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https://github.com/Covid19-GraphQL/covid-graph-graphql
A Neo4j-GraphQL API for the CovidGraph project
https://github.com/Covid19-GraphQL/covid-graph-graphql
api coronavirus covid-19 grandstack graphql graphs4good
Last synced: about 2 months ago
JSON representation
A Neo4j-GraphQL API for the CovidGraph project
- Host: GitHub
- URL: https://github.com/Covid19-GraphQL/covid-graph-graphql
- Owner: Covid19-GraphQL
- License: apache-2.0
- Created: 2020-03-25T21:47:42.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2022-12-13T18:36:13.000Z (about 2 years ago)
- Last Synced: 2024-08-04T01:27:24.168Z (5 months ago)
- Topics: api, coronavirus, covid-19, grandstack, graphql, graphs4good
- Language: JavaScript
- Homepage: https://covid-graph-graphql.now.sh/
- Size: 8.15 MB
- Stars: 22
- Watchers: 3
- Forks: 3
- Open Issues: 39
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-list - covid-graph-graphql - GraphQL API for the CovidGraph project | Covid19-GraphQL | 19 | (JavaScript)
README
[](https://circleci.com/gh/Covid19-GraphQL/covid-graph-graphql)
This project serves to develop and maintain a [Neo4j-GraphQL](https://grandstack.io/docs/neo4j-graphql-js) API for the Neo4j graph database used by the [CovidGraph](https://covidgraph.org/) project.
* [Demo](#demo)
* [GraphQL Playground](#graphql-playground)
* [GraphQL Voyager](#graphql-voyager)
* [Getting Started](#getting-started)
* [Schema](#schema)
* [Patents](#patents)
* [BioBERT](#biobert-nlp--ner)
* [BioMedical](#biomedical)
* [Papers](#papers)
* [Clinical Trials](#clinical-trials)
* [Statistical & Geographic](#statistical--geographic)
* [Tests](#tests)
[](https://covidgraph.org/ 'Image from covidgraph.org')
## 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](#tests).
Try this query 🚀
```graphql
query {
Paper(first: 50) {
_hash_id
cord_uid
journal
publish_time
source
title
url
}
}
```
[](https://covid-graph-graphql.now.sh/ 'GraphQL Playground')
### GraphQL Voyager
[GraphQL Voyager](https://www.npmjs.com/package/graphql-voyager) is available at: https://covid-graph-graphql.now.sh/voyager
[](https://covid-graph-graphql.now.sh/voyager 'GraphQL Voyager')
## Getting Started
Install root dependencies:
```sh
npm install
```
and install `/api` dependencies:
```sh
cd api
npm install
```
In the root directory, you can start the API server with:
```sh
run run start
```
To develop the API server and print Cypher translations to your terminal:
```sh
cd api
npm run start:dev
```
## Schema
The below links go to corresponding Neo4j-GraphQL type definitions:
### Patents
* [Patent](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/5f3d1da4fffe6bc6982f52caa73bfb463df72621/api/src/schemas/Patents/typeDefs/Patent.js#L5)
* [PatentTitle](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/5f3d1da4fffe6bc6982f52caa73bfb463df72621/api/src/schemas/Patents/typeDefs/Patent.js#L189)
* [PatentAbstract](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/5f3d1da4fffe6bc6982f52caa73bfb463df72621/api/src/schemas/Patents/typeDefs/Patent.js#L156)
* [PatentDescription](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/5f3d1da4fffe6bc6982f52caa73bfb463df72621/api/src/schemas/Patents/typeDefs/Patent.js#L217)
* [PatentClaim](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/5f3d1da4fffe6bc6982f52caa73bfb463df72621/api/src/schemas/Patents/typeDefs/Patent.js#L203)
* [PatentNumber](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/5f3d1da4fffe6bc6982f52caa73bfb463df72621/api/src/schemas/Patents/typeDefs/Patent.js#L46)
* [Entity](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/5f3d1da4fffe6bc6982f52caa73bfb463df72621/api/src/schemas/Patents/typeDefs/Patent.js#L170)
### BioBERT (NLP + NER)
* [Fragment](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/BioBERT/typeDefs/Fragment.js#L23)
* [Keyword](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/BioBERT/typeDefs/Keyword.js#L10)
* [NamedEntity](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/BioBERT/typeDefs/NamedEntity.js#L9)
* [GOTerm](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/BioBERT/typeDefs/GOTerm.js#L11)
* [Word](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/BioBERT/typeDefs/Word.js#L6)
### BioMedical
* [Gene](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/Gene.js#L5)
* [GeneSymbol](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/GeneSymbol.js#L5)
