"EDirect for PubMed" Class Materials

Upcoming Offerings

See upcoming offerings and a description of this class on the Classes page.

Recordings

March 2018 series:

• Part 1: Getting PubMed Data (March 5, 2018)
• Part 2: Extracting Data from XML (March 8, 2018)
• Part 3: Formatting Results and Unix Tools (March 12, 2018)
• Part 4: xtract Conditional Arguments (March 15, 2018)
• Part 5: Developing and Building Scripts (March 19, 2018)

Class Materials

Please feel free to re-use, redistribute, or modify these class materials:

• Handouts (text)
  • Part 1: Getting PubMed Data
  • Part 2: Extracting Data from XML
  • Part 3: Formatting Results and Unix Tools
  • Part 4: xtract Conditional Arguments
  • Part 5: Developing and Building Scripts
• Sample code for class examples
  • Part 1: Getting PubMed Data
  • Part 2: Extracting Data from XML
  • Part 3: Formatting Results and Unix Tools
  • Part 4: xtract Conditional Arguments
  • Part 5: Developing and Building Scripts
• Slides (PowerPoint)
  • Part 1: Getting PubMed Data
  • Part 2: Extracting Data from XML
  • Part 3: Formatting Results and Unix Tools
  • Part 4: xtract Conditional Arguments
  • Part 5: Developing and Building Scripts
• Slides, accessible versions (PowerPoint)
  • Part 1: Getting PubMed Data
  • Part 2: Extracting Data from XML
  • Part 3: Formatting Results and Unix Tools
  • Part 4: xtract Conditional Arguments
  • Part 5: Developing and Building Scripts
• Script (MS Word)
  • Part 1: Getting PubMed Data
  • Part 2: Extracting Data from XML
  • Part 3: Formatting Results and Unix Tools
  • Part 4: xtract Conditional Arguments
  • Part 5: Developing and Building Scripts

Online Resources

The following online resources are referenced in this class:

• Installing EDirect
• Insider’s Guide: EDirect Overview
• Insider’s Guide: EDirect Documentation
• NCBI Now! Lecture 3: Basic Linux commands
• PubMed XML Data Elements
• PubMed DTD Documentation
• Using EDirect to create a local copy of PubMed
• EDirect Cookbook on GitHub
• NCBI EDirect documentation