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Data from "Obstacles to the Reuse of Study Metadata in ClinicalTrials.gov"

dataset
posted on 03.11.2020, 20:58 authored by Laura MironLaura Miron, Rafael GonçalvesRafael Gonçalves, Mark A. Musen
This fileset provides supporting data and corpora for the empirical study described in:

Laura Miron, Rafael S. Goncalves and Mark A. Musen. Obstacles to the Reuse of Metadata in ClinicalTrials.gov

Description of files

Original data files:
- AllPublicXml.zip contains the set of all public XML records in ClinicalTrials.gov (protocols and summary results information), on which all remaining analyses are based. Set contains 302,091 records downloaded on April 3, 2019.
- public.xsd is the XML schema downloaded from ClinicalTrials.gov on April 3, 2019, used to validate records in AllPublicXML.

BioPortal API Query Results
- condition_matches.csv contains the results of querying the BioPortal API for all ontology terms that are an 'exact match' to each condition string scraped from the ClinicalTrials.gov XML. Columns={filename, condition, url, bioportal term, cuis, tuis}.
- intervention_matches.csv contains BioPortal API query results for all interventions scraped from the ClinicalTrials.gov XML. Columns={filename, intervention, url, bioportal term, cuis, tuis}.

Data Element Definitions
- supplementary_table_1.xlsx Mapping of element names, element types, and whether elements are required in ClinicalTrials.gov data dictionaries, the ClinicalTrials.gov XML schema declaration for records (public.XSD), the Protocol Registration System (PRS), FDAAA801, and the WHO required data elements for clinical trial registrations.

Column and value definitions:
- CT.gov Data Dictionary Section: Section heading for a group of data elements in the ClinicalTrials.gov data dictionary (https://prsinfo.clinicaltrials.gov/definitions.html)
- CT.gov Data Dictionary Element Name: Name of an element/field according to the ClinicalTrials.gov data dictionaries (https://prsinfo.clinicaltrials.gov/definitions.html) and (https://prsinfo.clinicaltrials.gov/expanded_access_definitions.html)
- CT.gov Data Dictionary Element Type: "Data" if the element is a field for which the user provides a value, "Group Heading" if the element is a group heading for several sub-fields, but is not in itself associated with a user-provided value.
- Required for CT.gov for Interventional Records: "Required" if the element is required for interventional records according to the data dictionary, "CR" if the element is conditionally required, "Jan 2017" if the element is required for studies starting on or after January 18, 2017, the effective date of the FDAAA801 Final Rule, "-" indicates if this element is not applicable to interventional records (only observational or expanded access)
- Required for CT.gov for Observational Records: "Required" if the element is required for interventional records according to the data dictionary, "CR" if the element is conditionally required, "Jan 2017" if the element is required for studies starting on or after January 18, 2017, the effective date of the FDAAA801 Final Rule, "-" indicates if this element is not applicable to observational records (only interventional or expanded access)
- Required in CT.gov for Expanded Access Records?: "Required" if the element is required for interventional records according to the data dictionary, "CR" if the element is conditionally required, "Jan 2017" if the element is required for studies starting on or after January 18, 2017, the effective date of the FDAAA801 Final Rule, "-" indicates if this element is not applicable to expanded access records (only interventional or observational)
- CT.gov XSD Element Definition: abbreviated xpath to the corresponding element in the ClinicalTrials.gov XSD (public.XSD). The full xpath includes 'clinical_study/' as a prefix to every element. (There is a single top-level element called "clinical_study" for all other elements.)
- Required in XSD? : "Yes" if the element is required according to public.XSD, "No" if the element is optional, "-" if the element is not made public or included in the XSD
- Type in XSD: "text" if the XSD type was "xs:string" or "textblock", name of enum given if type was enum, "integer" if type was "xs:integer" or "xs:integer" extended with the "type" attribute, "struct" if the type was a struct defined in the XSD
- PRS Element Name: Name of the corresponding entry field in the PRS system
- PRS Entry Type: Entry type in the PRS system. This column contains some free text explanations/observations
- FDAAA801 Final Rule FIeld Name: Name of the corresponding required field in the FDAAA801 Final Rule (https://www.federalregister.gov/documents/2016/09/21/2016-22129/clinical-trials-registration-and-results-information-submission). This column contains many empty values where elements in ClinicalTrials.gov do not correspond to a field required by the FDA
- WHO Field Name: Name of the corresponding field required by the WHO Trial Registration Data Set (v 1.3.1) (https://prsinfo.clinicaltrials.gov/trainTrainer/WHO-ICMJE-ClinTrialsgov-Cross-Ref.pdf)

Analytical Results:
- EC_human_review.csv contains the results of a manual review of random sample eligibility criteria from 400 CT.gov records. Table gives filename, criteria, and whether manual review determined the criteria to contain criteria for "multiple subgroups" of participants.
- completeness.xlsx contains counts and percentages of interventional records missing fields required by FDAAA801 and its Final Rule.
- industry_completeness.xlsx contains percentages of interventional records missing required fields, broken up by agency class of trial's lead sponsor ("NIH", "US Fed", "Industry", or "Other"), and before and after the effective date of the Final Rule
- location_completeness.xlsx contains percentages of interventional records missing required fields, broken up by whether record listed at least one location in the United States and records with only international location (excluding trials with no listed location), and before and after the effective date of the Final Rule

Intermediate Results:
- cache.zip contains pickle and csv files of pandas dataframes with values scraped from the XML records in AllPublicXML. Downloading these files greatly speeds up running analysis steps from jupyter notebooks in our github repository.

Funding

Clinical trials data to drive precision management of cardiovascular disease

American Heart Association

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