Distribution of trial registry numbers within full-text PubMed Central - full dataset of discovered links

Linking registered clinical trials with their published results continues to be a challenge. A variety of natural language processing (NLP)-based and machine learning-based models have been developed to assist users in identifying these connections. Articles from the PubMed Central full-text collection were scanned for mentions of ClinicalTrials.gov and international clinical trial registry identifiers. We analyzed the distribution of trial registry numbers within sections of the articles and characterized their publication type indexing and other metrics. Three supporting files are included herein: a pdf containing supplementary figures pertaining to the distribution of registry numbers found within the full text of articles, a csv dataset providing the registry numbers discovered and the corresponding XML path location within the document, and an example Python script to locate registry identifiers within an XML article document. It should be noted that the purpose of this study is to summarize clinical trial mentions within publications and specific registries or other nominative information contained in this dataset may contain errors.

Methods
These datasets and files are the results of scanning 6,901,686 XML documents within the Pubmed Central Open Access article datasets available at: https://ftp.ncbi.nlm.nih.gov/pub/pmc/

Each registry identifier match is represented by a row in the xmlScanOutput.csv file, along with PubMed identifiers, file information, XML path information, and several computed columns including a validation that an NCT number exists within ClinicalTrials.gov, a generalized article section, and publication types from multiple indexing sources. Summaries within the Distribution_of_Trial_Registry_Numbers_Additional_File.pdf were generated by counting distinct PMID values within the csv file across various groups.