5 Database and data sources
5.1 Database software
SysNDD currently uses the open-source MySQL relational database management system. The repository Compose stack uses the official MySQL Docker image, currently mysql:8.4.9.
5.2 Database schema
The design of our DB schema can be viewed in DB DESIGNER:
The diagram below is a documentation snapshot. The versioned schema source of truth is the migration history under db/migrations/ and the current database initialized by the migration runner.
5.3 Variant ontology
We use the “Variation Ontology” as ontology for the annotation of variation effects and mechanisms. Currently active terms include variant ontology terms for our curation. The list was extended to include additional terms for non-coding RNA variation.
The complete list of variation ontology terms can be accessed via:
- The SysNDD API endpoint for variation ontology lists
- The Variation Ontology (VariO) website
- The EBI OLS Vario terms
Reviewer-facing guidance for choosing among existing variation ontology terms is described in the re-review instructions.
5.4 Mode of Inheritance ontology
We use the “Human Phenotype Ontology” as ontology for the mode of inheritance.
The inheritance terms used in SysNDD follow the HPO standard and can be accessed via:
- The SysNDD API endpoint for inheritance lists
- The Human Phenotype Ontology website
For the complete and up-to-date list of ontology terms used in SysNDD, please refer to the SysNDD API documentation.