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@biothings-explorer/smartapi-kg
@biothings-explorer/smartapi-kg/built/index.js

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Readme

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

npm 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 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

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

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