Skip to content

Latest commit

 

History

History
33 lines (24 loc) · 2.99 KB

README.md

File metadata and controls

33 lines (24 loc) · 2.99 KB
Raw

Open Targets Extensible API

This repository template enables extending the OpenTargets Genetics API with custom data. This is intended to act as a backend data/API server. This is a good option if you have data that would be helpful to display alongside existing OpenTargets data. Please note that in order to view your data in a UI, you will have to modify an instance of the OpenTargets Genetics App, and point the API URL to this server instance.

This works by using a docker-compose setup to coordinate 2 services:

  1. The Node server backend that delegates calls to the OpenTargets API while augmenting response with custom data as necessary
  2. The Postgres SQL database storing the custom data to be served alongside OpenTargets data

Quickstart

Prerequisites: You must have Docker installed.

  1. Clone the repository
  2. From the main directory, run
docker compose up

This will run both services. You can verify the setup is working by making any normal graphql requests to your local API server running on port 4000. For example, through CURL:

curl -X POST -H 'Content-Type: application/json' localhost:4000 -d '{"operationName":"VariantPageQuery","variables":{"variantId":"1_154453788_C_T"},"query":"query VariantPageQuery($variantId: String!) {\n  variantInfo(variantId: $variantId) {\n    rsId\n    chromosome\n    position\n    chromosomeB37\n    positionB37\n    refAllele\n    altAllele\n    nearestGene {\n      id\n      symbol\n      __typename\n    }\n    nearestGeneDistance\n    nearestCodingGene {\n      id\n      symbol\n      __typename\n    }\n    nearestCodingGeneDistance\n    mostSevereConsequence\n    caddRaw\n    caddPhred\n    gnomadAFR\n    gnomadAMR\n    gnomadASJ\n    gnomadEAS\n    gnomadFIN\n    gnomadNFE\n    gnomadNFEEST\n    gnomadNFENWE\n    gnomadNFESEU\n    gnomadOTH\n    __typename\n  }\n}\n"}'

Should return:

{"data":{"variantInfo":{"rsId":"rs4129267","chromosome":"1","position":154453788,"chromosomeB37":"1","positionB37":154426264,"refAllele":"C","altAllele":"T","nearestGene":{"id":"ENSG00000163239","symbol":"TDRD10","__typename":"Gene"},"nearestGeneDistance":48431,"nearestCodingGene":{"id":"ENSG00000163239","symbol":"TDRD10","__typename":"Gene"},"nearestCodingGeneDistance":48431,"mostSevereConsequence":"intron_variant","caddRaw":0.705045,"caddPhred":11.13,"gnomadAFR":0.13748274275195582,"gnomadAMR":0.5094339622641509,"gnomadASJ":0.4517241379310345,"gnomadEAS":0.3795336787564767,"gnomadFIN":0.3019573978123201,"gnomadNFE":0.37592809691285656,"gnomadNFEEST":0.34029916410030797,"gnomadNFENWE":0.3897058823529412,"gnomadNFESEU":0.5283018867924528,"gnomadOTH":0.3318014705882353,"__typename":"Variant"}}}

Adding Custom Data

Please follow the guides in the docs folder for information on how to add and serve your own data.

Backend Design

See the Backend Server README for more information on the technologies used.