Package: pmparser 1.0.21

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_1.0.21.tar.gz
pmparser_1.0.21.zip(r-4.5)pmparser_1.0.21.zip(r-4.4)pmparser_1.0.21.zip(r-4.3)
pmparser_1.0.21.tgz(r-4.5-any)pmparser_1.0.21.tgz(r-4.4-any)pmparser_1.0.21.tgz(r-4.3-any)
pmparser_1.0.21.tar.gz(r-4.5-noble)pmparser_1.0.21.tar.gz(r-4.4-noble)
pmparser_1.0.21.tgz(r-4.4-emscripten)pmparser_1.0.21.tgz(r-4.3-emscripten)
pmparser.pdf |pmparser.html✨
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 site:https://pmparser.hugheylab.org

On CRAN:

5.23 score 17 stars 1 scripts 447 downloads 19 exports 17 dependencies

Last updated 1 months agofrom:f12a47670e. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 13 2025
R-4.5-win	OK	Feb 13 2025
R-4.5-mac	OK	Feb 13 2025
R-4.5-linux	OK	Feb 13 2025
R-4.4-win	OK	Feb 13 2025
R-4.4-mac	OK	Feb 13 2025
R-4.3-win	OK	Feb 13 2025
R-4.3-mac	OK	Feb 13 2025

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 Feb 13 2025.

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