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’s already in OBIS.

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.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: April 22-23, 2024. Add to your Google Calendar.

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

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Schedule

Times are in EDT.

Overview recordings of each lesson can be found in this playlist.

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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.

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.

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

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

• Two monitors: If you have two monitors, plan to have the tool you are learning 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) to follow along with the tool you will be learning about.
• Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) 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.