Review our current and previous class offerings below:
Welcome to E-utilities for PubMed
Want to do more with PubMed?
Want to extract just the PubMed data you need, in the format you want?
Dreaming of creating your own PubMed tool or interface, but don't know where to start?
Join us for an introduction to the Insider's Guide, a program designed to teach you more powerful and flexible ways of accessing NLM data, starting with the essentials of the Application Programming Interfaces (APIs) for PubMed and other NCBI databases. The Insider's Guide is geared toward librarians and other information specialists who have experience using PubMed via the traditional Web interface, but now want to dig deeper. This class will start with the very basics of APIs, before showing you how to get started using the E-utilities API to search and retrieve records from PubMed. The class will also showcase some specific tools and utilities that information specialists can use to work with E-utilities, helping to prepare you for subsequent Insider's Guide classes. We will finish by looking at some practical examples of E-utilities in the real world, and hopefully inspire you to get out and put these lessons to use!
No upcoming offerings of this class are currently scheduled. See below for recordings of previous offerings.
Tuesday, February 13, 2018: View recording
The slides, script, sample code and links referenced in this class are available on the Class Materials page.
EDirect for PubMed
This series of interactive workshops will introduce new users to the basics of using EDirect to access exactly the PubMed data you need, in the format you need. Over the course of five 90-minute sessions (plus an optional "office hours"), students will learn how to use EDirect commands in a Unix environment to access PubMed, design custom output formats, create basic data pipelines to get data quickly and efficiently, and develop simple strategies for solving real-world PubMed data-gathering challenges. No prior Unix knowledge is required; novice users are welcome!
This series of classes involves hands-on demonstrations and exercises, as well as homework exercises between sessions. We encourage students to follow along. Before registering for these classes, we strongly recommend that you:
- Be comfortable conducting basic searches in PubMed.
- Watch the first Insider's Guide class "Welcome to E-utilities for PubMed", or be familiar with the basic concepts of APIs and E-utilities.
- Be familiar with structured XML data (basic syntax, elements, attributes, etc.)
- Have access to a Unix command-line environment on your computer (for more information, see our Installing EDirect page).
- Install the EDirect software (for more information, see our Installing EDirect page).
March 2018 series:Register Now (Note: Before you register, you will be prompted to create a free account on the NNLM website and confirm that account using an existing e-mail address.)
- Session 1: Monday, March 5
- Session 2: Thursday, March 8
- Session 3: Monday, March 12
- Session 4: Thursday, March 15
- Session 5: Monday, March 19
- Office Hours: Thursday, March 22
Each session begins at 1 PM ET and runs approximately 90 minutes. Students are expected to attend all of the first five sessions; session six is an optional 90 minute "office hours" starting at 1 PM ET for students seeking help on the final exam.
Seven (7) hours of MLA CE credit are available for students who attend the first five sessions, complete the homework assignments, and complete the open-book exam no later than Monday, March 26.
July 2017 series:
- Part 1: Getting PubMed Data (July 10, 2017)
- Part 2: Extracting Data from XML (July 13, 2017)
- Part 3: Formatting Results and Unix Tools (July 17, 2017)
- Part 4: xtract Conditional Arguments (July 20, 2017)
- Part 5: Developing and Building Scripts (July 24, 2017)
The handouts, slides, script, sample code and links referenced in each session are available on the Class Materials page.