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. For ISRCTN, works only for "P", "A" or "E" but not mixed populations.
- 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)
#> * Found search query from EUCTR: query=antibody&phase=phase-three&dateFrom=2000-01-01
#> * Found search query from ISRCTN: &q=&filters=intervention:antibody,phase:Phase III,GT+overallStartDate:2000-01-01,primaryStudyDesign:Interventional
#> * Found search query from CTGOV2: intr=(antibody) AND (Drug OR Biological)&start=2000-01-01_&term=AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)&aggFilters=phase:3,studyType:int
#> * Found search query from CTGOV2: term=AREA[InterventionSearch]"antibody" AND (AREA[Phase]"PHASE3") AND AREA[StartDate]RANGE[2000-01-01,MAX] AND (AREA[StudyType]INTERVENTIONAL) AND (AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)) AND (AREA[InterventionSearch](DRUG OR BIOLOGICAL))
#> * Found search query from CTIS: searchCriteria={"containAll":"antibody","trialPhaseCode":[5],"eeaStartDateFrom":"2000-01-01"}
#> EUCTR
#> "https://www.clinicaltrialsregister.eu/ctr-search/search?query=antibody&phase=phase-three&dateFrom=2000-01-01#tabs"
#> ISRCTN
#> "https://www.isrctn.com/search?&q=&filters=intervention:antibody,phase:Phase III,GT+overallStartDate:2000-01-01,primaryStudyDesign:Interventional"
#> CTGOV2
#> "https://clinicaltrials.gov/search?intr=(antibody) AND (Drug OR Biological)&start=2000-01-01_&term=AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)&aggFilters=phase:3,studyType:int"
#> CTGOV2expert
#> "https://clinicaltrials.gov/expert-search?term=AREA[InterventionSearch]\"antibody\" AND (AREA[Phase]\"PHASE3\") AND AREA[StartDate]RANGE[2000-01-01,MAX] AND (AREA[StudyType]INTERVENTIONAL) AND (AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)) AND (AREA[InterventionSearch](DRUG OR BIOLOGICAL))"
#> CTIS
#> "https://euclinicaltrials.eu/ctis-public/search#searchCriteria={\"containAll\":\"antibody\",\"trialPhaseCode\":[5],\"eeaStartDateFrom\":\"2000-01-01\"}"
# For CTIS to accept such a search URL and show results, consider installing
# the Tampermonkey browser extension from https://www.tampermonkey.net/,
# click on the extension icon, "Create a new script", "Utility" and then
# "Import from this URL":
# https://raw.githubusercontent.com/rfhb/ctrdata/master/tools/ctrdataURLcopier.js
urls <- ctrGenerateQueries(
searchPhrase = "antibody AND covid",
recruitment = "completed",
)
# 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)
#> * Found search query from EUCTR: query="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"&dateFrom=2010-01-31&country=de&country=gb&country=3rd
#> * Found search query from ISRCTN: q="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"&filters=GT+overallStartDate:2010-01-31,primaryStudyDesign:Interventional,phase:Phase 0,phase:Phase I,phase:Phase II,phase:Phase III,phase:Phase IV,phase:Phase I/II,phase:Phase II/III,phase:Phase III/IV,recruitmentCountry:Germany,recruitmentCountry:United Kingdom,recruitmentCountry:United States of America
#> * Found search query from CTGOV2: term=("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") AND AREA[StartDate]RANGE[2010-01-31,MAX] AND (AREA[StudyType]INTERVENTIONAL) AND (AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)) AND (AREA[InterventionSearch](DRUG OR BIOLOGICAL)) AND (AREA[LocationCountry]"Germany" OR AREA[LocationCountry]"United Kingdom" OR AREA[LocationCountry]"United States of America")
#> * Found search query from CTGOV2: term=("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") AND AREA[StartDate]RANGE[2010-01-31,MAX] AND (AREA[StudyType]INTERVENTIONAL) AND (AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)) AND (AREA[InterventionSearch](DRUG OR BIOLOGICAL)) AND (AREA[LocationCountry]"Germany" OR AREA[LocationCountry]"United Kingdom" OR AREA[LocationCountry]"United States of America")
#> * Found search query from CTIS: searchCriteria={"containAny":"basket, platform, umbrella, master protocol, multiarm, multistage, subprotocol, substudy, multi-arm, multi-stage, sub-protocol, sub-study","eeaStartDateFrom":"2010-01-31","msc":[276,826,840]}
#> EUCTR
#> "https://www.clinicaltrialsregister.eu/ctr-search/search?query=\"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\"&dateFrom=2010-01-31&country=de&country=gb&country=3rd#tabs"
#> ISRCTN
#> "https://www.isrctn.com/search?q=\"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\"&filters=GT+overallStartDate:2010-01-31,primaryStudyDesign:Interventional,phase:Phase 0,phase:Phase I,phase:Phase II,phase:Phase III,phase:Phase IV,phase:Phase I/II,phase:Phase II/III,phase:Phase III/IV,recruitmentCountry:Germany,recruitmentCountry:United Kingdom,recruitmentCountry:United States of America"
#> CTGOV2
#> "https://clinicaltrials.gov/expert-search?term=(\"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\") AND AREA[StartDate]RANGE[2010-01-31,MAX] AND (AREA[StudyType]INTERVENTIONAL) AND (AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)) AND (AREA[InterventionSearch](DRUG OR BIOLOGICAL)) AND (AREA[LocationCountry]\"Germany\" OR AREA[LocationCountry]\"United Kingdom\" OR AREA[LocationCountry]\"United States of America\")"
#> CTGOV2expert
#> "https://clinicaltrials.gov/expert-search?term=(\"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\") AND AREA[StartDate]RANGE[2010-01-31,MAX] AND (AREA[StudyType]INTERVENTIONAL) AND (AREA[DesignPrimaryPurpose](DIAGNOSTIC OR PREVENTION OR TREATMENT)) AND (AREA[InterventionSearch](DRUG OR BIOLOGICAL)) AND (AREA[LocationCountry]\"Germany\" OR AREA[LocationCountry]\"United Kingdom\" OR AREA[LocationCountry]\"United States of America\")"
#> CTIS
#> "https://euclinicaltrials.eu/ctis-public/search#searchCriteria={\"containAny\":\"basket, platform, umbrella, master protocol, multiarm, multistage, subprotocol, substudy, multi-arm, multi-stage, sub-protocol, sub-study\",\"eeaStartDateFrom\":\"2010-01-31\",\"msc\":[276,826,840]}"
if (FALSE) { # \dontrun{
# count trials found
sapply(urls, ctrLoadQueryIntoDb, only.count = TRUE)
# load queries into database collection
dbc <- nodbi::src_sqlite(collection = "my_collection")
sapply(urls, ctrLoadQueryIntoDb, con = dbc)
} # }