esummary: Entrez database summaries

In cstubben/genomes2: Genome sequencing project metadata

Description

Summaries of Entrez database records at NCBI

Usage

esummary(id, db = "pubmed", parse = TRUE, ...)

Arguments

id	An EntrezHistory object or vector of Ids
db	An Entrez database, default pubmed
parse	Parse the XML results into a data.frame
...	Other key-value pairs passed to the esummary url string

Value

A data.frame or XML results if parse=FALSE

Note

If EntrezHistory results are the input, then the database listed in that object is used. If using a vector of Ids, the database option must be included. Also, do not pass more than 200 Ids to the url (use the History or see the NCBI help pages for other suggestions).

Some records may be missing fields and then constructing a data.frame will return warnings. For example, the DOI field is missing in many Pubmed records. You can also set the version="2.0" to return the version 2.0 ESummary XML.

Author(s)

Chris Stubben

References

http://www.ncbi.nlm.nih.gov/books/NBK25499

Examples

## Not run: 
# BioC articles published in the last year
x <- esearch("bioconductor[TITLE]", reldate=360)
y <- esummary(x, version="2.0")
y[, c(1, 42, 6, 3, 8, 10)]

# Y. pestis CO92 refseqs
x <- esearch( "Yersinia pestis CO92[ORGN] AND refseq[FILTER]", "nuccore")
y <- esummary(x)
y[, c(2,3,5,10)]
# Taxonomy database
esummary(esearch("Mouse[Subtree]", db="taxonomy"))

## End(Not run)

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.