pubmedR (version 1.0.2)

pmQueryBuild: Build a PubMed search query programmatically

Description

It helps to build a valid PubMed search query using the Entrez query language, combining multiple search terms with Boolean operators.

Usage

pmQueryBuild(
  terms = NULL,
  fields = "Title/Abstract",
  language = NULL,
  pub_type = NULL,
  date_range = NULL,
  mesh_terms = NULL,
  author = NULL,
  journal = NULL,
  operator = "AND"
)

Value

a character string containing the formatted PubMed query.

Arguments

terms

is a character or character vector. Search terms to look for in title and abstract fields.

fields

is a character or character vector. PubMed search tags to apply. Default is c("Title/Abstract"). Common fields include: "Title/Abstract", "Title", "Author", "MeSH Terms", "Affiliation", "Journal".

language

is a character or NULL. Language filter (e.g. "english", "french"). Default is NULL (no filter).

pub_type

is a character or NULL. Publication type filter (e.g. "Journal Article", "Review", "Clinical Trial"). Default is NULL (no filter).

date_range

is a character vector of length 2 or NULL. Date range in format c("YYYY", "YYYY") or c("YYYY/MM/DD", "YYYY/MM/DD"). Default is NULL (no filter).

mesh_terms

is a character or character vector or NULL. MeSH (Medical Subject Headings) terms. Default is NULL (no filter).

author

is a character or character vector or NULL. Author names. Default is NULL.

journal

is a character or character vector or NULL. Journal names or abbreviations. Default is NULL.

operator

is a character. Boolean operator to combine multiple terms. One of "AND", "OR". Default is "AND".

Details

The function constructs a query string compatible with NCBI's Entrez search system. Multiple terms within the same parameter are combined with the specified operator, while different parameters (terms, language, pub_type, etc.) are combined with AND.

For more information about PubMed search tags, visit: https://pubmed.ncbi.nlm.nih.gov/help/#search-tags

See Also

pmQueryTotalCount

pmApiRequest

Examples

# Simple query
q <- pmQueryBuild(terms = "bibliometrics", language = "english",
                  pub_type = "Journal Article", date_range = c("2000", "2023"))

# Multiple terms
q <- pmQueryBuild(terms = c("machine learning", "deep learning"),
                  operator = "OR", language = "english")

# MeSH terms query
q <- pmQueryBuild(mesh_terms = "COVID-19", pub_type = "Review",
                  date_range = c("2020", "2024"))

# Author search
q <- pmQueryBuild(terms = "bibliometrics", author = "Aria M")