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Type:

Package

Title:

Pubmed Unified REtrieval for Multi-Output Exploration

Version:

1.0.2

Maintainer:

Jason Timm <JaTimm@salud.unm.edu>

Description:

Access a variety of 'PubMed' data through a single, user-friendly interface, including abstracts https://pubmed.ncbi.nlm.nih.gov/, bibliometrics from 'iCite' https://icite.od.nih.gov/, pubtations from 'PubTator3' https://www.ncbi.nlm.nih.gov/research/pubtator3/, and full-text records from 'PMC' https://www.ncbi.nlm.nih.gov/pmc/.

License:

MIT + file LICENSE

Encoding:

UTF-8

Depends:

R (≥ 3.5)

Imports:

rentrez, textshape, xml2, data.table, httr, pbapply, jsonlite, rappdirs

Suggests:

knitr, rmarkdown

RoxygenNote:

7.3.1

URL:

https://github.com/jaytimm/puremoe, https://jaytimm.github.io/puremoe/

BugReports:

https://github.com/jaytimm/puremoe/issues

NeedsCompilation:

Packaged:

2024-10-15 16:22:19 UTC; jtimm

Author:

Jason Timm [aut, cre]

Repository:

CRAN

Date/Publication:

2024-10-15 18:30:02 UTC

Download and Process 'MeSH' and 'SCR' Embeddings

Description

This function downloads 'MeSH' and 'SCR' embeddings data from the specified URLs and processes it for use. The data is saved locally in RDS format. If the files do not exist, they will be downloaded and processed.

Usage

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

Arguments

path

A character string specifying the directory path where data should be stored. If not provided and persistent storage is requested, it defaults to a system-appropriate persistent location managed by 'rappdirs'.

use_persistent_storage

A logical value indicating whether to use persistent storage. If TRUE and no path is provided, data will be stored in a system-appropriate location. Defaults to FALSE, using a temporary directory.

force_install

A logical value indicating whether to force re-downloading of the data even if it already exists locally.

Details

This dataset is not viewable until it has been downloaded.

Citation

Noh, J., & Kavuluru, R. (2021). Improved biomedical word embeddings in the transformer era. Journal of biomedical informatics, 120, 103867.

Value

A data frame containing the processed Mesh and SCR embeddings data.

Examples


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

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

path

use_persistent_storage

A logical value indicating whether to use persistent storage. If TRUE and no path is provided, data will be stored in a system-appropriate location. Defaults to FALSE, using a temporary directory.

force_install

A logical value indicating whether to force re-downloading of the data even if it already exists locally.

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

path

use_persistent_storage

A logical value indicating whether to use persistent storage. If TRUE and no path is provided, data will be stored in a system-appropriate location. Defaults to FALSE, using a temporary directory.

force_install

A logical value indicating whether to force re-downloading of the data even if it already exists locally.

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

data <- data_mesh_trees()

Download and Load Pharmacological Actions Data

Description

This function downloads and loads pharmacological actions data from a specified URL.

Usage

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

Arguments

path

use_persistent_storage

A logical value indicating whether to use persistent storage. If TRUE and no path is provided, data will be stored in a system-appropriate location. Defaults to FALSE, using a temporary directory.

force_install

A logical value indicating whether to force re-downloading of the data even if it already exists locally.

Details

Value

A data frame containing pharmacological actions data.

Examples

data <- data_pharm_action()

Download and Process 'PMC Open Access' File List

Description

This function downloads the 'PubMed Central' (PMC) open access file list from the 'National Center for Biotechnology Information' (NCBI) and processes it for use.

Usage

data_pmc_list(
  path = NULL,
  use_persistent_storage = FALSE,
  force_install = FALSE,
  timeout = 300
)

Arguments

path

use_persistent_storage

A logical value indicating whether to use persistent storage. If TRUE and no path is provided, data will be stored in a system-appropriate location. Defaults to FALSE, using a temporary directory.

force_install

A logical value indicating whether to force re-downloading of the data even if it already exists locally.

timeout

An integer indicating the timeout in seconds for the download. Defaults to 300 seconds.

Details

The data is sourced from the specified URL 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 processed PMC open access file list.

Examples


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

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_abstracts",
    "pmc_fulltext"),
  cores = 3,
  sleep = 1,
  ncbi_key = NULL
)

Arguments

pmids

A vector of PMIDs for which data is to be retrieved.

endpoint

A character vector specifying the type of data to retrieve ('pubtations', 'icites', 'affiliations', 'pubmed', 'pmc').

cores

Number of cores to use for parallel processing (default is 3).

sleep

Duration (in seconds) to pause after each batch

ncbi_key

(Optional) NCBI API key for authenticated access.

Value

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

Examples

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

Arguments

x

Character string, the search query.

start_year

Integer, the start year of publication date range (used if 'use_pub_years' is TRUE).

end_year

Integer, the end year of publication date range (used if 'use_pub_years' is TRUE).

retmax

Integer, maximum number of records to retrieve, defaults to 9999.

use_pub_years

Logical, whether to filter search by publication years, defaults to TRUE.

Value

Numeric vector of unique PubMed IDs.

Examples

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