Accessing NCBI Biology Resources Using EDirect for Command Line Novices
This workshop concluded on July 18, 2023. The workshop materials are available here, and the video recording will also be made available here about two weeks after the event: https://www.nlm.nih.gov/ncbi/workshops/2023-07_intro-to-edirect/workshop-details.html
This workshop is for life scientists, including educators and research students, who would like to learn to use the command line for searching and fetching NCBI data. 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 biological data from several NCBI databases. You do not need to have had prior experience with the command line, but we do recommend that you have some familiarity with NCBI databases get the most of this workshop.
In this workshop you will learn how to:
- Write Bash commands with parameters
- Construct search queries using NCBI’s EDirect to search in a specific database
- Download selected data in chosen file formats
- Link to related data in another database
- Combine commands into reproducible workflows
Note: This workshop is appropriate for both student researchers themselves as well as educators and mentors who want to help their students learn to use these resources.