Use of terms from well-known domain-specific ontologies is one of the fundamental guidelines enumerated by the FAIR principles for making scientific data and metadata Findable, Accessible, Interoperable, and Reusable56. MeSH provides the best coverage of any single ontology, but it does not cover significantly more terms than MEDDRA, which contains matches for 230,639 conditions (46%), or SNOMED-CT, which contains matches for 224,008 conditions (45%). We performed a comprehensive search for concepts in UMLS ontologies that matched the values given for the condition field. All interventions have an associated intervention type, one of the eleven choices in Fig. Hosting the NIH CDE Task Force (CDETF), a trans-NIH community of practice. Including registry metadata in systematic reviews can help to identify selective reporting bias by comparing published outcomes to prespecified outcomes8,9, and adverse events are more likely to be reported in clinical trial registries than in published literature10,11. Python notebooks which reproduce all other analyses, tables, and figures are available at https://github.com/lauramiron/CTMetadataAnalysis. CAS PubMedGoogle Scholar. (Agency: National Institutes of Health, Department of Health and Human Services; Action: Final rule; Publication Date: 09/21/2016, 2016). Curr. Internet Explorer). The fields for which the difference in the number of records missing a value for the field across agency class is the greatest are displayed in Fig. Res. Indications of Recruitment Challenges in Research with U.S. Military Service Members: A ClinicalTrials.gov Review. Bernardez-Pereira, S. et al. These data were chosen from the discharge summaries of patients who were . F1000Research 4, 80 (2015). Data 6, 190021 (2019). 103, 2230 (2018). 7, 6569 (2020). Giel, J. L. Comparison of results reporting on ClinicalTrials.gov by funding source. re3data.org. Genet. Alternative spellings (tumor vs tumour) and synonyms (breast cancer vs malignant neoplasm of the breast) are not harmonized. 54, 232239 (2020). Until then, the Ministerial Order 221/1984, that only required the drawing up of a discharge report for patients seen in . Lets look at a current example where health data standards, a common data language, have had a real impact. For our analyses of type consistency and usage of ontology terms, we considered all 149 elements listed in the two data dictionaries. Many of the fields that are shared between the WHO data set and FDAAA801 have different names and definitions within the two standards. We conducted our analysis of the PRS system using a test environment, which allows records to be created but never submitted, maintained by Stanford University. NEWS: New NIH Policy for Data Management and Sharing (effective January 25, 2023) NIH has issued a new Final NIH Policy for Data Management and Sharing, which will require NIH funded researchers to prospectively submit a plan outlining how scientific data from their research will be managed and shared.On January 25, 2023, the new policy will come into effect and replace the 2003 NIH Data . However, first name, middle name, and degrees are missing in all investigators and contacts in all records, and instead the individuals full name and degrees all appear within the value of the last name field (e.g., Sarah Smith, M.D.). PubMed Association between 25(OH)D Level, Ultraviolet Exposure, Geographical Location, and Inflammatory Bowel Disease Activity: A Systematic Review and Meta-Analysis. Med. National Library of Medicine8600 Rockville PikeBethesda, MD 20894, Web PoliciesFOIAHHS Vulnerability Disclosure, Health Data Standards: A Common Language to Support Research and Health Care, Office of the National Coordinator for Health Information Technology (ONC), A Journey to Spur Innovation and Discovery, Health Data Standards: A Common Language to Support Research and Health Care Psychiatry Intel Real-Time Evidence-Based Psychiatry and Mental Health Research Online, Common Data Elements: Increasing FAIR Data Sharing NLM Musings from the Mezzanine. For any given disease, information from these organizational scales is scattered across publications, non-standardized data repositories, evolving ontologies, and clinical guidelines.. Baldi, I., Lanera, C., Berchialla, P. & Gregori, D. Early termination of cardiovascular trials as a consequence of poor accrual: analysis of ClinicalTrials.gov 20062015. A table containing the exact mapping between element names in the data dictionary, XML element names, field names in FDAAA801, and WHO data element names is provided in the supplementary material. We counted the number of records missing each field for 28 of the 41 fields required by the FDAAA801 Final Rule. Our long-standing efforts to establish common health terminology supported the COVID-19 response by allowing access to near-real time clinical information to guide the diagnosis, treatment, and prevention of this disease. We assigned each metadata field in the data dictionary to a category, and, for each category, we determined the type of validation that we would perform: Simple type (date, integer, age, Boolean) Validate records against the XSD. We provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration. & Musen, M.A. These detected synonyms are always included and the user cannot choose to search for an exact phrase. Hart, B., Lundh, A. We ignored five fields that are conditionally required based on information unavailable to us (e.g., secondary outcome measures must be listed, but only if they exist) (Pediatric Postmarket Surveillance, Other Names for Interventions, Post Prior to FDA