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Summarize an XML record from pubmed.

Source: R/parse_pubmed_xml.r
parse_pubmed_xml.Rd

Note: this function assumes all records are of the type "PubmedArticle" and will return an empty record for any other type (including books).

Usage

parse_pubmed_xml(record)

Arguments

record

Either and XMLInternalDocument or character the record to be parsed ( expected to come from entrez_fetch)

Value

Either a single pubmed_record object, or a list of several

Examples

# \donttest{
hox_paper <- entrez_search(db="pubmed", term="10.1038/nature08789[doi]")
hox_rel <- entrez_link(db="pubmed", dbfrom="pubmed", id=hox_paper$ids)
recs <- entrez_fetch(db="pubmed", 
                       id=hox_rel$links$pubmed_pubmed[1:3], 
                       rettype="xml")
#> Error: HTTP failure: 400
#> <?xml version="1.0" encoding="UTF-8" ?>
#> <!DOCTYPE eEfetchResult PUBLIC "-//NLM//DTD efetch 20131226//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20131226/efetch.dtd">
#> <eFetchResult>
#> 	<ERROR> Error: External viewer error: Empty Response. Bytes read: 0 Status: Timeout</ERROR>
#> </eFetchResult>
parse_pubmed_xml(recs)
#> Error: object 'recs' not found
# }