Welcome to @biothings-explorer/smartapi-kg 👋

Generate a meta knowledge graph of how biomedical concepts are connected based on SmartAPI Specifications with built-in filtering capabilities

🏠 Homepage

Install

pnpm i @biothings-explorer/smartapi-kg

Usage

• Import and Initialize

  const kg = require("@biothings-explorer/smartapi-kg")
  //initiate a new knowledge graph class
  let meta_kg = new kg.default()

• Load the Meta Knowledge Graph (meta-kg)

  • Option 1: Load Meta-KG from SmartAPI specs with translator tag specified

    //async load knowledge graph from SmartAPI
    await meta_kg.constructMetaKG()

  • Option 2: Load Meta-KG from SmartAPI specs with translator tag as well as ReasonerStdAPI with /predicates endpoint

    await meta_kg.constructMetaKG(includeReasoner=true);

  • Option 3: Load Meta-KG from SmartAPI specs with tags equal to biothings

    await meta_kg.constructMetaKG(includeReasoner = false, {tag: "biothings"});

  • Option 4: Load Meta-KG from SmartAPI specs with team name equal to Text Mining Provider

    await meta_kg.constructMetaKG(includeReasoner = false, {teamName: "Text Mining Provider"});

  • Option 5: Load Meta-KG from SmartAPI specs with component equal to KP

    await meta_kg.constructMetaKG(includeReasoner = false, {component: "KP"});

  • Option 6: Load Meta-KG for a specific SmartAPI spec with SmartAPI ID

    await meta_kg.constructMetaKG(includeReasoner = false, {smartAPIID: "5076f09382b38d56a77e376416b634ca"});

  • Option 7: Load Meta-KG from a local copy of SmartAPI specs included in the package

    //Alternatively, you can also sync load SmartAPI specs from a local copy within the package
    meta_kg.constructMetaKGSync();

  • Option 8: Load Meta-KG from file path you specify

      const path = require("path");
      // provide file path storing your SmartAPI file
      const file_path = path.resolve(__dirname, '../data/smartapi_multiomics_kp_query.json');
      let meta_kg = new MetaKG(file_path);
      meta_kg.constructMetaKGSync();

  • Option 9: Load Meta-KG from data you specify

      const smartapiSpecs = {} // This should contain your smartapi specs: could be from file read, redis, etc.
      const predicates = [] // This should contain predicates data on TRAPI APIs (optional)
    
      let meta_kg = new MetaKG();
      meta_kg.constructMetaKGSync(includeReasoner = true, { predicates, smartapiSpecs });

  • Option 10: Load Meta-KG from operations you specify

      const meta_kg_old = new MetaKG();
      meta_kg_old.constructMetaKGSync();
      const ops = meta_kg_old.ops; // ops can be transfered over a network/threads since it just stores JSON
    
      // loading a new MetaKG from the operations
      const meta_kg = new MetaKG(undefined, undefined, ops);

  • Option 11: Load Meta-KG with an api list

    meta_kg.constructMetaKGSync(includeReasoner=true, {apiList: [
      {
        id: '09c8782d9f4027712e65b95424adba79',
        name: 'MyVariant.info API'
      },
      {
        id: '59dce17363dce279d389100834e43648',
        name: 'MyGene.info API'
      }
    ]});

• Filter the Meta-KG for specific associations based on input, output, predicate, or api combinations.

  //filter based on predicate
  meta_kg.filter({predicate: 'treats'})
  //filter based on predicate and input_id
  meta_kg.filter({predicate: 'treats', input_id: 'CHEMBL.COMPOUND'})
  //filter based on predicate and input_type
  meta_kg.filter({predicate: ['treats', 'physically_interacts_with'], input_type: 'SmallMolecule'})
  //filter based on input_type, output_type and api
  meta_kg.filter({ api: "Automat PHAROS API", input_type: "SmallMolecule", output_type: "Gene" });

Runkit Notebook Demo

Run tests

pnpm run test

Author

👤 Jiwen Xin

• Website: http://github.com/kevinxin90
• Github: @kevinxin90

🤝 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 © 2020 Jiwen Xin.
This project is ISC licensed.

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