Approval/Clearance, Product Manufactured in or Exported from the U.S., Secondary Outcome Measure Information), three fields stored internally by ClinicalTrials.gov but not made public FDA IND or IDE, Human Subject Protection Board Review Status, Responsible Party Contact Information), three fields which were not added to ClinicalTrials.gov until November 2017 concerning FDA regulations (Studies an FDA-regulated Device Product, Studies an FDA-regulated drug product, Device or Product Not Approved/Cleared by FDA), and two fields that represent administrative data present in all records (Unique Protocol Identification Number, Record Verification Date). You are using a browser version with limited support for CSS. The responsible party element contains sub-fields investigator affiliation, investigator full name, and investigator title with no field for degrees. Registries . Geographic Accessibility to Clinical Trials for Advanced Cancer in the United States. Oncol. The method aims to identify a subset of genes in a subset of samples from input data sets that jointly explain the expression of genes . Error types include: Missing one or both inclusion/exclusion headers, Misspelled or alternative inclusion/exclusion headers, Criteria not formatted, or only partially formatted as a bulleted list, Criteria defined for sub-groups of participants, and/or defined for non-subjects. Of the 190,927 condition terms that have no match in MeSH, 96,678 conditions (51%) do have an exact match in another ontology. The Ontology of Clinical Research (OCRe): An informatics foundation for the science of clinical research. & Platts-Mills, T. F. Clinical trials registries are under-utilized in the conduct of systematic reviews: a cross-sectional analysis. Large datasets may benefit from cloud-based data repositories for data access, preservation, and sharing. Out of the 117,906 records in group 2 and group 3, we manually reviewed a convenience sample of 400 records, selected at random, allowing us to extrapolate (with 95+/5% confidence) the number of eligibility definitions that failed to parse because they listed criteria for more than one sub-group of participants (e.g., different criteria for subjects with the studied condition and for healthy participants, different criteria for participants assigned to surgical and non-surgical intervention arms), which is not permitted in the current format. The most common cause of criteria failing to parse according to the expected format was paragraph-style sentences interspersed with bulleted criteria. Sharing and archiving data on the platform is fee-based. Some data quality issues at ClinicalTrials.gov. For a list of NIH-supported repositories, visit. Fed (US governmental agency other than NIH), 69,100 trials sponsored by industry, and 160,291 trials with agency class other. Nat. L.M. The largest source of metadata that describes the experimental protocol, funding, and scientific leadership of clinical studies is ClinicalTrials.gov. Important fields for search, such as condition and intervention, are not restricted to ontologies, and almost half of the conditions are not denoted by MeSH terms, as recommended. J. Clin. Using ORCIDs also would allow for a researchers name, degrees, and affiliation to change with time and to be simultaneously updated in all records. The ClinicalTrials.gov XSD schema contained type definitions for all Boolean, integer, date, and age fields, and all records validated against this XSD (Table3). Williams, R. Engaging Users to Support the Modernization of ClinicalTrials.gov, Https://nlmdirector.nlm.nih.gov/2019/08/13/engaging-users-to-support-the-modernization-of-clinicaltrials-gov/ (2019). Another rule checks both the chosen value for study phase (Phase 1), and the (lack of) interventions that are enumerated on a separate page of the entry system. Most required fields are present in nearly all records submitted after the January 2017 update to ClinicalTrials.gov because automated PRS validation rules prevent the submission of records with missing required fields. Google Scholar. 51, 203211 (2015). 27 (2011). Some required data element definitions were updated by the Final Rule, an amendment to FDAAA801 released on September 09, 2016. Moreover, the inclusion of synonyms in searches cannot be toggled off, and users may disagree with ClinicalTrials.govs definition of synonymy. If your data contains a patient whose complete clinical record contains one or more encounters that have been filtered out by this policy . Non-publication of large randomized clinical trials: cross sectional analysis. Our results demonstrate that there is no single ontology that covers the majority of needed terms (Fig. Arm information consists of a label (e.g., the name of the experimental intervention used or placebo), type (Experimental, active comparator, placebo comparator, or other), and description. Only synonyms for the query term are provided, and users cannot browse from their original query to more or less general concepts (e.g., in the MeSH hierarchy) in order to refine their search. The expected format for eligibility criteria in ClinicalTrials.gov is a bulleted list of strings that enumerate the criteria below the headers Inclusion Criteria and Exclusion Criteria. However, contact information was frequently missing or underspecified both before and after the Final Rule. McCray, A. T. & Ide, N. C. Design and Implementation of a National Clinical Trials Registry. Because FDAAA801 only defines required fields for interventional trials, we conducted analyses of missing fields only on the set of 239,274 interventional records, and