Enhancing FAIR data practices in China: An integrated strategy for biomedical research

Abstract

The construction of scientific data compliant with FAIR (Findability, Accessibility, Interoperability, and Reusability) principles has become a consensus in the biomedical field. However, FAIR is often implemented at the data submission stage, leading to suboptimal outcomes, such as incomplete metadata, limited semantic consistency, and high costs of post hoc FAIRification. We developed a comprehensive data service to support the application of data standards at the project onset, facilitating efficient FAIR-aligned metadata and data management. We developed two resource platforms for terminology and metadata. MedPortal, built on the OntoPortal framework, provides ontology resources using application programming interface (API) and web-based tools for ontology querying, annotation, and mapping. CDE Portal employs a standard metadata model and leverages MedPortal for semantic support, offering tools for common data element (CDE) storage, query, construction, reuse, and management. To enhance accessibility for domain scientists, we developed CDE Tools, an easy-to-use Microsoft® Excel® add-in, utilizing APIs from MedPortal and CDE Portal, allowing the reuse of CDEs and case report forms (CRFs) from CDE Portal, and supporting standardization during data collection through value constraints and term queries via MedPortal. MedPortal now has 62 ontologies, including 9 bilingual Chinese-English ontologies, with 3,590,080 ontology terms available. There are 88,289 CDEs and 107 CRFs stored in the CDE Portal from research projects and data-dictionary standards in China. A functional assessment was conducted to examine how the platform services and managed resources support selected FAIR indicators. Our biomedical data standard application service provides scientists with data standards resources and application tools for constructing, publishing, managing, and applying biomedical metadata standards from the beginning of research projects.