Beacon API for CARE-SM patient data

Beacon API for CARE Semantic Model. to perform anonymous patient counts from data registries. This implementation converts Beacon Requests into CARE-SM SPARQL counting query, retrieving a Beacon-compliant JSON Response with the anonymous outcome.

Considerations:

Beacon-API4CARE-SM is only compatible with Triplestore repositories that contain CARE-Semantic Model patient data.

Documentation:

This implementation follows the EJPRD Virtual Platform API specifications for Beacon API v.2.0 at Github.

Usage and Docker

This whole implementation is Dockerized at Docker hub, check our public image here. Feel free to implement our docker image next to your TripleStore with CARE-SM patient data.

This beacon API consumes environmental variables for all required parameters related to triplestore credentials (endpoint/username/password) and all available filters to query.

You can run the docker image in a docker-compose file that contains your environmental variables with your credentials, like this:

version: '3'
services:
  api:
    image: pabloalarconm/beacon-api4care-sm:0.1.0
    ports:
      - "8000:8000"
    environment:
      - TRIPLESTORE_URL=http://localhost:7200/repositories/exemplar_vp_api_repo
      - TRIPLESTORE_USERNAME=admin
      - TRIPLESTORE_PASSWORD=root
      - URL_SERVER=http://0.0.0.0:8000/

      - FILTER_SEX=True
      - FILTER_DISEASE=True
      - FILTER_SYMPTOM=True
      - FILTER_GENE_VARIANT=True
      - FILTER_BIRTHYEAR=True
      - FILTER_AGE_SYMPTOM_ONSET=True
      - FILTER_AGE_DIAGNOSIS=True

This beacon-API4CARE-SM is already deployed at FAIR-in-a-box (Fiab) interface.

Beacon Request

Exemplar Beacon JSON complaint request containing filter. For more examples, please check your exemplar_body folder.

{ 
  "meta":{
    "apiVersion": "v2.0",
    "returnedSchemas": []

},
    "query": {
         "filters": [
          {
            "type": "obo:NCIT_C124353",
            "id": "7",
            "operator": ">"
          },
          {
            "type": "obo:NCIT_C28421",
            "id": "obo:NCIT_C16576",
            "operator": "="
          },
          {
            "type": "sio:SIO_010056",
            "id": "obo:HP_0003131",
            "operator": "="
          }
        ]
       }
   }