How to: Download a large, custom set of records from NCBI

Starting with...

A TEXT QUERY (and I prefer to download them using a web browser)

  1. Use the text query to retrieve the records from the appropriate Entrez database. For guidance on creating an Entrez text query, see the Entrez Help or help documents linked to the home page of the Entrez database that contains the data you want.
  2. If desired, change the display format using the Display pulldown menu.
  3. Choose File from the "Send to" menu, then select the desired format and click "Create File."

A TEXT QUERY (and I prefer to download them using a computer program or script)

  1. Use the esearch and efetch Entrez Programming Utilities E-utilities.
  2. See Application 3 in the E-utilities Practical Guide for instructions.

A SET OF UNIQUE IDENTIFIERS (and I prefer to download them using a web browser)

  1. Create a plain text file containing each identifier on a separate line.
  2. Upload this file using Batch Entrez. Click the Browse button to search for your file or enter the full path of the file name in the input box. Be sure to set the database pulldown menu to the correct database.
  3. If desired, change the display format using the Display pulldown menu.
  4. Choose File from the "Send to" menu, then select the desired format and click "Create File."

A SET OF UNIQUE IDENTIFIERS (and I prefer to download them using a computer program or script)

  1. Use the epost and efetch Entrez Programming Utilities E-utilities.
  2. See the "epost->esummary/efetch" example under "Basic Pipelines" in the E-utilities Practical Guide.
  3. See Application 3 in the E-utilities Practical Guide for instructions on using efetch.
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