@biothings-explorer/api-response-transform NPM

Welcome to @biothings-explorer/api-response-transform 👋

A NodeJS module to transform the JSON output from API into BioLink-compatible JSON structure

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Install

npm i @biothings-explorer/api-response-transform

Usage

This package is desgined to be used as a downstream consumer of @biothings-explorer/smartapi-kg nodejs package. @biothings-explorer/smartapi-kg provides knowledge graph operation info, and when combined with API JSON response, can be consumed as input of the @biothings-explorer/api-response-transform package.

Import and Initialize

const tf = require("@biothings-explorer/api-response-transform")
const axios = require("axios");

Transform

Get API Response

let res = await axios({
    method: 'post',
    url: 'https://biothings.ncats.io/semmedgene/query',
    data: 'q=C1332823, C1332824, 123&scopes=umls',
    params: {
        fields: 'name,umls,positively_regulates',
        size: '5'
    }
});

Bind with edge info from @biothings-explorer/smartapi-kg

let input = {
    response: res.data,
    edge: {
        "input": ["C1332824", "C1332823"],
        "query_operation": {
            "params": {
                "fields": "positively_regulates"
            },
            "request_body": {
                "body": {
                    "q": "{inputs[0]}",
                    "scopes": "umls"
                }
            },
            "path": "/query",
            "path_params": [],
            "method": "post",
            "server": "https://biothings.ncats.io/semmedgene",
            "tags": [
                "disease",
                "annotation",
                "query",
                "translator",
                "biothings",
                "semmed"
            ],
            "supportBatch": true,
            "inputSeparator": ","
        },
        "association": {
            "input_id": "UMLS",
            "input_type": "Gene",
            "output_id": "UMLS",
            "output_type": "Gene",
            "predicate": "positively_regulates",
            "source": "SEMMED",
            "api_name": "SEMMED Gene API",
            "smartapi": {
                "id": "81955d376a10505c1c69cd06dbda3047",
                "meta": {
                    "ETag": "f94053bc78b3c2f0b97f7afd52d7de2fe083b655e56a53090ad73e12be83673b",
                    "github_username": "kevinxin90",
                    "timestamp": "2020-05-27T16:53:40.804575",
                    "uptime_status": "good",
                    "uptime_ts": "2020-06-12T00:04:31.404599",
                    "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_gene.yaml"
                }
            }
        },
        "response_mapping": {
            "positively_regulates": {
                "pmid": "positively_regulates.pmid",
                "umls": "positively_regulates.umls"
            }
        },
        "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
    }
}

Transform into biolink-compatible format

let transformer = new tf.default(input);
let res = transformer.transform();

//returns [
//{
//  HGNC: '10956',
//  pubmed: [ '21685912', '30089514', sequence: true ],
//  relation: 'contributes to condition',
//  source: [ 'https://archive.monarchinitiative.org/#gwascatalog' ],
//  taxid: 'NCBITaxon:9606',
//  '$reasoner_edge': undefined,
//  '$association': {
//    input_id: 'MONDO',
//    input_type: 'Disease',
//    output_id: 'HGNC',
//    output_type: 'Gene',
//    predicate: 'related_to',
//    api_name: 'BioLink API',
//    smartapi: [Object]
//  },
//  '$input': 'MONDO:678',
//  '$output': 'HGNC:10956',
//  '$original_input': undefined,
//  '$input_resolved_identifiers': undefined,
//  publications: [ 'PMID:21685912', 'PMID:30089514' ]
//  },
//  ...]