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Semantic data model of the set of common data elements for rare disease registration

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Status: The rdf model is still in an early development stage. The current version of the model is intended for internal use and testing purpose only.

There are two versions of the model(s). One captures the features/facets of the JRC as free-form entity-relationship diagrams (see the top set of models in the navigation box to the right of the screen). The second version of the model(s) uses the SemanticScience Integrated Ontology as an overarching framework for scholarly knowledge representation, into which these facets are mapped and organized.

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To make rare disease registry data Interoperable (the 'I' in FAIR). Version 0.2.0. License CC0.

Here, we present a semantic data model of the set of common data elements for rare diseases registration recommended by the European commission joint research centre. There are 16 data elements: ‘Pseudonym’, ‘Date of Birth’, ‘Sex’, ‘Patient’s status’, ‘Date of death’, ‘First contact with specialised centre’, ‘Age at onset’, Age at diagnosis’, ‘Diagnosis of the rare disease’, ‘Genetic diagnosis’, ‘Undiagnosed case’, ‘Agreement to be contacted for research purposes’, ‘Consent to the reuse of data’, ’Biological sample’, ‘Link to a biobank’, ‘Classification of functioning/disability’.

The semantic data model is presented below in 11 modules describing the different 16 data elements. Central to each module is the 'person'. Each module has in addition different characteristics assigned to the person.

Modules (free-form)

• Person
• Pseudonym
• Personal information
• Patient status
• Care pathway
• Disease history and diagnosis
• Genetic diagnosis
• Undiagnosed
• Consent
• Biobanks
• Disability

Modules (SIO framework)

• Pseudonym
• Personal information
• Patient status
• Care pathway
• Disease history and diagnosis
• Genetic diagnosis
• Undiagnosed
• Consent
• Biobanks
• Disability

General notes

• The relationships defined in this semantic data model are all based on assigning characteristics to the patient/person. If multiple forms are filled in per patient/person we need to include clinical visits, including dates etc.
• In this data model we have used snomed, which has a licence, which considerations do we need to take here when thinking about reusability within multiple countries?

Feedback

Your feedback is more than welcome it will help us improve our semantic data model. Please use github issues to provide your feedback. If you are new to github please see this video to know more about github issues.