├── .github ├── ISSUE_TEMPLATE │ ├── bug-report.md │ ├── dataset-request.md │ └── feature-request.md └── workflows │ └── qc.yml ├── .gitignore ├── .idea └── .gitignore ├── .spp_cache └── badges.json ├── CONTRIBUTING.md ├── Jenkinsfile ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── curated └── ORFs │ ├── merge_KGCOVID_COVIDscholar_syns.out │ ├── merge_KGCOVID_COVIDscholar_syns.py │ ├── synonyms_list_COVIDscholar.txt │ └── uniprot_sars-cov-2.gpi ├── data ├── .gitkeep ├── raw │ └── .gitkeep └── transformed │ └── .gitkeep ├── docs ├── .nojekyll ├── _sources │ ├── getting_started.md.txt │ ├── getting_started.rst.txt │ ├── index.rst.txt │ ├── kg_covid_19.rst.txt │ ├── kg_covid_19.transform_utils.chembl.rst.txt │ ├── kg_covid_19.transform_utils.drug_central.rst.txt │ ├── kg_covid_19.transform_utils.gocam_transform.rst.txt │ ├── kg_covid_19.transform_utils.intact.rst.txt │ ├── kg_covid_19.transform_utils.ontology.rst.txt │ ├── kg_covid_19.transform_utils.pharmgkb.rst.txt │ ├── kg_covid_19.transform_utils.rst.txt │ ├── kg_covid_19.transform_utils.sars_cov_2_gene_annot.rst.txt │ ├── kg_covid_19.transform_utils.scibite_cord.rst.txt │ ├── kg_covid_19.transform_utils.string_ppi.rst.txt │ ├── kg_covid_19.transform_utils.ttd.rst.txt │ ├── kg_covid_19.transform_utils.zhou_host_proteins.rst.txt │ ├── kg_covid_19.utils.rst.txt │ ├── modules.rst.txt │ ├── run.rst.txt │ └── tests.rst.txt ├── _static │ ├── basic.css │ ├── css │ │ ├── badge_only.css │ │ ├── fonts │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ └── theme.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── fonts │ │ ├── FontAwesome.otf │ │ ├── Lato │ │ │ ├── lato-bold.eot │ │ │ ├── lato-bold.ttf │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-bolditalic.eot │ │ │ ├── lato-bolditalic.ttf │ │ │ ├── lato-bolditalic.woff │ │ │ ├── lato-bolditalic.woff2 │ │ │ ├── lato-italic.eot │ │ │ ├── lato-italic.ttf │ │ │ ├── lato-italic.woff │ │ │ ├── lato-italic.woff2 │ │ │ ├── lato-regular.eot │ │ │ ├── lato-regular.ttf │ │ │ ├── lato-regular.woff │ │ │ └── lato-regular.woff2 │ │ ├── Roboto-Slab-Bold.woff │ │ ├── Roboto-Slab-Bold.woff2 │ │ ├── Roboto-Slab-Light.woff │ │ ├── Roboto-Slab-Light.woff2 │ │ ├── Roboto-Slab-Regular.woff │ │ ├── Roboto-Slab-Regular.woff2 │ │ ├── Roboto-Slab-Thin.woff │ │ ├── Roboto-Slab-Thin.woff2 │ │ ├── RobotoSlab │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ └── roboto-slab-v7-regular.woff2 │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── lato-bold-italic.woff │ │ ├── lato-bold-italic.woff2 │ │ ├── lato-bold.woff │ │ ├── lato-bold.woff2 │ │ ├── lato-normal-italic.woff │ │ ├── lato-normal-italic.woff2 │ │ ├── lato-normal.woff │ │ └── lato-normal.woff2 │ ├── jquery-3.5.1.js │ ├── jquery.js │ ├── js │ │ ├── badge_only.js │ │ ├── html5shiv-printshiv.min.js │ │ ├── html5shiv.min.js │ │ ├── modernizr.min.js │ │ └── theme.