The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

puremoe

PubMed Unified REtrieval for Multi-Output Exploration. An R package that provides a single interface for accessing a range of NLM/PubMed databases, including:

This unified interface simplifies the data retrieval process, allowing users to interact with multiple PubMed services/APIs/output formats through a single R function.

The package also includes MeSH thesaurus resources as simple data frames, including Descriptor Terms, Descriptor Tree Structures, and Supplementary Concept Terms. Via the mesh-resources library.

Installation

Get the released version from CRAN:

install.packages('puremoe')

Or the development version from GitHub with:

remotes::install_github("jaytimm/puremoe")

Usage

The package has two basic functions: search_pubmed and get_records. The former fetches PMIDs from the PubMed API based on user search; the latter scrapes PMID records from a user-specified PubMed endpoint – pubmed_abstracts, pubmed_affiliations, pubtations, icites, or pmc_fulltext.

Search syntax is the same as that implemented in standard PubMed search.

pmids <- puremoe::search_pubmed('("political ideology"[TiAb])',
                                 use_pub_years = F)

# pmids <- puremoe::search_pubmed('immunity', 
#                                  use_pub_years = T,
#                                  start_year = 2022,
#                                  end_year = 2024)

Get record-level data

pubmed <- pmids |> 
  puremoe::get_records(endpoint = 'pubmed_abstracts', 
                       cores = 3, 
                       sleep = 1) 

affiliations <- pmids |> 
  puremoe::get_records(endpoint = 'pubmed_affiliations', 
                       cores = 1, 
                       sleep = 0.5)

icites <- pmids |>
  puremoe::get_records(endpoint = 'icites',
                       cores = 3,
                       sleep = 0.25)

pubtations <- pmids |> 
  puremoe::get_records(endpoint = 'pubtations',
                       cores = 2)

# For PMC full text, first convert PMIDs to PMC IDs
pmc_ids <- puremoe::pmid_to_pmc(pmids, sleep = 0.5)
pmc_fulltext <- pmc_ids$url[!is.na(pmc_ids$url)] |> 
  puremoe::get_records(endpoint = 'pmc_fulltext', 
                       cores = 1, 
                       sleep = 1)

For the pmc_fulltext endpoint, first use pmid_to_pmc() to convert PMIDs to PMC IDs and full URLs, then pass the url column to get_records().

Summary

Output Colname Description
pubmed_abstracts pmid PMID
pubmed_abstracts year Publication year
pubmed_abstracts journal Journal name
pubmed_abstracts articletitle Article title
pubmed_abstracts abstract Article abstract
pubmed_abstracts annotations Mesh/Chem/Keywords annotations
pubmed_affiliations pmid PMID
pubmed_affiliations Author Author name
pubmed_affiliations affiliation Author affiliation
pubtations pmid PMID
pubtations tiab Title or abstract
pubtations id Entity ID
pubtations entity Extracted entity
pubtations identifier Knowledge base link (KB link)
pubtations type Entity type
pubtations start Start position (char)
pubtations end End position (char)
pmc_fulltext pmid PMID
pmc_fulltext section Full text section
pmc_fulltext text Full text content
icites pmid PMID
icites is_research_article Research article indicator
icites nih_percentile NIH percentile rank
icites is_clinical Clinical article indicator
icites citation_count Citation count
icites ref_count Reference count
icites citation_net Citation network (to/from edgelist)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.