An Introduction to Accessing NCBI Resources on the Command Line using EDirect for Biologists
NCBI Faculty: E. Sally Chang, PhD
Workshop Duration: 2 hours
Content Difficulty: Beginner
Target Audience:
Workshop Description:
In this workshop, we will begin with an introduction to working in a command line environment and then show you how to use the EDirect suite to access data programmatically from several NCBI databases.
In this workshop you will learn how to:
- Write Bash commands with parameters
- Download and store data files in an organized directory structure
- Construct search queries using NCBI’s EDirect to search in a specific database, link to related data in another database, and download selected information.
- Chain together multiple command line calls in a reusable workflow which can quickly and reproducibly access the latest information.
Data Access Technology: Jupyter Notebook, Command-line
NCBI Resources: Entrez Direct (EDirect)
Last Reviewed: March 15, 2023