ethnexus/disgenet-ms repository overview

⁠Disgenet Micro Service

A reusable micro service to provide Disgenet apis and data on a local machine.

⁠Usage

To use the microservice in your application you need to integrate the following configuration into your docker-compose.yml

version: "3"

services:
  disgenet:
      image: ethnexus/disgenet-ms
      volumes:
        - ./data:/data:z
      ports:
        - "9077:9077"
      secrets:
        - disgenet_creds
      env_file: .env
  secrets:
    disgenet_creds:
      file: ./.disgenet_creds

In your .env file adjust the required environment variables (if the values are not set the defaults as below are taken):

DISGENET_DB_URL=https://www.disgenet.org/static/disgenet_ap1/files/sqlite_downloads/current/disgenet_2020.db.gz
DISGENET_UMLS_URL=https://www.disgenet.org/static/disgenet_ap1/files/downloads/disease_mappings_to_attributes.tsv.gz

Create the disgenet credentials file:

echo "${DISGENET_USERNAME}:${DISGENET_PASSWORD}" | base64 > .disgenet_creds

Run the container using:

docker-compose up -d

⁠Using the API

⁠All VDA's

/api/vda/variants

⁠Example url for a single VDA

/api/vda/variants/rs295

⁠Filter parameters

• year: some description (e.g. Examplevalue)
• source: some description (e.g. Examplevalue)
• score: some description (e.g. Examplevalue)
• ei: some description (e.g. Examplevalue)
• pmid: some description (e.g. Examplevalue)

You can provide multiple of those parameters as query parameters in the url:

/api/vda/variant?year=2000&source=UNIPROT