conducted all other analyses on the full set of 302,091 records. Research questions, such as, What date did the patient first display COVID-19 symptoms? arose continuously. Google Scholar. Subset analyses. Thiers, F. A., Sinskey, A. J. CDEs are in use across NIH, to varying degrees. Clinical trial design and dissemination: comprehensive analysis of clinicaltrials.gov and PubMed data since 2005. Robin Taylor, MLIS, joined NLM in 2016. Because a CDR is intended to support multiple uses, we do not categorize the database within any single application as a CDR. Perspect. Sci. The only field currently restricted to terms from an ontology is the condition field. Genomic Data Sharing Expectations by NIH Institute & Center, Completing an Institutional Certification Form, How to Register and Submit A Study in dbGaP, NIH Institute and Center Data Sharing Policies, Intramural Human Data Sharing Policy (Staff Only), Accessing Genomic Data from NIH Repositories, How to Request and Access Datasets from dbGaP, Supplemental Policy Information: Selecting a Repository for Data Resulting from NIH-Supported Research. Special care should be taken when parsing these dates because the behavior of many date parsing libraries when given input without a day number is undefined. Such an . Eligibility criteria are stored as semi-structured text; they are recommended to be formatted as a bulleted list of individual criteria, but nearly 49% of values fail to parse according to the expected format. & Ghersi, D. The Quality of Registration of Clinical Trials: Still a Problem. Descriptions of the sources will refer to repository traits (Table 1) that make them more or less useful and available for research.The first two traits are quantitative ones that we use later (Figure 1) to compare all the repository types.The first trait is the number of patients or research subjects observed. We downloaded all public XML trial records (n=302,091) on April 3, 2019. Hu, W., Zaveri, A., Qiu, H. & Dumontier, M. Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. ClinicalTrials.gov records, like metadata records from other widely used biomedical data repositories41,42, are plagued by quality issues. What influences recruitment to randomised controlled trials? ClinicalTrials.gov records are available as Web pagesaccessible through the systems search portaland as XML files (https://clinicaltrials.gov/AllPublicXML.zip). Every day we benefit from data standards, and every day most of us dont even notice it! The Final Rule eliminates the single-arm control element, makes interventional model, allocation, enrollment, and masking required sub-elements of study design, and makes number of arms and arm information separate required elements. Correspondence to Further, the PRS should allow users to enter multiple blocks of inclusion and exclusion criteria and an associated criteria group name, such as the label of the corresponding study arm. and determining whether ORCID and ROR entries should be created for entities if they do not exist. McDonald, A. M. et al. Nat. Some examples of the types of data found in a clinical data repository include demographics, lab results, radiology images, admissions, transfers, and diagnoses. Ed. Heart J. Our work is limited to the clinical-trial protocols stored in ClinicalTrials.gov, and could be expanded to cover adherence to schema, missing fields, and usage of ontology terms in the summary results of ClincialTrials.gov records, which are required to be submitted within one year of the study completion date. PubMed Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. biotab.manager - Manage TCGA clinical tables . 10, e1001566 (2013). Therefore, all records contain correctly typed values for all occurrences of these elements. This study creates a conceptual framework for predicting how various properties of these systems will scale as they continue to expand. The ontologies that provide the most coverage for condition values are MeSH (62%), MedDRA (46%), and SNOMED-CT (45%). Wagner, D. E., Turner, L., Panoskaltsis-Mortari, A., Weiss, D. J. BioPortal: Enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Get real time updates on the latest news and events. Compliance with legal requirement to report clinical trial results on ClinicalTrials.gov: a cohort study. meet criteria that merit their recommendation for use in NIH-funded research. Cite this article. CAS Trials 10, 56 (2009). CRHD Releases include unprocessed multimodal imaging data for all released subjects (all projects) and minimally preprocessed data for a subset of subjects (including PDC, BANDA and HCP-EP). Tse et al. JAMA 307, 1838 (2012). We also counted the number of interventional trial records missing values from each of the 41 fields required by the Final Rule after categorizing the records based on the agency class of the lead sponsor. PLoS One 10, e0132036 (2015). Sim, I. et al. 4). Abstract. A principal investigator may be listed within a ClinicalTrials.gov record either in the responsible party element when the responsible party type is Principal Investigator or Sponsor-Investigator, or in the overall official element. Timing and Completeness of Trial Results Posted at ClinicalTrials.gov and Published in Journals. Friends of Cancer Research https://www.focr.org/blog/engaging-innovation/data (2017). A searchable database of more than 2,000 research data repositories, including 100+ relating to cancer. PLoS Med. Dates are permitted to be Unknown, or similar to January 3, 2004 or March, 2005 where the day number is optional. Similar levels of security are a best practice for any data from human subjects or . This enables reuse of data across multiple sources, which increases statistical power and accelerates our understanding of this disease. 