imProving Agent

imProving Agent is Autonomous Reasoning Agent built on top of Scalable Precision Medicine Oriented Knowledge Engine (SPOKE) and is part of the NCATS Biomedical Data Translator Network. It aims to improve user queries by utilizing EHR and multi-omic cohorts to extract the best knowledge for a given concept. Use these links to find out more about imProving Agents's Data, its algorithms, or some of its multi-omic cohort data.

Using imProving Agent as a client

Find a Jupyter notebook with some basic examples of appropriate Translator Reasoner API queries here.

Deploying

SPOKE database

imProving Agent relies on a bolt connection to a Neo4j instance of SPOKE

PSEVs

For ranking, imProving Agent relies on PSEVs. PSEVs are accessed via the psev-service

Environment variables

Depending on the environment in which imProving Agent is to be run, a number of environment variables must be set.

ITRB deployment

The following variables must be set for deployment in the ITRB test, staging, and production environments:

• APP_ENV_IA should be set to itrb
• AWS_REGION should be set to the AWS region in which the secrets noted below are stored.
• NEO4J_SPOKE_HOSTNAME should be set to the environment-specific (CI, Production, Test) hostname of the instance hosting SPOKE
• NEO4J_SECRETS_NAME should be set to the environment-specific name of the secret that contains the authentication credentials for SPOKE
• PSEV_SECRETS_NAME should be set to the environment-specific name of the secrets that will be used to authenticate with the psev-service
• PSEV_SERVICE_HOSTNAME the environment-specific hostname of the instance hosting the psev-service. In most cases, this should be set to the same value as the NEO4J hostname above

Local and dev deployment

• APP_ENV_IA should be set to local or dev
• NEO4J_SPOKE_HOSTNAME should be set to the docker network name of the SPOKE instance to which imProving Agent will connect. In some cases, e.g. when running against remote databases, this can be set to the remote hostname
• NEO4J_SPOKE_PASS should be set to the password of the local SPOKE Neo4j instance
• NEO4J_SPOKE_USER should be set to the user of the local SPOKE Neo4j instance
• PSEV_API_KEY should be set to the value of the key that will be used to connect with the local psev-service instance
• PSEV_SERVICE_HOSTNAME should be set to the docker network name of the psev-service to which imProving Agent will connect
• AWS_SHARED_CREDENTIALS_FILE if running locally against remote resources in AWS, this should be set to the location where boto3 can find your AWS credentials

Networking

The imProving Agent HTTP service will be exposed on port 3031 and uwsgi stats will be exposed on port 3032. When running locally via docker-compose, these ports are bound to host ports 3033 and 3034, respectively.

Running imProving Agent

Given the depedencies described above, start the service with docker-compose up web