The virtual microbial resource is a database to store metadata of samples, isolates, and sequences collected as part of the Government of Canada's GRDI-AMR2 project. It implements the GRDI-AMR OneHealth data standard as a relational database in PostGres.
This repo contains the sql code to generate a mostly-empty database. The GRDI-AMR OneHealth ontology, which definesontology terms that are allowed to be selected in various the metadata fields, is also implemented in this repo.
Requirements:
- Postgres
On a local machine, ensure a postgres cluster is initialized. Then, create a database from the baseline sql code:
cd src
bash make_from_baseline.sh database_name
This will generate a schema with empty data tables, but with ontology terms and associated lookup tables filled according to the GRDI OneHealth data standard.