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Fetch NCBI BioSample and BioProject metadata for project samples

Source: R/ncbi_db.R
fetch_ncbi.Rd

Looks up each sample's NCBI BioSample, directly or through an SRA accession (SRR/ERR/DRR run, SRX experiment, or SRS sample), plus the BioProject(s) it belongs to, and stores everything in the project database for viewing in the app and use at export. The NCBI API key comes from the project's .config file (ncbi_api_key), the NCBI_API_KEY environment variable, or ENTREZ_KEY.

Usage

fetch_ncbi(path = ".", ids = NULL, ncbi_ids = NULL, link_sources = NULL)

Arguments

path

Path to the project directory (default = current working directory)

ids

Sample IDs to fetch. Default: every sample with a BioSample value.

ncbi_ids

Optional BioSample or SRA accessions to set for ids first (same length as ids). A blank value removes that sample's BioSample and its NCBI data.

Follow links to GEOME, GBIF, or NCBI records named in the fetched records, filling in IDs a sample does not have yet. NULL (default) uses the project setting.

Value

Invisibly, a data frame of ID, status, and message.