Intro to APIs: Case study to match taxonomic names in Python

Woods Hole Oceanographic Institution


October 26, 2021

8:30 - 12:30 EST

Instructors: Amber York

Helpers: Karen Soenen, Stace Beaulieu, Andrew Reed, Brett Longworth, Ariel Vardi-Chouchana

Learn about APIs to tap into data sources!

Do you want to learn how to pull from existing data sources to accelerate your own research and development? Let's learn how to do that with APIs. We will de-mystify terms commonly thrown around with APIs like REST and cover practical examples of interacting with APIs.

This is a 4 hour workshop tailored to the ocean sciences. We will cover that basics of what APIs are, common types you will encounter, and how to use these communication tools to pull from data sources. We will learn how to use APIs to make requests, get responses in a variety of ways (web browser, command line, programs (e.g. python).

General Information

The need for general coding skills as well as domain-specific training in programming skills to accomplish scientific and engineering goals permeates all departments and levels at WHOI. These skills are often learned on the job in a self-directed way. Formal training in modern coding and reproducible data science is a more efficient way to learn, leads to code adhering to best practices for readability and reproducibility, and most importantly, leads to a community of practice of scientific programming that reinforces these ideas and methods. WHOI also has a need for domain-specific training in programming skills.

The Ocean Informatics Work Group strives to obtain such data community at WHOI and encourages the community to help one another and to apply what they have learned to their own research problems. The workshop is sponsored by a DDVPR Technical Staff Training Award

For more information on upcoming events on data and workshops see the Ocean Informatics Working Group events logs.

Who: This workshop is targeted towards the technical WHOI staff in order to improve project efficiency and build technical skills. It will only be held for 20 people at a time through an online Zoom meeting. There is no need to have background in API's or python, however some basic python understanding is necessary to get the most out of the usecase (Using an API in python to match taxonomic names).

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

When: October 26, 2021. Add to your Google Calendar.


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 or for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

How to register?: Please register using the following link.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Below you can find the workshop outline. Please go to the the lesson landing page for an interactive page of the whole workshop.

Workshop Outline

08:30 Intro to APIs
9:15 Morning break
9:30 How can I use an API?
11:00 Afternoon break
11:30 Working in Python Taxa name matching and ERDDAP
12:00 Usecase: Taxa name matching
12:15 Wrap-up
12:30 END


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:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

Please check the "Setup" page of [the lesson site]() for instructions to follow to obtain the software and data you will need to follow the lesson.