Marine Biological Data Mobilization Workshop 2025
OBIS-USA, IOOS, Hakai, CIOOS, MBON, OTN, OBIS Secretariat, Caribbean-OBIS, OBIS-Chile
Online
November 4-6, 2025
13:00 - 17:00 EDT
Instructors: Mathew Biddle, Laura Brenskelle, Steve Formel, Elizabeth Lawrence, Tylar Murray, Carolina Peralta, Jonathan Pye, Tim van der Stap
Helpers: Pedro Pablo Aros, Caitlin Bate, Nicolás Bralic, Bruce Delo, Angela Dini, Braulio Fernandez, Pamela Fierro, Ignacio Ibanez, Brian Jones, Shannon Landovskis, YingHuan Niu, Kyla Richards, Joxmer Scott-Frias
General Information
This workshop is intended to be a small hands-on, interactive virtual workshop focused on mobilizing marine biological observation datasets to the Ocean Biodiversity Information System (OBIS) by helping data providers standardize their data using Darwin Core including species observations from any type of sampling methodologies (e.g. visual surveys, net tows, microscopy, fish trawls, imaging, ’omics, acoustics, telemetry).
What this workshop will cover:
- Darwin Core and the required terms for OBIS and GBIF.
- Typical data cleaning tasks needed to standardize the data.
- Getting your data into a final Darwin Core format.
- Common QA/QC steps, data enhancement, and validation tools.
- Help you improve your understanding of controlled vocabulary.
- Required metadata information.
- How to get your data into the Integrated Publishing Toolkit.
- Tools that will help in all of the above processes.
The goal is that by the end of the workshop you will have a dataset in a final standardized state and shared to OBIS. We are hoping to address some of the blockers that you identified, including: lack of time, training, and specific formatting questions.
We have a short time together therefore our focus will be hands-on work in breakout rooms using the dataset you bring to the workshop. We will not have many presentations and they will be relatively short. Instead we will have large portions of time for you to work on your data and ask questions when you hit a stumbling block. Therefore, if you do not have a dataset to work on you may not find this workshop a good use of your time.
What this workshop will not cover:
- What is OBIS?
- Rationale for sharing data with OBIS.
- Using data that is already in OBIS.
- Data analysis.
- Use of programs or software.
If you would like to learn more about OBIS and a short rationale for sharing data to it, please watch this two minute video and this two minute video and share them with those you want to work with to share data.
When: November 4-6, 2025
Requirements:
- Must have a dataset to work on.
- Must have some R or Python experience.
- Must have a basic knowledge of GitHub.
- Participants must have the software they wish to use for data standardization installed (e.g., R and RStudio, Python, or Excel software).
Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.
Contact: Please contact us via email or Slack if you have any questions.
Schedule
Times are in EST.
The videos created for the Marine Biological Data Mobilization Workshop can be found in this playlist.
November 4
| 13:00 | Welcome and Housekeeping |
|---|---|
| 13:10 | Introduction to Darwin Core |
| 13:30 | Breakout Rooms |
| 14:30 | Social Break |
| 15:00 | Data Cleaning and Taxon Matching |
| 15:10 | Breakout Rooms |
| 16:30 | Return to Main Room |
| 17:00 | Finish |
Software Setup
To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.
Install the videoconferencing client
If you haven’t used Zoom before, go to the official website to download and install the Zoom client for your computer.
Set up your workspace
This workshop is hands-on with minimal presentations. You will likely need to have both the window for your dataset, the tool you will use to standardize it (a terminal, RStudio, spreadsheet software, etc..), and the window for the Zoom video conference client open. In order to see all at once, we recommend using one of the following set up options:
- Two monitors: If you have two monitors, plan to have your dataset and the tool you will use up on one monitor and the video conferencing software on the other.
- Two devices: If you don’t have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) for your data.
- Divide your screen: If you only have one device and one screen, practice having two windows (e.g. the video conference program and your dataset) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.
This blog post includes detailed information on how to set up your screen to follow along during the workshop.