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A nodejs library for generate knowledge graphs based on SmartAPI Specifications

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biothings/smartapi-kg.js

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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

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

🤝 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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