bio_mobilization_workshop

OBIS-USA, IOOS, Hakai, CIOOS, MBON, OTN, OBIS, Caribbean-OBIS, OBIS-Chile

Online

November 4-6, 2025

12:00 - 15:00 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.
• 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. November 6th will be an optional day to attend for Workshop Participants if they require additional help.

Requirements:

• Must have a dataset to work on.
• Must have some R or Python experience.
• Must have a basic knowledge of GitHub.
• Participants must bring a laptop with R and RStudio or Python software installed.

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 visit https://obis.org/contact/ for more information.

Schedule

Times are in EDT.

The videos created for the Marine Biological Data Mobilization Workshop can be found in this playlist.

November 4

Time	Session
12:00	Quick intro to Darwin Core. Event Core: eventIDs, cleaning date/time, lat/long
13:30	Break
15:00	Occurrence: WoRMS (API), matching names, QA/QC
17:00	Finish

November 5

Time	Session
12:00	eMOF: controlled vocab
13:30	Break
14:00	Publishing / IPT
15:00	Finish
End	Post-workshop help & survey

November 6

Time	Session
12:00	Special presentations on specific observation types
13:30	Break
14:00	Working session, Q&A
15:00	Finish

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