Elements are parsed according to the MEDLINE®PubMed® XML Element
Descriptions and their Attributes
here.
These functions should not normally be called directly, as they are called by
modifyPubmedDb().
Usage
parsePmidStatus(rawXml, filename, con = NULL, tableSuffix = NULL)
parseArticleId(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseArticle(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parsePubHistory(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseJournal(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parsePubType(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseMesh(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseKeyword(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseGrant(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseChemical(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseDataBank(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseComment(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseAbstract(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseOther(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseAuthor(pmXml, dPmid, con = NULL, tableSuffix = NULL)
parseInvestigator(pmXml, dPmid, con = NULL, tableSuffix = NULL)Arguments
- rawXml
An xml document obtained by loading a PubMed XML file using
xml2::read_xml().- filename
A string that will be added to a column
xml_filename.- con
Connection to the database, created using
DBI::dbConnect().- tableSuffix
String to append to the table names.
- pmXml
An xml nodeset derived from
rawXml, such as that returned byparsePmidStatus(), where each node corresponds to a PMID.- dPmid
A data.table with one row for each node of
pmXml, should have columnspmid,version, and possiblyxml_filename.
Value
parsePmidStatus() returns a list of two objects. The first is an
xml nodeset in which each node corresponds to a PubmedArticle in the
rawXml object. The second is a data.table with columns pmid, version,
xml_filename, and status, in which each row corresponds to a
PubmedArticle in the rawXml object or a deleted pmid. The status column
is parsed from the DeleteCitation and MedlineCitation sections.
The following functions return a data.table or list of data.tables with
columns from dPmid plus the columns specified.
parseArticleId(): a data.table with columns id_type and id_value,
parsed from the ArticleIdList section. Only id_types "doi"
and "pmc" are retained.
parseArticle(): a data.table with columns title, language,
vernacular_title, pub_model, and pub_date, parsed from the Article
section.
parsePubHistory(): a data.table with columns pub_status and pub_date,
parsed from the History section.
parseJournal(): a data.table with columns journal_name, journal_iso,
pub_date, pub_year, pub_month, pub_day, medline_date, volume,
issue, and cited_medium, parsed from the Journal section.
parsePubType(): a data.table with columns type_name and type_id,
parsed from the PublicationTypeList section.
parseMesh(): a list of three data.tables parsed mostly from the
MeshHeadingList section. The first has column indexing_method (parsed
from the MedlineCitation section), the second has columns descriptor_pos,
descriptor_name, descriptor_ui, and descriptor_major_topic, the
third has columns descriptor_pos, qualifier_name, qualifier_ui, and
qualifier_major_topic.
parseKeyword(): a list of two data.tables parsed from the KeywordList
section. The first has column list_owner, the second has columns
keyword_name and major_topic.
parseGrant(): a list of two data.tables parsed from the GrantList
section. The first has column complete, the second has columns
grant_id, acronym, agency, and country.
parseChemical(): a data.table with columns registry_number,
substance_name, and substance_ui, parsed from the ChemicalList section.
parseDataBank(): a data.table with columns data_bank_name and
accession_number, parsed from the DataBankList section.
parseComment(): a data.table with columns ref_type and ref_pmid,
parsed from the CommentsCorrectionsList section.
parseAbstract(): a list of two data.tables parsed from the Abstract
section. The first has column copyright. The second has columns text,
label, and nlm_category.
parseAuthor(): a list of data.tables parsed from the AuthorList section.
The first is for authors and has columns author_pos, last_name,
fore_name, initials, suffix, valid, equal_contrib, and
collective_name. The second is for affiliations and has columns
author_pos, affiliation_pos, and affiliation. The third is for author
identifiers and has columns author_pos, source, and identifier. The
fourth is for author affiliation identifiers and has columns author_pos,
affiliation_pos, source, and identifier. The fifth is for the author
list itself and has a column complete.
parseInvestigator(): a list of data.tables similar to those returned by
parseAuthor(), except parsed from the InvestigatorList section, with
column names containing "investigator" instead of "author", and where the
first data.table lacks columns for equal_contrib and collective_name
and the fifth data.table does not exist.
parseOther(): a list of data.tables parsed from the OtherAbstract and
OtherID sections. The first has columns text, type, and language. The
second has columns source and id_value.
Examples
library('data.table')
library('xml2')
filename = 'pubmed20n1016.xml.gz'
rawXml = read_xml(system.file('extdata', filename, package = 'pmparser'))
pmidStatusList = parsePmidStatus(rawXml, filename)
pmXml = pmidStatusList[[1L]]
dPmidRaw = pmidStatusList[[2L]]
dPmid = dPmidRaw[status != 'Deleted', !'status']
dArticleId = parseArticleId(pmXml, dPmid)
dArticle = parseArticle(pmXml, dPmid)
dJournal = parseJournal(pmXml, dPmid)
dPubType = parsePubType(pmXml, dPmid)
dPubHistory = parsePubHistory(pmXml, dPmid)
meshRes = parseMesh(pmXml, dPmid)
keywordRes = parseKeyword(pmXml, dPmid)
grantRes = parseGrant(pmXml, dPmid)
dChemical = parseChemical(pmXml, dPmid)
dDataBank = parseDataBank(pmXml, dPmid)
dComment = parseComment(pmXml, dPmid)
abstractRes = parseAbstract(pmXml, dPmid)
authorRes = parseAuthor(pmXml, dPmid)
investigatorRes = parseInvestigator(pmXml, dPmid)
otherRes = parseOther(pmXml, dPmid)