├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── binder ├── apt.txt ├── postBuild ├── requirements.txt └── start ├── data ├── README.md ├── nodes │ ├── Admin1.csv │ ├── Admin2.csv │ ├── City.csv │ ├── Country.csv │ ├── Host.csv │ ├── PersonAnimal.csv │ └── Strain.csv └── relationships │ ├── Pathogen-HAS-Strain.csv │ ├── PersonAnimal-CARRIES-Strain.csv │ ├── PersonAnimal-IS_A-Host.csv │ ├── PersonAnimal-LOCATED_IN-Admin1.csv │ ├── PersonAnimal-LOCATED_IN-Admin2.csv │ ├── PersonAnimal-LOCATED_IN-City.csv │ ├── PersonAnimal-LOCATED_IN-Country.csv │ ├── Strain-FOUND_IN-Admin1.csv │ ├── Strain-FOUND_IN-Admin2.csv │ ├── Strain-FOUND_IN-City.csv │ └── Strain-FOUND_IN-Country.csv ├── docs ├── coronavirus_kg.png ├── genome.png ├── locations.png └── strains.png ├── environment.yml ├── notebooks ├── 1a-Strains.ipynb ├── 2-CreateGraph.ipynb └── 3-ExampleQueries.ipynb └── reference_data ├── Outbreak.csv ├── Pathogen-CAUSES-Outbreak.csv ├── Pathogen.csv ├── ReferenceGenome-ENCODES-Pathogen.csv ├── ReferenceGenome.csv └── nextstrain_ncov_metadata.tsv /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/.gitignore -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/README.md -------------------------------------------------------------------------------- /binder/apt.txt: -------------------------------------------------------------------------------- 1 | openjdk-8-jdk 2 | -------------------------------------------------------------------------------- /binder/postBuild: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/binder/postBuild -------------------------------------------------------------------------------- /binder/requirements.txt: -------------------------------------------------------------------------------- 1 | py2neo 2 | pandas 3 | -------------------------------------------------------------------------------- /binder/start: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/binder/start -------------------------------------------------------------------------------- /data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/README.md -------------------------------------------------------------------------------- /data/nodes/Admin1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/nodes/Admin1.csv -------------------------------------------------------------------------------- /data/nodes/Admin2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/nodes/Admin2.csv -------------------------------------------------------------------------------- /data/nodes/City.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/nodes/City.csv -------------------------------------------------------------------------------- /data/nodes/Country.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/nodes/Country.csv -------------------------------------------------------------------------------- /data/nodes/Host.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/nodes/Host.csv -------------------------------------------------------------------------------- /data/nodes/PersonAnimal.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/nodes/PersonAnimal.csv -------------------------------------------------------------------------------- /data/nodes/Strain.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/nodes/Strain.csv -------------------------------------------------------------------------------- /data/relationships/Pathogen-HAS-Strain.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/Pathogen-HAS-Strain.csv -------------------------------------------------------------------------------- /data/relationships/PersonAnimal-CARRIES-Strain.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/PersonAnimal-CARRIES-Strain.csv -------------------------------------------------------------------------------- /data/relationships/PersonAnimal-IS_A-Host.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/PersonAnimal-IS_A-Host.csv -------------------------------------------------------------------------------- /data/relationships/PersonAnimal-LOCATED_IN-Admin1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/PersonAnimal-LOCATED_IN-Admin1.csv -------------------------------------------------------------------------------- /data/relationships/PersonAnimal-LOCATED_IN-Admin2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/PersonAnimal-LOCATED_IN-Admin2.csv -------------------------------------------------------------------------------- /data/relationships/PersonAnimal-LOCATED_IN-City.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/PersonAnimal-LOCATED_IN-City.csv -------------------------------------------------------------------------------- /data/relationships/PersonAnimal-LOCATED_IN-Country.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/PersonAnimal-LOCATED_IN-Country.csv -------------------------------------------------------------------------------- /data/relationships/Strain-FOUND_IN-Admin1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/Strain-FOUND_IN-Admin1.csv -------------------------------------------------------------------------------- /data/relationships/Strain-FOUND_IN-Admin2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/Strain-FOUND_IN-Admin2.csv -------------------------------------------------------------------------------- /data/relationships/Strain-FOUND_IN-City.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/Strain-FOUND_IN-City.csv -------------------------------------------------------------------------------- /data/relationships/Strain-FOUND_IN-Country.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/data/relationships/Strain-FOUND_IN-Country.csv -------------------------------------------------------------------------------- /docs/coronavirus_kg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/docs/coronavirus_kg.png -------------------------------------------------------------------------------- /docs/genome.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/docs/genome.png -------------------------------------------------------------------------------- /docs/locations.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/docs/locations.png -------------------------------------------------------------------------------- /docs/strains.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/docs/strains.png -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/environment.yml -------------------------------------------------------------------------------- /notebooks/1a-Strains.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/notebooks/1a-Strains.ipynb -------------------------------------------------------------------------------- /notebooks/2-CreateGraph.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/notebooks/2-CreateGraph.ipynb -------------------------------------------------------------------------------- /notebooks/3-ExampleQueries.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/notebooks/3-ExampleQueries.ipynb -------------------------------------------------------------------------------- /reference_data/Outbreak.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/reference_data/Outbreak.csv -------------------------------------------------------------------------------- /reference_data/Pathogen-CAUSES-Outbreak.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/reference_data/Pathogen-CAUSES-Outbreak.csv -------------------------------------------------------------------------------- /reference_data/Pathogen.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/reference_data/Pathogen.csv -------------------------------------------------------------------------------- /reference_data/ReferenceGenome-ENCODES-Pathogen.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/reference_data/ReferenceGenome-ENCODES-Pathogen.csv -------------------------------------------------------------------------------- /reference_data/ReferenceGenome.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/reference_data/ReferenceGenome.csv -------------------------------------------------------------------------------- /reference_data/nextstrain_ncov_metadata.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbl-sdsc/coronavirus-knowledge-graph/HEAD/reference_data/nextstrain_ncov_metadata.tsv --------------------------------------------------------------------------------