The de novo FAIRification process of a registry for vascular anomalies

Background Patient data registries that are FAIR—Findable, Accessible, Interoperable, and Reusable for humans and computers—facilitate research across multiple resources. This is particularly relevant to rare diseases, where data often are scarce and scattered. Specific research questions can be asked across FAIR rare disease registries and other FAIR resources without physically combining the data. Further, FAIR implies well-defined, transparent access conditions, which supports making sensitive data as open as possible and as closed as necessary. Results We successfully developed and implemented a process of making a rare disease registry for vascular anomalies FAIR from its conception—de novo. Here, we describe the five phases of this process in detail: (i) pre-FAIRification, (ii) facilitating FAIRification, (iii) data collection, (iv) generating FAIR data in real-time, and (v) using FAIR data. This includes the creation of an electronic case report form and a semantic data model of the elements to be collected (in this case: the “Set of Common Data Elements for Rare Disease Registration” released by the European Commission), and the technical implementation of automatic, real-time data FAIRification in an Electronic Data Capture system. Further, we describe how we contribute to the four facets of FAIR, and how our FAIRification process can be reused by other registries. Conclusions In conclusion, a detailed de novo FAIRification process of a registry for vascular anomalies is described. To a large extent, the process may be reused by other rare disease registries, and we envision this work to be a substantial contribution to an ecosystem of FAIR rare disease resources.

341The birth of an electronic chronic disease registry bank in Nigeria

Background Nigeria is rapidly undergoing epidemiological transition resulting in a double burden of infectious and chronic diseases. Efforts have been concentrated on addressing infectious diseases, neglecting chronic diseases. However, the benefit of targeted chronic disease investigation cannot be overemphasized. Methods We conducted a literature search to identify ongoing chronic disease registry efforts in Nigeria. We then contacted the researchers and obtained additional information on the projects including information on the process for data management and number of contributing institutions. Results We found several single institutional efforts but were able to identify five efforts that were cross institutional and promising. These were the Cancer, Paediatric Cardiology, Adult Cardiology, Nephrology and Cardiac Surgery registries. Of the five, the cancer registry was well established with an electronic system and several publications from this registry. Next was the cardiac surgery registry with an online repository. Others did not have proper electronic archives and were often made of single institution efforts. Conclusions To address the data management need, we built a bank of chronic disease registries https://disreg.org/ and established partnerships with research teams. The bank is designed with multiple levels of access control. Additional registries can be plugged into the bank with ease. It provides a warehouse for chronic disease researchers to archive their data in Nigeria and potentially beyond. Key messages The bank will enrich the data available for investigating risk factors of chronic diseases pertinent in our environment.

Semantic modelling of Common Data Elements for Rare Disease registries, and a prototype workflow for their deployment over registry data

Background: The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Disease (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles. Results: Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR. Conclusions: Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.

A Medical Report Feature for OSSE Rare Disease Registries

Web-based patient registries support clinicians by providing a way to effectively store and process data. Here, we present a new feature for the open-source registry software OSSE: medical reports generated with R Markdown. As part of a rare disease research project, we describe the process from requirements assessment to the current state of technical implementation. The feature offers clinicians the possibility to download customised as well as generic reports from an OSSE rare disease registry.

Decongestant use and the risk of myocardial infarction and stroke: a case-crossover study

Pharmacovigilance reports of cerebral and cardiovascular events in those who use decongestants have triggered alerts related to their use. We aimed to assess the risk of stroke and myocardial infarction (MI) associated with the use of decongestants. We conducted a nested case-crossover study of patients with incident stroke and MI identified in France between 2013 and 2016 in two systematic disease registries. Decongestant use in the three weeks preceding the event was assessed using a structured telephone interview. Conditional logistic multivariable models were used to estimate the odds of incident MI and stroke, also accounting for transient risk factors and comparing week 1 (index at-risk time window, immediately preceding the event) to week 3 (reference). Time-invariant risk factors were controlled by design. In total, 1394 patients with MI and 1403 patients with stroke, mainly 70 years old or younger, were interviewed, including 3.2% who used decongestants during the three weeks prior to the event (1.0% definite exposure in the index at-risk time window, 1.1% in the referent time window; adjusted odds ratio (aOR), 0.78; 95%CI, 0.43–1.42). Secondary analysis yielded similar results for individual events (MI/stroke). We observed no increased risk of MI or stroke for patients 70 years of age and younger without previous MI or stroke who used decongestants.