CDERD

CDERD standardizes and semantically models 16 Common Data Elements (CDEs to enable interoperable, FAIR-compliant integration of rare disease (RD) registry data using the SemanticScience Integrated Ontology (SIO) and ontology mappings).

Key Features:

• Semantic Modeling: Creates semantically grounded models for 16 Common Data Elements (CDEs) using the SemanticScience Integrated Ontology (SIO).
• Ontological Mapping: Maps CDE concepts to the Orphanet Rare Disease Ontology (ORDO), Human Phenotype Ontology (HPO), and National Cancer Institute Thesaurus (NCIt).
• FAIR Data Principles Compliance: Aligns models and outputs with the FAIR principles (Findable, Accessible, Interoperable, Reusable) to support FAIR-compliant data publication.
• Reusable ETL Pipeline: Provides an exemplar Extract, Transform, Load (ETL) pipeline for transforming registry raw data into model-compliant, FAIR-formatted outputs deployable across independent repositories.

Scientific Applications:

• Interoperability of RD Patient Data: Enables semantic integration of rare disease patient data across independent registries and the European Platform on Rare Disease Registration.
• FAIR Data Publication: Supports publication of expressive, semantically rich FAIR data by rare disease registries and biomedical domain experts to facilitate data sharing and reuse.

Methodology:

Semantic modeling of 16 CDEs using the SemanticScience Integrated Ontology (SIO); mapping CDE concepts to Orphanet Rare Disease Ontology, Human Phenotype Ontology, and National Cancer Institute Thesaurus; and an exemplar Extract, Transform, Load (ETL) pipeline to convert raw registry data into model-compliant, FAIR formats.