eFetch

eFetch is a utility within the NCBI Entrez Programming Utilities (E-utilities) that retrieves records from NCBI databases. It provides programmatic access to full records or portions of records for databases such as PubMed, nucleotide, protein, and GenBank. Users can fetch individual records by their identifiers or operate on batches produced by a prior search.

The service is accessed via an HTTP GET request to the efetch.fcgi endpoint. Required parameters typically include the database (db) and the identifiers to fetch (id), or a web environment (webenv) and query key (query_key) for batch retrieval. Optional parameters control the output format: rettype selects the record format (for example, fasta, gb, or abstract), while retmode selects the output wrapper (such as xml or text). Some databases support additional rettype values tailored to their data type. When using E-utilities, it is common to supply tool and email parameters to identify the client and provide contact information in case of issues; this helps with rate limiting and support.

Common usage examples include retrieving a PubMed record in XML, or downloading a nucleotide sequence in FASTA format. Example: efetch.fcgi?db=pubmed&id=31762132&retmode=xml, and efetch.fcgi?db=nucleotide&id=NC_000852.1&rettype=fasta&retmode=text. eFetch is frequently used in scripts and pipelines, and is also accessible through libraries such as Biopython’s Entrez module for programmatic retrieval and parsing.

Overall, eFetch serves as a flexible means to obtain NCBI data in chosen formats for automated analysis and integration into computational workflows.