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Entrez Programming Utilities Help Entrez Programming Utilities Help Last Updated: February 8, 2021 National Center for Biotechnology Information (US) Bethesda (MD) National Center for Biotechnology Information (US), Bethesda (MD) NLM Citation: Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-. iii • E-utilities Introduction • Please see the Release Notes for details and changes. The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL syntax that translates a standard set of input parameters into the values necessary for various NCBI software components to search for and retrieve the requested data. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three- dimensional molecular structures, and the biomedical literature. iv Entrez Programming Utilities Help Table of Contents E-utilities Quick Start..................................................................................................................................................................................... 1 Release Notes........................................................................................................................................................................................................ 1 Announcement...................................................................................................................................................................................................... 1 Introduction............................................................................................................................................................................................................ 1 Searching a Database ........................................................................................................................................................................................ 1 Uploading UIDs to Entrez................................................................................................................................................................................... 3 Downloading Document Summaries................................................................................................................................................................ 4 Downloading Full Records ................................................................................................................................................................................. 7 Finding Related Data Through Entrez Links.................................................................................................................................................... 8 Getting Database Statistics and Search Fields .............................................................................................................................................. 9 Performing a Global Entrez Search................................................................................................................................................................. 10 Retrieving Spelling Suggestions ........................................................................................................................................................................ 11 Demonstration Programs.................................................................................................................................................................................... 12 For More Information .......................................................................................................................................................................................... 16 A General Introduction to the E-utilities............................................................................................................................................ 17 Introduction............................................................................................................................................................................................................ 17 Usage Guidelines and Requirements............................................................................................................................................................... 17 The Nine E-utilities in Brief................................................................................................................................................................................. 19 Understanding the E-utilities Within Entrez.................................................................................................................................................... 20 Combining E-utility Calls to Create Entrez Applications ............................................................................................................................. 24 Demonstration Programs.................................................................................................................................................................................... 25 For More Information .......................................................................................................................................................................................... 25 Sample Applications of the E-utilities ................................................................................................................................................. 27 Introduction............................................................................................................................................................................................................ 27 Basic Pipelines....................................................................................................................................................................................................... 27 ESearch – ESummary/EFetch............................................................................................................................................................................ 27 EPost – ESummary/EFetch ................................................................................................................................................................................. 28 ELink – ESummary/Efetch .................................................................................................................................................................................. 29 ESearch – ELink – ESummary/EFetch.............................................................................................................................................................. 30 EPost – ELink – ESummary/EFetch................................................................................................................................................................... 31 EPost – ESearch .................................................................................................................................................................................................... 32 ELink – ESearch .................................................................................................................................................................................................... 33 Contents v Application 1: Converting GI numbers to accession numbers................................................................................................................... 33 Application 2: Converting accession numbers to data................................................................................................................................ 34 Application 3: Retrieving large datasets......................................................................................................................................................... 35 Application 4: Finding unique sets of linked records for each member of a large dataset................................................................ 35 Demonstration Programs.................................................................................................................................................................................... 37 For More Information .......................................................................................................................................................................................... 37 The E-utilities In-Depth: Parameters, Syntax and More ......................................................................................................... 39 Introduction............................................................................................................................................................................................................ 39 General Usage Guidelines................................................................................................................................................................................. 39 E-utilities DTDs .....................................................................................................................................................................................................
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