Chapter | 4 Database and data sources
4.1 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).
4.2 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:
4.3 Variant ontology
We use the “Variation Ontology” as ontology for the annotation of variation effects and mechanisms. Currently active terms are represented in following table. Initially we used 85 variant ontology terms. This was extended to include 11 additional terms for non-coding RNA variation. The column ‘use’ depicts the variant ontology terms used for our curation. The column ‘sort’ is used to display the most commonly used ontology terms first.