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https://github.com/sbl-sdsc/coronavirus-knowledge-graph
OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (see NEW VERSION: https://github.com/covid-19-net/covid-19-community)
https://github.com/sbl-sdsc/coronavirus-knowledge-graph
binder coronavirus coronavirus-analysis covid-19 jupyter-notebook
Last synced: 15 days ago
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OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (see NEW VERSION: https://github.com/covid-19-net/covid-19-community)
- Host: GitHub
- URL: https://github.com/sbl-sdsc/coronavirus-knowledge-graph
- Owner: sbl-sdsc
- License: mit
- Created: 2020-02-12T09:07:44.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2020-11-25T08:27:16.000Z (about 4 years ago)
- Last Synced: 2023-02-28T19:26:30.030Z (almost 2 years ago)
- Topics: binder, coronavirus, coronavirus-analysis, covid-19, jupyter-notebook
- Language: Jupyter Notebook
- Homepage:
- Size: 3.13 MB
- Stars: 18
- Watchers: 5
- Forks: 13
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# Coronavirus-Knowledge-Graph
This project is obsolete.
**The current version of this project is here:** [COVID-19-Net Knowledge Graph](https://github.com/covid-19-net/covid-19-community)
**WORK IN PROGRESS**
[![Binder](https://aws-uswest2-binder.pangeo.io/badge_logo.svg)](https://aws-uswest2-binder.pangeo.io/v2/gh/pwrose/coronavirus-knowledge-graph/master?urlpath=lab)
![](docs/strains.png)
Fig. Strain subgraph
# Documentation below is obsolete
Prototype to create a [Neo4j](https://neo4j.com/) Knowledge Graph for Coronavirus outbreaks.
The goal of this Knowledge Graph project is to link heterogeneous data from publically available resources relevant to the COVID-19 outbreak. By linking disparate datasets, new insights may be gained.
Currently, this project integrates data from:
* Daily reported COVID-19 cases from [Coronavirus COVID-19 Global Cases by Johns Hopkins CSSE](https://github.com/CSSEGISandData/COVID-19)
* Real-time tracking of COVID-19 evolution from [Nextstrain](https://github.com/nextstrain/ncov)
* Genome, gene, and protein data from [NCBI](https://www.ncbi.nlm.nih.gov/nuccore/NC_045512)The initial focus of this repo is on the Novel Coronavirus COVID-19 (2019-nCoV). In the future we will include data for SARS and MERS.
## How to use this project?
1. Launch this repo on [MyBinder.org](https://mybinder.org/). Binder lets you run Jupyter Notebooks in your web browser without software installation.
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sbl-sdsc/coronavirus-knowledge-graph/master?urlpath=lab)
2. Once Jupyter Lab launches (this may take a couple of minutes), navigate to the notebooks directory.
3. Run the following Jupyter Notebooks:
* 1-PrepareDatasets.ipynb (downloads public data about COVID-19)
* 2-CreateKnowledgeGraph (creates a Neo4j Knowledge Graph)
* 3-AddGeneProteinInfo (adds genome, gene, and protein information)
* 4-ExampleQueries (runs [Cypher](https://neo4j.com/developer/cypher-query-language/) queries on the Knowledge Graph)
## Coronavirus KG Views displayed in Neo4j Browser
![](docs/coronavirus_kg.png)Fig. 1: The whole Coronavirus KG
![](docs/locations.png)
Fig. 2: Outbreaks by Country, State/Province, and City
![](docs/genome.png)
Fig. 3: Pathogen, Genome, Genes, and Proteins
![](docs/strains.png)
Fig. 4: Strains found in Hubei province
## How can you help?
* Suggest complementary publically accessible datasets to include in this Knowledge Graph
* Suggest queries and analyses
* Report bugs or issues
* Submit a pull requestPlease send [feedback or feature requests](https://github.com/sbl-sdsc/coronavirus-knowledge-graph/issues/new).