ctrGenerateQueries: Generates queries that work across registers

In ctrdata: Retrieve and Analyze Clinical Trials Data from Public Registers

Generates queries that work across registers

Description

From high-level search terms provided by the user, generate specific queries for each registers with which ctrdata works, see ctrdata-registers. Search terms that are expanded to concepts such as from MeSH and MedDRA by the search implementations in registers include the 'intervention' and 'condition'. Logical operators only work with 'searchPhrase'.

Usage

ctrGenerateQueries(
  searchPhrase = NULL,
  condition = NULL,
  intervention = NULL,
  phase = NULL,
  population = NULL,
  recruitment = NULL,
  startBefore = NULL,
  startAfter = NULL,
  completedBefore = NULL,
  completedAfter = NULL,
  onlyMedIntervTrials = TRUE,
  onlyWithResults = FALSE,
  countries = NULL
)

Arguments

searchPhrase	String with optional logical operators ("AND", "OR") that will be searched in selected fields of registers that can handle logical operators (general or title fields), should not include quotation marks
condition	String with condition / disease
intervention	String with intervention
phase	String, e.g. "phase 2" (note that "phase 2+3" is a specific category, not the union set of "phase 2" and "phase 3")
population	String, e.g. "P" (paediatric), "A" (adult), "P+A" (adult and paediatric), "E" (elderly), "P+A+E" participants can be recruited
recruitment	String, one of "ongoing", "completed", "other" ( which includes "ended early" but this cannot be searched; use trial concept f.statusRecruitment to identify this status)
startBefore	String that can be interpreted as date (for EUCTR, when trial was first registered)
startAfter	String that can be interpreted as date (for EUCTR, when trial was first registered)
completedBefore	String that can be interpreted as date (does not work with EUCTR)
completedAfter	String that can be interpreted as date (does not work with EUCTR)
onlyMedIntervTrials	Logical, default TRUE, which indicates if queries should search only for medicine interventional clinical trial
onlyWithResults	Logical
countries	Vector of country names, two- or three-letter ISO 3166 codes

Value

Named vector of URLs for finding trials in the registers and as input to functions ctrLoadQueryIntoDb and ctrOpenSearchPagesInBrowser

Examples

urls <- ctrGenerateQueries(
  intervention = "antibody",
  phase = "phase 3",
  startAfter = "2000-01-01")

# open queries in register web interface
sapply(urls, ctrOpenSearchPagesInBrowser)

urls <- ctrGenerateQueries(
  searchPhrase = "antibody AND covid",
  recruitment = "completed",
  )

# count trials found
sapply(urls, ctrLoadQueryIntoDb, only.count = TRUE)

# load queries into database collection
# sapply(urls, ctrLoadQueryIntoDb, con = dbc)

# find research platform and platform trials
urls <- ctrGenerateQueries(
  searchPhrase = paste0(
   "basket OR platform OR umbrella OR master protocol OR ",
   "multiarm OR multistage OR subprotocol OR substudy OR ",
   "multi-arm OR multi-stage OR sub-protocol OR sub-study"),
 startAfter = "01/31/2010",
 countries = c("DE", "US", "United Kingdom"))

# open queries in register web interface
sapply(urls, ctrOpenSearchPagesInBrowser)

ctrdata documentation built on April 15, 2025, 1:34 a.m.