Download and Combine 'MeSH' and Supplemental Thesauruses

Description

This function downloads and combines the 'MeSH' (Medical Subject Headings) Thesaurus and a supplemental concept thesaurus. The data is sourced from specified URLs and stored locally for subsequent use. By default, the data is stored in a temporary directory. Users can opt into persistent storage by setting 'use_persistent_storage' to TRUE and optionally specifying a path.

Usage

data_mesh_thesaurus(
  path = NULL,
  use_persistent_storage = FALSE,
  force_install = FALSE
)

Arguments

Value

A data.table containing the combined MeSH and supplemental thesaurus data.

Examples

if (interactive()) {
  data <- data_mesh_thesaurus()
}

Download and Load 'MeSH' Trees Data

Description

This function downloads and loads the 'MeSH' (Medical Subject Headings) Trees data.

Usage

data_mesh_trees(
  path = NULL,
  use_persistent_storage = FALSE,
  force_install = FALSE
)

Arguments

Details

The data is sourced from specified URLs and stored locally for subsequent use. By default, the data is stored in a temporary directory. Users can opt into persistent storage by setting 'use_persistent_storage' to TRUE and optionally specifying a path.

Value

A data frame containing the MeSH Trees data.

Examples

if (interactive()) {
  data <- data_mesh_trees()
}

Download and Load 'PMC' Open Access File List

Description

This function downloads and loads the 'PMC' (PubMed Central) Open Access file list. The file list contains mappings between PMC IDs, PMIDs, and file paths for open access articles available for download.

Usage

data_pmc_list(
  path = NULL,
  use_persistent_storage = FALSE,
  force_install = FALSE
)

Arguments

Details

The data is sourced from NCBI's FTP server and stored locally for subsequent use. By default, the data is stored in a temporary directory. Users can opt into persistent storage by setting 'use_persistent_storage' to TRUE and optionally specifying a path.

Value

A data.table containing the PMC file list with columns: file_path, citation, pmcid, pmid, and license_code.

Examples

if (interactive()) {
  data <- data_pmc_list()
}

Get Information About Available Endpoints

Description

This function provides detailed information about the available endpoints in the package, including column descriptions, parameters, rate limits, and usage notes.

Usage

endpoint_info(endpoint = NULL, format = c("list", "json"))

Arguments

Value

If endpoint is NULL, returns a character vector of available endpoint names. If endpoint is specified, returns a list (or JSON string) with detailed information about that endpoint including description, columns, parameters, rate limits, and notes.

Examples

if (interactive()) {
  # List all available endpoints
  endpoint_info()
  
  # Get information about a specific endpoint
  endpoint_info("pubmed_abstracts")
  
  # Get information in JSON format
  endpoint_info("icites", format = "json")
}

Retrieve Data from 'NLM'/'PubMed' databases Based on PMIDs

Description

This function retrieves different types of data (like 'PubMed' records, affiliations, 'iCites 'data, etc.) from 'PubMed' based on provided PMIDs. It supports parallel processing for efficiency.

Usage

get_records(
  pmids,
  endpoint = c("pubtations", "icites", "pubmed_affiliations", "pubmed_references",
    "pubmed_abstracts", "pmc_fulltext"),
  cores = 3,
  sleep = 1,
  ncbi_key = NULL
)

Arguments

Details

For the 'pmc_fulltext' endpoint, provide full URLs to PMC tar.gz files. Use pmid_to_pmc to convert PMIDs to PMC IDs and full URLs first.

Value

A data.table containing combined results from the specified endpoint.

Examples

pmids <- c("38136652")
results <- get_records(pmids, endpoint = "pubmed_abstracts", cores = 1)

Convert PubMed IDs (PMIDs) to PMC IDs and Full-Text URLs

Description

This function converts PMIDs to PMC IDs, then fetches the full-text file URLs from the PMC Open Access service. It combines both steps into a single workflow.

Usage

pmid_to_ftp(
  pmids,
  batch_size = 200L,
  sleep = 0.5,
  verbose = FALSE,
  ncbi_key = NULL
)

Arguments

Value

A data.table with columns:

• pmid: The input PubMed ID

• pmcid: The corresponding PMC ID

• doi: The corresponding DOI (NA if not available)

• url: The full HTTPS URL for downloading PMC full text

Results are filtered to only include rows with valid URLs (open access articles), ordered by PMID. Returns NULL with a message if the API is unavailable or returns invalid data.

Examples

if (interactive()) {
  # Convert PMIDs to PMC IDs and get full-text URLs
  result <- pmid_to_ftp(c("11250746", "11573492"))
}

Convert PubMed IDs (PMIDs) to PMC IDs

Description

This function converts a vector of PubMed IDs (PMIDs) to their corresponding PubMed Central (PMC) IDs and DOIs using the NCBI ID Converter API.

Usage

pmid_to_pmc(pmids, batch_size = 200L, sleep = 0.5)

Arguments

Value

A data.table with columns:

• pmid: The input PubMed ID

• pmcid: The corresponding PMC ID (NA if not available in PMC)

• doi: The corresponding DOI (NA if not available)

Results are ordered by PMID. Returns NULL with a message if the API is unavailable or returns invalid data.

Examples

if (interactive()) {
  # Convert a single PMID to PMC ID
  result <- pmid_to_pmc("12345678")
  
  # Convert multiple PMIDs
  pmids <- c("12345678", "23456789", "34567890")
  result <- pmid_to_pmc(pmids, batch_size = 10, sleep = 1)
}

Search 'PubMed' Records

Description

Performs a 'PubMed' search based on a query, optionally filtered by publication years. Returns a unique set of 'PubMed' IDs matching the query.

Usage

search_pubmed(
  x,
  start_year = NULL,
  end_year = NULL,
  retmax = 9999,
  use_pub_years = FALSE
)

Arguments

Value

Numeric vector of unique PubMed IDs.

Examples

ethnob1 <- search_pubmed("ethnobotany", 2010, 2012)