IT for Advanced Bioinformatics Applications: Variant Database

A variant database created with Django and MongoDB as part of BIOL60860.

Team

• George Doyle (@gdoy1)
• Robert Wilson (@RSWilson1)
• Ben Bunce (@bbunce)
• Becky Locke (@rklocke)

Set up

Clone the repo and install the requirements using requirements.txt:

cd uom_mongodb
pip install -r requirements.txt

Pull the official MongoDB Docker image from DockerHub:

docker pull mongo

Run the container and copy the JSON containing variants into the container:

docker run -p 27017:27017 -d mongo --name variant_db
docker cp <path_to_file>/all_variants.json variant_db:/all_variants.json

Set env variable for the IP address of the Docker container:

nano ~/.bashrc
export UOM_DOCKER_IP="mongodb://<your_ip_address>:27017"

Run interactively:

docker exec -it variant_db bash

Import the JSON into my_database into the collection variants:

mongoimport --db mydatabase --collection variants --file /all_variants.json

Exit and finally, run the server:

python manage.py runserver

Features

Query the variants in the database

To query the variants that are present in the database, use the form present on the Query Variants page.

Example of querying with SNP, variant consequence and coordinate range, variant counter shows a subset of the whole database.

View summary of variant consequence from query

The summary of variant consequences from the query can be view by clicking on the Query Summary Graph button.

Example of query results summary graph of variant consequences.

Add variants to the database

Add a single variant

A single variant can be added via a form using the 'Add Single Variant' page from the navigation bar.

• The form will validate your entries and check if your variant already exists in the database by the genome assembly, chromosome, start, end, ancestral and minor alleles provided.
• If the variant already exists, the form will produce an error, otherwise your variant will be uploaded and a success message will be displayed.

Bulk upload variants

Variants can be uploaded in bulk via a JSON file using the Upload page.

A success message will confirm everything has been uploaded correctly.

This form will check if any variants in the JSON are already present in the database, have any missing mandatory field or do not conform to the correct format.