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Entrez Direct: E-utilities on the UNIX command line

ncbi.nlm.nih.govsite

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Bioinformatics
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2026-10-10
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  1. NCBI E-utilities ncbi.nlm.nih.gov
    site category #computational-biology link ↗

    Unified APIs for accessing NCBI databases (Gene, GEO, SRA, PubChem, etc).

  2. rentrez github.com
    tool category #bioie link ↗

    R utilities for accessing NCBI resources, including PubMed.

  3. PubMed E-utilities (esearch/efetch) nlm.nih.gov
    site category #computational-biology link ↗

    APIs for searching and retrieving biomedical literature from PubMed.

  4. A New Online Computational Biology Curriculum doi.org
    site category #bioinformatics link ↗
  5. D-GENIES dgenies.toulouse.inra.fr
    site category #bioinformatics link ↗
  6. COMBINE combine.org.au
    site category #bioinformatics link ↗

Bioinformatics › Database Access: “UNIX command line tools to access NCBI's databases programmatically. Instructions to install and examples are found in the link.”