3). Even when values for fields in ClinicalTrials.gov records are drawn from an ontology, they are not specified using globally unique and persistent identifiers, which would enable the interoperability of data with systems that expect these well-defined terms as input. Whether captured during product development activities such as clinical research trials and studies, or as a part . BMJ 344, d7202d7202 (2012). It's a vast database infrastructure that gathers, manages, and stores varying data sets for analysis, distribution, and reporting. Clinical Data Repository It collects comprehensive data on large patient cohorts, assembled and stored over time, which not only permit these institutions to examine trends in utilization and outcomes, but also perform sophisticated quality assurance and medical management queries The FAIR Guiding Principles for scientific data management and stewardship. Rare Dis. The mapping between data dictionary elements and XML elements is mostly trivial, but several dictionary/XML elements can map to a single field required by FDAAA801, and others are optional and not included in FDAAA801. The data dictionary says to use, if available, appropriate descriptors from NLMs Medical Subject Headings (MeSH)-controlled vocabulary or terms from another vocabulary, such as the Systemized Nomenclature of MedicineClinical Terms (SNOMED-CT), that has been mapped to MeSH within the Unified Medical Language System (UMLS) Metathesaurus58. Several studies have analyzed ClinicalTrials.gov records for missing fields required by the Food and Drug Administration Amendments Act of 2007, which governs US trial registries, and the World Health Organization (WHO) minimum data set, which provides guidelines for registries internationally43,44,45,46. Official title, why study stopped (for a study that is suspended, terminated or withdrawn prior to its planned completion), study start date, and study completion date were recommended but not required for studies with start dates before the effective date of the Final Rule. Informatics Assoc. PubMed Google Scholar. Hill, K. D., Chiswell, K., Califf, R. M., Pearson, G. & Li, J. S. Characteristics of pediatric cardiovascular clinical trials registered on ClinicalTrials.gov. In the meantime, to ensure continued support, we are displaying the site without styles 3). Metanalyses involving the principal investigators of trials are further hindered by the fact that principal investigator information may be listed as part of either the responsible party field, the overall official field, both, or neither. Syst. We used regular expressions to test whether values for eligibility criteria conformed to the expected semi-structured format. Additional instructions are provided for study phase and masking fields, and automated validation messages of levels Note, Warning and Error can be seen. . BMJ j448 (2017). Jones, C. W. et al. Software used to query the BioPortal API extends an existing suite of metadata analysis tools maintained by the Center for Expanded Data Annotation and Retrieval (CEDAR) and is available at https://github.com/metadatacenter/metadata-analysis-tools/. Further, responsible party uses a single sub-field (investigator full name) to store the entire name, but overall official has sub-fields first name, middle name, and last name. Since 2018, she has been the lead for the NIH Common Data Elements Repository. The advantage of CEDAR is that it provides tight integration with biomedical ontologies to control both field names and values, while not being tied to a single repository or metadata schema. This dataset contains three clinic examination and 20 year follow-up data on a large subset of the original Framingham cohort participants. We noticed irregularities in the structure of both investigator and contact-related elements. Opin. Informatics Assoc. When choosing a repository to manage and share data resulting from Federally funded research, here are some desirable characteristics to look for: When working with human participant data, including de-identified human data, here are some additional characteristics to look for: See Repositories for Sharing Scientific Data for a listing of NIH-affiliated data repositories. Does the Genomic Data Sharing Policy Apply to My Research? Oral Oncol. In accordance with HIPAA and various contractual obligations, the STARR data repository filters out certain patients and clinical encounters that are deemed not permissible for research use. Emerg. Chaturvedi et al.47 found that information about the principal investigators of trials in ClinicalTrials.gov are inconsistent both within multiple occurrences in the same record and across records. Apart from minor irregularities in some fields with enumerated values, ClinicalTrials.gov metadata were entirely free from these issues. Wilkinson, M. D. et al. We found that records from trials with a lead sponsor of NIH contain significantly more missing values than do those from the other three agency classes. Thadani, S. R., Weng, C., Bigger, J. T., Ennever, J. F. & Wajngurt, D. Electronic Screening Improves Efficiency in Clinical Trial Recruitment. In past work, we documented similar quality issues with the NCBI BioSample and EBI BioSamples repositories: records used many syntactic variants for the same field, and values did not conform to the expected type, including where ontology term identifiers are expected42.
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