README.md

This project serves to develop and maintain a Neo4j-GraphQL API for the Neo4j graph database used by the CovidGraph project.

• Demo
  • GraphQL Playground
  • GraphQL Voyager
• Getting Started
• Schema
  • Patents
  • BioBERT
  • BioMedical
  • Papers
  • Clinical Trials
  • Statistical & Geographic
• Tests

Demo

GraphQL Playground

The API is currently hosted by Vercel at: https://covid-graph-graphql.now.sh/. For example queries, please see the below integration tests.

Try this query 🚀

query {
  Paper(first: 50) {
    _hash_id
    cord_uid
    journal
    publish_time
    source
    title
    url
  }
}

GraphQL Voyager

GraphQL Voyager is available at: https://covid-graph-graphql.now.sh/voyager

Getting Started

Install root dependencies:

npm install

and install /api dependencies:

cd api
npm install

In the root directory, you can start the API server with:

run run start

To develop the API server and print Cypher translations to your terminal:

cd api
npm run start:dev

Schema

The below links go to corresponding Neo4j-GraphQL type definitions:

Patents

• Patent
• PatentTitle
• PatentAbstract
• PatentDescription
• PatentClaim
• PatentNumber
• Entity

BioBERT (NLP + NER)

• Fragment
• Keyword
• NamedEntity
• GOTerm
• Word

BioMedical

• Gene
  • GeneSymbol
  • GtexTissue
  • Pathway
  • Disease
    • Anatomy
  • Transcript
    • Protein

Papers

• Paper
  • Author
    • Affiliation
      • Location
  • ReferenceCollection
    • BodyText
    • Reference
    • Abstract
      • Citation

Clinical Trials

• ClinicalTrial
  • Design
  • InclusionCriteria
  • ExclusionCriteria
  • Status
  • Description
  • Contact
  • Phase
  • Facility
• Compound

Statistical & Geographic

• Country
  • City
  • Province
    • DailyReport
  • AgeGroup

Tests

Integration tests are run using Ava. To run the below tests, start the API server and run:

npm run test

If you're in /api, you can run:

npm run integration

Patents

• Patent

BioBERT (NLP + NER)

• NamedEntity path: (NamedEntity)<-[MENTIONS]-(Abstract)-[HAS_FRAGMENT]->(FromAbstract:Fragment)-[MENTIONS]->(GeneSymbol)

BioMedical

• Gene
  • GeneSymbol
  • Disease
  • Protein

Papers

• Paper

Clinical Trials

• ClinicalTrial
• Compound

Statistical & Geographic

• Country path: (Country)<-[LOCATED_IN]-(City)<-[LOCATED_IN]-(Facility)
• Country path: (Country)<-[PART_OF]-(Province)-[REPORTED]->(DailyReport)
• Country to AgeGroups