* [GtexTissue](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/Gene.js#L84)
* [Pathway](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/Gene.js#L164)
* [Disease](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/Disease.js#L5)
* [Anatomy](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/Disease.js#L41)
* [Transcript](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/Gene.js#L44)
* [Protein](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Biomedical/typeDefs/Protein.js#L5)
### Papers
* [Paper](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L5)
* [Author](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L32)
* [Affiliation](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L44)
* [Location](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L52)
* [ReferenceCollection](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L92)
* [BodyText](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L161)
* [Reference](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L77)
* [Abstract](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L122)
* [Citation](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Papers/typeDefs/Paper.js#L145)
### Clinical Trials
* [ClinicalTrial](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L5)
* [Design](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L162)
* [InclusionCriteria](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L206)
* [ExclusionCriteria](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L211)
* [Status](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L121)
* [Description](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L156)
* [Contact](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L216)
* [Phase](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L98)
* [Facility](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/ClinicalTrial.js#L55)
* [Compound](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/ClinicalTrials/typeDefs/Compound.js#L5)
### Statistical & Geographic
* [Country](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Cases/typeDefs/Country.js#L5)
* [City](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Cases/typeDefs/Country.js#L15)
* [Province](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Cases/typeDefs/Country.js#L28)
* [DailyReport](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Cases/typeDefs/Country.js#L43)
* [AgeGroup](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/076ffb5423a79331a51d8e192016a926bf78f04d/api/src/schemas/Cases/typeDefs/Country.js#L67)
## Tests
Integration tests are run using [Ava](https://github.com/avajs/ava). To run the below tests, start the API server and run:
```sh
npm run test
```
If you're in `/api`, you can run:
```sh
npm run integration
```
[](./img/integration-tests.png 'Integration tests')
### Patents
* [Patent](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Patents/tests/Patent.test.js#L5)
### BioBERT (NLP + NER)
* [NamedEntity path: (NamedEntity)<-[MENTIONS]-(Abstract)-[HAS_FRAGMENT]->(FromAbstract:Fragment)-[MENTIONS]->(GeneSymbol)](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/BioBERT/tests/NamedEntity.test.js#L5)
### BioMedical
* [Gene](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Biomedical/tests/Gene.test.js#L5)
* [GeneSymbol](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Biomedical/tests/GeneSymbol.test.js#L5)
* [Disease](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Biomedical/tests/Disease.test.js#L5)
* [Protein](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Biomedical/tests/Protein.test.js#L5)
### Papers
* [Paper](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Papers/tests/Paper.test.js#L5)
### Clinical Trials
* [ClinicalTrial](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/ClinicalTrials/tests/ClinicalTrial.test.js#L5)
* [Compound](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/ClinicalTrials/tests/Compound.test.js#L5)
### Statistical & Geographic
* [Country path: (Country)<-[LOCATED_IN]-(City)<-[LOCATED_IN]-(Facility)](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Cases/tests/Country.test.js#L5)
* [Country path: (Country)<-[PART_OF]-(Province)-[REPORTED]->(DailyReport)](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Cases/tests/Country.test.js#L133)
* [Country to AgeGroups](https://github.com/Covid19-GraphQL/covid-graph-graphql/blob/6d6581ce73909bc7c975bd0490410135f7032fd5/api/src/schemas/Cases/tests/Country.test.js#L911)