README.md

In bgcarlisle/trn2doi: A data set of Trial Registration Numbers (TRNs) matched to Digital Object Identifiers (DOIs) for their primary results publications

ctlookup

A data set of Trial Registration Numbers (TRNs) matched to Digital Object Identifiers (DOIs) for their primary results publications

To install and use

Install from Github:

install.packages("devtools")
library(devtools)
install_github("bgcarlisle/ctlookup")

After installation:

library(ctlookup)
data(lookup)

This package provides a data frame, lookup, which can be loaded via the R package with data(lookup). The same data frame is also provided as a CSV in this repository as inst/extdata/lookup.csv.

lookup contains four columns:

| trn | doi | preprint_doi | search_date | |-------|-------|----------------|---------------|

Each row in this data frame contains a Trial Registration Number (TRN, the trn column) and a date on which the literature was searched (search_date column as an ISO-8601 formatted date).

If a full journal publication reporting the results of the primary outcome was found, the corresponding Digital Object Identifier (DOI) is provided, otherwise this column is NA. Abstract-only publications, protocols, systematic reviews, combined or pooled reports of multiple trials, subgroup analyses, or other secondary publications using the data from the trial in question are not included. In the case of multiple publication of the primary outcome of a clinical trial, the first publication will be included.

If there is a DOI in the doi column, it corresponds to a single full journal publication of the trial's primary outcome results, and if that column contains NA, there was no such publication found on the date of search.

Similarly, if a preprint is found that reports a trial's primary outcome results, it will be reported in the preprint_doi column, otherwise that column will contain NA.

The trn column contains unique entries, as there can only be one first full journal publication and one first preprint of a trial's primary outcome results. Due to multiple registration (a clinical trial that is registered in multiple registries and reported in a single publication or preprint), the doi and preprint_doi columns are not unique.

Every entry in this data set represents a manual search that has been manually double-coded to ensure data quality. In many cases, these data have been taken from previously completed projects, checked for accuracy and added. See help(lookup) for a full list of data sources.

To contribute

If you completed a project in which you matched clinical trial registrations to publications and you would like to contribute your data:

1. Fork this repository locally.
2. Add a CSV to the data-raw/ folder with the same four columns as the lookup data frame (see above). Name the file as follows: [publication year]-[first author]-[first word in publication title].csv, e.g. 2016-carlisle-benefit.csv. Each row should contain data that match the definitions and criteria as specified above, and should include only manually-curated literature searches, not data that has been scraped automatically from Pubmed or ClinicalTrials.gov.
3. Cite the source of these data in R/lookup.R using a @source item, formatted as follows: @source [First author] et al. [Title]. [Journal abbreviation], [Year]. doi: [doi].
4. Make a pull request.
5. Your submission will be checked for accuracy and consistency with the definitions and inclusion criteria for this data set and merged on completion.

How to cite ctlookup

Here is a BibTeX entry for ctlookup:

@Manual{ctlookup-carlisle,
  Title          = {ctlookup},
  Author         = {Carlisle, Benjamin Gregory},
  Organization   = {The Grey Literature},
  Address        = {Berlin, Germany},
  url            = {https://github.com/bgcarlisle/ctlookup},
  year           = 2022
}

If you use this data set and you found it useful, I would take it as a kindness if you cited it.

Best,

Benjamin Gregory Carlisle PhD

bgcarlisle/trn2doi documentation built on April 25, 2022, 5:31 a.m.