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The best way to use GraphQL with an Amazon Neptune backend is to leverage AWS AppSync. With AppSync, you don't have to manage an Apollo server and you can define your GraphQL schema and resolvers within the AppSync service. We don't yet have the ability to automatically generate the resolvers for Neptune, so you'll have to manually create a resolver using AWS Lambda and the appropriate graph query using either Gremlin or openCypher (1).
(1) https://docs.aws.amazon.com/appsync/latest/devguide/tutorial-lambda-resolvers.html
There are some great examples of how to use AppSync with Neptune here:
https://github.com/dabit3/cdk-appsync-neptune
https://github.com/aws-samples/aws-appsync-calorie-tracker-workshop
https://github.com/jkahn117/aws-appsync-session-manager-neptune
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