efetch

The efetch command uses the EFetch utility to download records from an NCBI database in a specified format.

Input

One or more unique identifiers (UIDs; when fetching from PubMed, PMIDs). These UIDs can be specified in the -id argument (see below), or can be retrieved from the History server.

Output

One or more records displayed in a chosen format:

• A list of UIDs (i.e. PMIDs).
• Abstract view, formatted in plain text.
• MEDLINE view, including the field indicators.
• The full XML of the record.

Arguments

The efetch command allows the following arguments:

• -db: The database from which you wish to retrieve records.
  • Example: -db pubmed
• -id: One or more UIDs (PMIDs, if your -db argument is pubmed), separated by commas.
  • Example: -id 24102982,21171099,17150207
  • Example: -id 26287646
• -format: Specifies the format in which you wish to display the records.
  • For PubMed, the valid formats include:
    • uid: displays a list of UIDs (i.e. PMIDs).
    • abstract: displays the Abstract view, formatted in plain text.
    • medline: displays the MEDLINE view, including the field indicators.
    • xml: displays the full PubMed XML.
  • Example: -format uid
  • Example: -format xml

Examples:

Retrieve the record for PMID 25359968 in MEDLINE format:

efetch -db pubmed -id 25359968 -format medline

Retrieve the record for PMID 26287646 in XML format:

efetch -db pubmed -id 26287646 -format xml

Retrieve the records for PMIDs 24102982, 21171099, and 17150207 in abstract view:

efetch -db pubmed -id 24102982,21171099,17150207 -format abstract