Package: pmparser 1.0.20

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_1.0.20.tar.gz
pmparser_1.0.20.zip(r-4.5)pmparser_1.0.20.zip(r-4.4)pmparser_1.0.20.zip(r-4.3)
pmparser_1.0.20.tgz(r-4.4-any)pmparser_1.0.20.tgz(r-4.3-any)
pmparser_1.0.20.tar.gz(r-4.5-noble)pmparser_1.0.20.tar.gz(r-4.4-noble)
pmparser_1.0.20.tgz(r-4.4-emscripten)pmparser_1.0.20.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

On CRAN:

5.68 score 16 stars 1 scripts 310 downloads 19 exports 17 dependencies

Last updated 10 months agofrom:fe86e9355b. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 13 2024
R-4.5-win	OK	Oct 13 2024
R-4.5-linux	OK	Oct 13 2024
R-4.4-win	OK	Oct 13 2024
R-4.4-mac	OK	Oct 13 2024
R-4.3-win	OK	Oct 13 2024
R-4.3-mac	OK	Oct 13 2024

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 Oct 13 2024.

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