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:

• PubMed abstract records,

• iCite bibliometric data,

• PubTator3 named entity annotations, and

• full-text entries from PubMed Central (PMC).

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

Also included are MeSH thesaurus resources as simple data frames: Descriptor Terms, Descriptor Tree Structures, and Supplementary Concept Terms, via the mesh-resources library.

The package provides a straightforward retrieval interface for PubMed literature, with utility in LLM workflows and RAG applications requiring access to abstracts, full-text articles, entity annotations, and bibliometric data.

Installation

Get the released version from CRAN:

install.packages('puremoe')

Or the development version from GitHub with:

remotes::install_github("jaytimm/puremoe")

PubMed search

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])') 

Get record-level data

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

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)

PMC full text

Full-text articles can be retrieved for PMIDs if available in PMC’s open-access collection. Use pmid_to_ftp() to get download URLs, then pass these to get_records(endpoint = 'pmc_fulltext') — useful for quick retrieval in LLM/chat contexts.

For bulk downloads, use data_pmc_list().

pmcs <- puremoe::pmid_to_ftp(pmids = pmids, ncbi_key = ncbi_key)
pmc_fulltext <- puremoe::get_records(pmcs[1:5]$url, endpoint = 'pmc_fulltext', cores = 1)

Endpoint information

Returns schema, columns, and rate limits for each endpoint. Useful in LLM app contexts for tool schemas.

endpoint_info() lists endpoints; endpoint_info('endpoint_name') returns details; format = 'json' for machine-readable output.

puremoe::endpoint_info()

## [1] "pubmed_abstracts"    "pubmed_affiliations" "icites"             
## [4] "pubtations"          "pmc_fulltext"

puremoe::endpoint_info('pmc_fulltext')

## $description
## [1] "Full-text articles from PubMed Central"
## 
## $returns
## [1] "data.frame"
## 
## $columns
## $columns$pmid
## [1] "PubMed ID (character)"
## 
## $columns$section
## [1] "Section heading (character)"
## 
## $columns$text
## [1] "Section text content (character)"
## 
## 
## $parameters
## $parameters$cores
## [1] "parallel workers"
## 
## 
## $input
## [1] "Requires FTP URLs from pmid_to_ftp()"
## 
## $rate_limit
## [1] "NCBI FTP: be respectful"
## 
## $notes
## [1] "One row per section; use after pmid_to_ftp() to get URLs. Not all PMIDs have PMC full text available."

License

MIT © [Jason Timm, MA, PhD]

Citation

If you use this package in your research, please cite:

citation("puremoe")

Issues

Report bugs or request features at https://github.com/username/puremoe/issues

Contributing

Contributions welcome! Please open an issue or submit a pull request.