EUtilsGet: Results of an NCBI EUtils query

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/EUtils.R

Description

Download results of a query for any database of the National Center for Biotechnology Information (NCBI).

Usage

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EUtilsGet(x,type="efetch",db="pubmed")

Arguments

x

Either vector of NCBI records ids, i.e. returned ids from EUtilsSummary, or the EUtilsSummary object itself

type

string indicating type of NCBI Eutility, efetch, esummary, etc.

db

string indicating the NCBI database used in query

Details

Possible E-utilities to supply to type are efetch, esummary, and elink.

The database name supplied to db can be any valid Entrez database, such as pubmed, protein, nlm, etc.

For further details on available E-utilities and databases visit http://www.ncbi.nlm.nih.gov/books/NBK25499/.

Note on usage:

In order not to overload the E-utility servers, NCBI recommends that users post no more than three URL requests per second and limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays. Failure to comply with this policy may result in an IP address being blocked from accessing NCBI.

Value

For queries to PubMed, a list by article, with named vectors for each field of the article result.

For all other database, a vector with each element name the field returned from XML output.

Author(s)

Stephanie Kovalchik [email protected]

References

Summary help:

http://www.ncbi.nlm.nih.gov/books/NBK3827/

MEDLINE/PubMed Field Descriptions

http://www.nlm.nih.gov/bsd/mms/medlineelements.html

See Also

EUtilsSummary

Examples

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# PUBMED QUERY FOR MYELOMA ARTICLES FOR LAST YEAR
res <- EUtilsSummary("myeloma[ti]",retmax=2,reldate=365)

summary(res)

fetch <- EUtilsGet(res)

# PUBMED RETURNS A MEDLINE OBJECT
fetch

PMID(fetch)

Author(fetch)[[1]]

RISmed documentation built on June 6, 2017, 5:03 p.m.