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@biothings-explorer/api-response-transform
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1.12.0 • Public • Published

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

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

🏠 Homepage

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' ]
      //  },
      //  ...]

Run tests

npm run test

Author

👤 BioThings team

🤝 Contributing

Contributions, issues and feature requests are welcome!
Feel free to check issues page.

Show your support

Give a ⭐️ if this project helped you!

📝 License

Copyright © 2021 BioThings Team.
This project is ISC licensed.

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Install

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

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Version

1.12.0

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Collaborators

  • ericz1803
  • kevinxin
  • marcocano
  • newgene