{"id":22645351,"url":"https://github.com/sbl-sdsc/coronavirus-knowledge-graph","last_synced_at":"2025-04-12T00:33:53.838Z","repository":{"id":48064072,"uuid":"239968905","full_name":"sbl-sdsc/coronavirus-knowledge-graph","owner":"sbl-sdsc","description":"OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (see NEW VERSION: https://github.com/covid-19-net/covid-19-community)","archived":false,"fork":false,"pushed_at":"2020-11-25T08:27:16.000Z","size":3287,"stargazers_count":18,"open_issues_count":0,"forks_count":13,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-25T20:15:46.140Z","etag":null,"topics":["binder","coronavirus","coronavirus-analysis","covid-19","jupyter-notebook"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sbl-sdsc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-02-12T09:07:44.000Z","updated_at":"2022-09-27T00:12:46.000Z","dependencies_parsed_at":"2022-08-12T17:50:20.912Z","dependency_job_id":null,"html_url":"https://github.com/sbl-sdsc/coronavirus-knowledge-graph","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbl-sdsc%2Fcoronavirus-knowledge-graph","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbl-sdsc%2Fcoronavirus-knowledge-graph/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbl-sdsc%2Fcoronavirus-knowledge-graph/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbl-sdsc%2Fcoronavirus-knowledge-graph/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sbl-sdsc","download_url":"https://codeload.github.com/sbl-sdsc/coronavirus-knowledge-graph/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248501696,"owners_count":21114676,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["binder","coronavirus","coronavirus-analysis","covid-19","jupyter-notebook"],"created_at":"2024-12-09T06:05:07.872Z","updated_at":"2025-04-12T00:33:53.814Z","avatar_url":"https://github.com/sbl-sdsc.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Coronavirus-Knowledge-Graph\n\nThis project is obsolete.\n\n**The current version of this project is here:** [COVID-19-Net Knowledge Graph](https://github.com/covid-19-net/covid-19-community)\n\n\n\n**WORK IN PROGRESS**\n\n[![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)\n\n\u003c!--- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pwrose/coronavirus-knowledge-graph/master?urlpath=lab) ---\u003e\n\n![](docs/strains.png)\n\nFig. Strain subgraph\n\n\n\n\n# Documentation below is obsolete\n\nPrototype to create a [Neo4j](https://neo4j.com/) Knowledge Graph for Coronavirus outbreaks. \n\nThe 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.\n\nCurrently, this project integrates data from:\n* Daily reported COVID-19 cases from [Coronavirus COVID-19 Global Cases by Johns Hopkins CSSE](https://github.com/CSSEGISandData/COVID-19)\n* Real-time tracking of COVID-19 evolution from [Nextstrain](https://github.com/nextstrain/ncov)\n* Genome, gene, and protein data from [NCBI](https://www.ncbi.nlm.nih.gov/nuccore/NC_045512)\n\nThe 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.\n\n## How to use this project?\n\n1. Launch this repo on [MyBinder.org](https://mybinder.org/). Binder lets you run Jupyter Notebooks in your web browser without software installation.\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sbl-sdsc/coronavirus-knowledge-graph/master?urlpath=lab)\n\n2. Once Jupyter Lab launches (this may take a couple of minutes), navigate to the notebooks directory.\n\n3. Run the following Jupyter Notebooks:\n\n* 1-PrepareDatasets.ipynb (downloads public data about COVID-19)\n\n* 2-CreateKnowledgeGraph (creates a Neo4j Knowledge Graph)\n\n* 3-AddGeneProteinInfo (adds genome, gene, and protein information)\n\n* 4-ExampleQueries (runs [Cypher](https://neo4j.com/developer/cypher-query-language/) queries on the Knowledge Graph)\n\n## Coronavirus KG Views displayed in Neo4j Browser\n![](docs/coronavirus_kg.png)\n\nFig. 1: The whole Coronavirus KG\n\n![](docs/locations.png)\n\nFig. 2: Outbreaks by Country, State/Province, and City\n\n![](docs/genome.png)\n\nFig. 3: Pathogen, Genome, Genes, and Proteins\n\n![](docs/strains.png)\n\nFig. 4: Strains found in Hubei province\n\n## How can you help?\n\n* Suggest complementary publically accessible datasets to include in this Knowledge Graph\n* Suggest queries and analyses\n* Report bugs or issues\n* Submit a pull request\n\nPlease send [feedback or feature requests](https://github.com/sbl-sdsc/coronavirus-knowledge-graph/issues/new).\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbl-sdsc%2Fcoronavirus-knowledge-graph","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsbl-sdsc%2Fcoronavirus-knowledge-graph","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbl-sdsc%2Fcoronavirus-knowledge-graph/lists"}