Package: pmparser 1.0.26

Jake Hughey

pmparser: Create and Maintain a Relational Database of Data from PubMed/MEDLINE

Provides a simple interface for extracting various elements from the publicly available PubMed XML files, incorporating PubMed's regular updates, and combining the data with the NIH Open Citation Collection. See Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.

Authors:Jake Hughey [aut, cre], Josh Schoenbachler [aut], Elliot Outland [aut]

pmparser_1.0.26.tar.gz
pmparser_1.0.26.zip(r-4.7)pmparser_1.0.26.zip(r-4.6)pmparser_1.0.26.zip(r-4.5)
pmparser_1.0.26.tgz(r-4.6-any)pmparser_1.0.26.tgz(r-4.5-any)
pmparser_1.0.26.tar.gz(r-4.7-any)pmparser_1.0.26.tar.gz(r-4.6-any)
pmparser_1.0.26.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pmparser/json (API)
NEWS

# Install 'pmparser' in R:

install.packages('pmparser', repos = c('https://hugheylab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hugheylab/pmparser/issues

Pkgdown/docs site:https://pmparser.hugheylab.org

On CRAN:

5.98 score 19 stars 1 scripts 179 downloads 19 exports 17 dependencies

Last updated from:7a70bbcb64. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	205
source / vignettes	OK	193
linux-release-x86_64	OK	153
macos-release-arm64	OK	95
macos-oldrel-arm64	OK	111
windows-devel	OK	222
windows-release	OK	211
windows-oldrel	OK	205
wasm-release	OK	117

Exports:getCitation getPgParams modifyPubmedDb parseAbstract parseArticle parseArticleId parseAuthor parseChemical parseComment parseDataBank parseGrant parseInvestigator parseJournal parseKeyword parseMesh parseOther parsePmidStatus parsePubHistory parsePubType

Dependencies:bitops cli codetools curl data.table DBI foreach glue iterators jsonlite R.methodsS3 R.oo R.utils RCurl rlang withr xml2

Data Dictionary

Rendered fromdata_dictionary.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2022-04-13
Started: 2020-11-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get public-domain citation data	getCitation
Get Postgres connection parameters	getPgParams
Create or update a PubMed database	modifyPubmedDb
Parse elements from a PubMed XML file	parseAbstract parseArticle parseArticleId parseAuthor parseChemical parseComment parseDataBank parseElement parseGrant parseInvestigator parseJournal parseKeyword parseMesh parseOther parsePmidStatus parsePubHistory parsePubType