5 Database and data sources
5.1 Database software
SysNDD currently uses the open-source MySQL 8.0 relational database management system (RDBMS). The database runs in a docker container using the official mysql docker image (version 8.0.29).
5.2 Database schema
The design of our DB schema can be viewed in DB DESIGNER:
As of 2022-06-07 the database schema looks like this:
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
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.