MBON Data Mobilization Workshop 2025

Coordinators: Casey Godwin, Connie Kot, Felimon Gayanilo, Katherine Silliman, Kathleen Pitz, Laura Brenskelle, Luke Thompson, Mathew Biddle, Ana Peralta Brichtova, Stephen Formel, Frank Muller-Karger, Daniel Otis, Tylar Murray, Michael Lonneman, Dylan Pugh

When:

08:30 - 16:30 EDT April 7th, 2025

08:30 - 11:30 EDT April 8th, 2025 Optional

Where:

Memorial Union Building
University of New Hampshire, Durham, NH 03824
3rd Level - Rooms 330-340

General Information

This workshop is intended to be a small hands-on, interactive in-person 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 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.

Requirements:

  • Must have a dataset to work on. See data setup for details on what minimum requirements your data should meet at the time of the workshop.
  • 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

All times are in EDT.

April 7

Time Activity
08:30 - 09:00 Arrival
Light continental breakfast
09:00 - 09:15 Introductions to you and your data
09:15 - 09:30 OBIS-USA IPT Introduction
09:30 - 10:30 Occurrence Core Working Session
10:30 - 10:45 Break
Coffee and tea
10:45 - 11:00 Occurrence Core + IPT Q&A / Wrap-up
11:00 - 12:00 Event Core Working Session
12:00 - 13:00 Lunch
Provided
13:00 - 13:15 Event Core Q&A / Wrap-up
13:15 - 14:30 Extensions Working Session
14:30 - 14:45 Break
Coffee and tea
14:45 - 15:00 Extensions Q&A / Wrap-up
15:00 - 16:00 Observation Method-Specific Recommendations
16:00 - 16:30 Final Q&A / Wrap-up

April 8 - optional

Note: There is no provided breakfast this morning.

Time Activity
08:30 - 11:30 Data Social Hour
Optional time for further data discussions
11:30 - 12:00 Lunch
Holloway Commons Dining Hall - ticketed
13:00 - onward MBON All Hands Meeting

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Data Setup

Before attending the workshop we ask that you have:

  1. Your “raw” data files:
    1. these are tables with your data.
    2. Data should include latitude, longitude, time, and taxonomic identification, among other things.
  2. A programming environment: Participants should be ready to run python and/or R code to transform their data. Please set up an environment in advance as troubleshooting installation can take significant time.
    1. Recommended python setup guide: link.
    2. Recommended R setup guide: link.
  3. Created a GitHub issue using this form. This helps us track datasets and document our work.

For ’Omics/eDNA data, see the NOAA Omics Data Management Guide section on Study Data Templates.