDT) was developed to address this need.

The GBIF Metabarcoding Data Programme

In October 2024, GBIF launched a pilot phase for the Metabarcoding Data programme, intended to improve GBIF’s integration of DNA metabarcoding data on biodiversity. The pilot programme is open to GBIF node managers who wish to manage an instance of the MDT. Participating nodes are provided a hosted installation of the MDT. An MDT can be configured to operate in one of two modes:

  • Publishing mode: MDT users can register datasets for publication through GBIF through the organizations to which they’re associated. This mode functions similarly to an installation of GBIF’s [ipt].

  • Conversion-only mode: MDT users can use it to reshape their dataset into a GBIF-ready [dwc-a] but must download them for hosting and publication on another repository, such as an IPT.

Apply to manage an MDT in the pilot programme (GBIF node managers only).

Target audiences and scope

This user guide is for anyone interested in learning to use the MDT for formatting and publishing DNA metabarcoding data to GBIF (or OBIS, etc.).

What the Metabarcoding Data Toolkit can do:

  • Handle DNA metabarcoding datasets – specifically OTU tables and their associated metadata.

  • Accept dataset uploads in a few supported template formats.

What the MDT cannot do:

  • Bioinformatic processing/analysis of raw sequencing data (Fastq files, etc.). Use dedicated bioinformatic tools and pipelines for that (dada2, Qiime2, Vsearch, Usearch, etc.).

  • Handle DNA metagenomic dataset (e.g., shotgun sequencing) -

  • Handle other DNA-associated biodiversity data types (e.g., specimen barcodes, qPCR).

Getting started

If you already know about DNA metabarcoding data and/or just want to learn the basics of using the MDT:

If you already know the basics of the MDT and want to prepare your own dataset:

More context about MDT and DNA-derived data in GBIF:

Selected learning resources on eDNA and DNA metabarcoding (videos, podcasts):

  • How we can detect pretty much anything - Hélène Morlon and Anna Papadopoulou - TED-Ed. (video)

  • Biomonitoring using eDNA (environmental DNA) - Henrik’s Lab. (video)

  • What is Environmental DNA (eDNA)? – Illumina AMEA. (video)

  • Environmental DNA - World Wildlife Fund. (video)

  • Environmental DNA - Towards Next-Generation Biomonitoring - LeeseLab. (video)

  • What is Environmental DNA (eDNA) and How Can it Help? - A Conversation with Dr Shaun Wilkinson – Dr Adam Forbes. (podcast)

Essential terms

Quick reference to essential terms for new users. Links to [glossary].