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Data Services: Workshop Series_Archived Events

Vincent Scalfani

February 3, 2021 2:00-3:30 pm on Zoom

Introduction to NCBI's EDirect Software: Learn how to programmatically search and compile PubMed and related data directly in a Unix Shell

National Center for Biotechnology Information - WikipediaThe National Center for Biotechnology Information (NCBI) offers programmatic access to biomedical literature and molecular data through their Entrez Programming Utilities (E-Utilities, https://www.ncbi.nlm.nih.gov/books/NBK25501/).

EDirect is a free software program from NCBI that provides access to E-Utilities in a Unix Shell. In my experience, EDirect has a lower learning curve than trying to develop your own custom separate shell logo ยป Vasanth Blogprogramming scripts; that is, with a basic knowledge of the Unix Shell (e.g., Bash), programmatic access to NCBI data is highly accessible to new users without prior programming experience.

This workshop will be useful to any researcher interested in accessing NCBI literature and data programmatically. Specifically, we will cover the following in this introductory workshop:

  1. Brief introduction of the Unix Shell and what you will need to know for EDirect
  2. Overview of EDirect
  3. Searching PubMed with EDirect
  4. Retrieving PubMed journal metadata in XML format, and extracting out specific information fields for bibliometric analysis
  5. Creating Unix scripts for automation of multiple EDirect searches and workflows
  6. Using EDirect to find related linked NCBI data.

Attendees that want to follow along on their own computers should download and install EDirect before the workshop. The Instructor will be using Linux, however, EDirect can be installed on Mac and Windows as well: https://www.ncbi.nlm.nih.gov/books/NBK179288/

 

About the Instructors:

Dr. Vincent F. Scalfani is an Associate Professor in the Rodgers Library for Science and Engineering at The University of Alabama. He is the information specialist for Chemistry, Chemical Engineering, and Mathematics. Before joining The University of Alabama in 2012, he studied block copolymer phase behavior and earned a Ph.D. in Chemistry from Colorado State University (2012) and a B.S. in Chemistry from SUNY Oswego (2007). His research interests include chemical information and cheminformatics.