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4.0.0 • Public • Published

Welcome to @biothings-explorer/smartapi-kg 👋

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

🏠 Homepage


npm i @biothings-explorer/smartapi-kg


  • 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
    • 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);
    • Option 9: 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

npm run test


👤 Jiwen Xin

🤝 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.

This README was generated with ❤️ by readme-md-generator


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