MBON+USF+Moore BioData Mobilization Workshop

University of South Florida

15-17 June 2026

08:30-17:00

Instructors: Carolina Peralta, Tylar Murray, Cara Estes

Helpers:

General Information

workshop logo image

The University of South Florida (USF), Moore Marine College, and the Marine Biodiversity Observation Network (MBON) will host a small, hands-on, interactive workshop focused on mobilizing marine biological observation datasets to the Ocean Biodiversity Information System (OBIS). The objective is to help data holders understand the value of following good practices for standardizing biological data, using widely accepted biodiversity standards like Darwin Core. This would include records of different biological attributes and ecosystem observations from different types of sampling methodologies.

By the end of the workshop, attendees will have a clear understanding of the process of mobilizing biological data to OBIS and will have brought one of their datasets to a final maturity state that aligns with best practices for data sharing and biodiversity documentation. The workshop will also enhance awareness of improving the quality of marine biodiversity data and will increase the availability of marine biological data for scientific research, species conservation, and ecosystem-based management by promoting data publication through OBIS. Additionally, the workshop will foster collaborative research efforts among participants and contribute to the MBON community of practice by increasing capacity in the implementation of coordinated and standardized biodiversity observing and publishing efforts.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: STG 115, University of South Florida St Petersburg. Get directions with OpenStreetMap or Google Maps.

When: 15-17 June 2026; 08:30-17:00 Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. Participants are expected to have familiarity with:

  • Working with taxonomic occurrence data
  • Using spreadsheet tools (e.g., Excel, LibreOffice, Google Sheets).
  • File handling & different file formats (Working with CSV, TXT, and Excel formats).
  • Basic Python or R programming.
  • Basic data wrangling skills for marine biodiversity data management (e.g., data structuring).
    • Familiarity with a few specific software packages are recommended (listed below).

    Contact: Please email peraltabrichtova@usf.edu for more information.

    Please report any issues or feedback here.

    Schedule

    Reference materials for each section are linked in the schedule below.

    Day 1

    Before starting Complete Setup (see below)
    08:30 Welcome and Opening of the workshop
  • [OBIS Data life cycle video]
  • [Workshop Slides]
  • [Moore Marine Overview]
    		•
    10:30 COFFEE BREAK
    11:00 Data Access from OBIS
  • [OBIS data from the Mapper and Portal]
  • [OBIS data with R]
  • [the OBIS API]
  • [OBIS Manual on Access]
  • [OBIS Manual on IPT]
    		•
    12:30 LUNCH
    13:30 About Your Data
  • [Creating a New GitHub Repository]
    • 14:30 Data Access Coding With AI & Colab
  • [CoLab Notebook Examples]
    • 15:30 COFFEE BREAK
    16:00 OBIS Data standards and formatting
  • [OBIS Manual DwC]
  • [Intro DwC: More Than The Sum Of Its Parts]
    		•
    17:30 Adjourn

    Day 2

    08:30 OBIS standards, formatting, & quality control
  • [Day 2 Slide Deck]
  • [DwC Example Template]
  • [What are the Aphia, LSIDs? - paper]
  • [Open Taxonomic nomenclature (for uncertain taxa) ]
    		•
    10:30 COFFEE BREAK
    11:00 Dataset curation and processing
  • [OBIS Manual on QC]
  • [OBIS Manual on GeoSpatial QC]
    		•
    12:30 LUNCH
    13:30 Dataset curation and processing
  • [DwC Occurrence Table]
  • [DwC Event Table]
  • [DwC Measurment or Facts]
    		•
    15:30 COFFEE BREAK
    16:00 Dataset curation and processing
  • [WoRMS ID Taxon Match Tool]
  • [WoRMS ID Ambiguity]
  • [WoRMS ID Synonyms]
  • [QC Checks with R]
  • [OBIS Manual on eDNA
  • [OBIS & eDNA (video)]
  • [OBIS Manual on eDNA]
  • [Latest Archive Structure Proposal]
    		•
    17:30 Adjourn

    Day 3

    08:30 Dataset curation and processing
  • [Day 3 Slide Deck]
    		•
    10:30 COFFEE BREAK
    11:00 Before publishing your data in OBIS
  • [OBIS Manual on Publication]
  • [OBIS Manual on IPT]
  • [Intro to OBIS Nodes]
    		•
    12:30 LUNCH
    13:30 Publishing your data in OBIS
    16:00 CONCLUSIONS AND CLOSURE
    17:30 End

    Additional reference materials:

  • OBIS Manual

    • Setup

    To participate in a Software Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

    We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

    The installation steps below should be reviewed before starting the workshop. The workshop will focus on the use of Google Colab, which requires minimal software setup.

    Google Colab

    Google CoLab is a Google-specialized Jupyter notebook server. Like other JupyterHub implementations, CoLab allows you to run code on a server instead of your local machine. This allows you skip over setup on your local machine. Although other programming language kernels are available with CoLab pro, we will be using the python kernel. Common tasks that can be accomplished with CoLab and python include:

    To use Google CoLab you must have a google account. Please have a google account created before attending the workshop and ensure you can access https://colab.research.google.com

    Within Google CoLab you are able to

    The following resources provide additional documentation, tutorials, and reference material for working with Python, Jupyter notebooks, and Google Colab.

    Git

    Git is a version control system that lets you track who made changes to what when. Using git you can publish your code on a git repository hosting service like github.com. You will need a supported web browser .

    We will be using git within the Google Colab environment. Git is pre-installed on Google Colab servers, so no setup is needed. The instructions below will allow you to use git on your local machine, but for this workshop you do not necessarily need git installed on your laptop.

    You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

    Local Git Installation (optional)

    Git can be installed from the git website. Alternatively, git will be installed on your computer as part of most Bash emulator installations. If you have a Bash shell (such as MobaXTerm), you may already have git installed.

    Please open the Terminal app, type git --version and press Enter/Return. If it's not installed already, follow the instructions to Install the "command line developer tools". Do not click "Get Xcode", because that will take too long and is not necessary for our Git lesson. After installing these tools, there won't be anything in your /Applications folder, as they and Git are command line programs. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here. (Note: this project is no longer maintained.) Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open in the pop-up dialog.

    If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.