GBIF North America eDNA Publishing Workshop
OBIS-USA, IOOS, Hakai, CIOOS, MBON, OTN, OBIS, Caribbean-OBIS, OBIS-Chile
Online
April 22-23, 2024
13:00 - 17:00 EDT
Instructors: Chandra Earl, Steve Formel
Helpers: TBD
General Information
The GBIF-NA DNA Publishing Workshop is designed for researchers and collection managers looking to publish DNA-derived data using established biodiversity data standards. This workshop will introduce key data standards, tools, and workflows for sharing environmental and specimen-derived DNA data through the biodiversity data aggregator GBIF.
Participants will gain hands-on experience with data mapping in IPT, learn how to enable DNA extensions, and explore the GBIF Metabarcoding Data Toolkit (MDT). This is not a beginner’s workshop—attendees should have their own data and a basic understanding of biodiversity informatics.
For background on best practices in publishing DNA data, we recommend reading “Publishing DNA-derived data through biodiversity data platforms”.
Who: This workshop is designed for collection managers and researchers who are already familiar with DNA science but need guidance on publishing DNA-derived data using community standards. Participants should be aware of the Integrated Publishing Toolkit (IPT) and have their own dataset to work with, though a standard dataset will also be provided for examples. This is not a beginner’s workshop—attendees should have a working knowledge of DNA barcoding, environmental DNA (eDNA), or related molecular techniques but may be unfamiliar with data standards such as MIxS, DwC, and MDT.
Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
When: Friday May 9, 2025; 10:00am - 4:00pm CST Add to your Google Calendar.
Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).
Contact: Please email sformel@usgs.gov or chandra.earl@asu.edu for more information.
Schedule
Before starting Pre-workshop survey 10:00 - 12:00 PM CT Introduction to DNA Data Review of key literature and standards (MIxS, DwC, MDT, NCBI, iBOL) Overview of DNA data types and publishing challenges Introduction to example datasets 12:00 - 12:10 PM CT Break 12:10 - 2:30 PM CT Deep Dive into Data Standards & Modeling Introduction to Darwin Core (DwC) DNA extension Exploring real-world datasets and metadata structures Conceptual modeling of participant datasets 2:30 - 2:45 PM CT Break 2:45 - 4:00 PM CT Publishing DNA Data Demo: Using IPT to publish data with the DNA extension Demo: Using the Metabarcoding Data Toolkit (MDT) for DNA data 4:00 - 4:15 PM CT Post-workshop survey 4:15 PM CT End of Workshop
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introduction to DNA Data |
Where do DNA data come from? What do the look like? ::: |
| Duration: 02h 04m | 2. Example Datasets | How do you write a lesson using R Markdown and sandpaper? |
| Duration: 02h 16m | 3. The MDT | How do you write a lesson using R Markdown and sandpaper? |
| Duration: 02h 28m | 4. Suggested Reading and References |
How can I learn more? ::: |
| Duration: 02h 38m | 5. Introduction to DwC DNA extension | How do you write a lesson using R Markdown and sandpaper? |
| Duration: 02h 50m | 6. Conceptual modeling of datasets | How do you write a lesson using R Markdown and sandpaper? |
| Duration: 03h 02m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
The learners should have a GBIF account, and access to the Test IPT and MDT installations.
Account Setup
If you don’t have accounts, instructions to create them are below.
Data Sets
Download the data zip file and unzip it to your Desktop