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── underscore-1.3.1.js │ └── underscore.js ├── genindex.html ├── getting_started.html ├── index.html ├── kg_covid_19.html ├── kg_covid_19.transform_utils.chembl.html ├── kg_covid_19.transform_utils.drug_central.html ├── kg_covid_19.transform_utils.gocam_transform.html ├── kg_covid_19.transform_utils.html ├── kg_covid_19.transform_utils.intact.html ├── kg_covid_19.transform_utils.ontology.html ├── kg_covid_19.transform_utils.pharmgkb.html ├── kg_covid_19.transform_utils.sars_cov_2_gene_annot.html ├── kg_covid_19.transform_utils.scibite_cord.html ├── kg_covid_19.transform_utils.string_ppi.html ├── kg_covid_19.transform_utils.ttd.html ├── kg_covid_19.transform_utils.zhou_host_proteins.html ├── kg_covid_19.utils.html ├── modules.html ├── objects.inv ├── py-modindex.html ├── run.html ├── search.html ├── searchindex.js └── tests.html ├── download.yaml ├── example-KG-COVID-19-usage.ipynb ├── kg_covid_19 ├── __init__.py ├── download.py ├── make_holdouts.py ├── merge_utils │ └── merge_kg.py ├── query.py ├── transform.py ├── transform_utils │ ├── __init__.py │ ├── chembl │ │ ├── __init__.py │ │ ├── chembl_activity_query.json │ │ ├── chembl_assay_query.json │ │ ├── chembl_document_query.json │ │ ├── chembl_molecule_query.json │ │ └── chembl_transform.py │ ├── drug_central │ │ ├── __init__.py │ │ └── drug_central.py │ ├── gocam_transform │ │ ├── __init__.py │ │ └── gocam_transform.py │ ├── intact │ │ ├── __init__.py │ │ └── intact.py │ ├── ontology │ │ ├── __init__.py │ │ └── ontology_transform.py │ ├── pharmgkb │ │ ├── __init__.py │ │ └── pharmgkb.py │ ├── sars_cov_2_gene_annot │ │ ├── __init__.py │ │ └── sars_cov_2_gene_annot.py │ ├── scibite_cord │ │ ├── __init__.py │ │ └── scibite_cord.py │ ├── string_ppi │ │ ├── __init__.py │ │ ├── edge_additional_headers.json │ │ ├── edge_core_header.json │ │ ├── node_header.json │ │ └── string_ppi.py │ ├── transform.py │ ├── ttd │ │ ├── __init__.py │ │ └── ttd.py │ └── zhou_host_proteins │ │ ├── __init__.py │ │ └── zhou_transform.py └── utils │ ├── __init__.py │ ├── download_utils.py │ ├── normalize_utils.py │ └── transform_utils.py ├── maps └── drugcentral-maps-kg_covid_19-0.1.sssom.tsv ├── merge.yaml ├── merge_jenkins.yaml ├── poetry.lock ├── pyproject.toml ├── queries ├── query-01-bl-cat-counts.rq ├── query-02-sars-cov-2-prot.rq ├── query-03-sars-cov-2-interactors.rq ├── query-04-sars-cov-2-interactors_2nd_order.rq ├── query-05-sars-cov-2-interactors_druggable_2nd_order.rq ├── query-06-provided_by_counts.rq ├── query-07-drug-to-drug-target.rq └── urls.yml ├── run.py ├── sonar-project.properties ├── sphinx ├── Makefile ├── conf.py ├── getting_started.rst ├── index.rst ├── kg_covid_19.rst ├── kg_covid_19.transform_utils.chembl.rst ├── kg_covid_19.transform_utils.drug_central.rst ├── kg_covid_19.transform_utils.gocam_transform.rst ├── kg_covid_19.transform_utils.intact.rst ├── kg_covid_19.transform_utils.ontology.rst ├── kg_covid_19.transform_utils.pharmgkb.rst ├── kg_covid_19.transform_utils.rst ├── kg_covid_19.transform_utils.sars_cov_2_gene_annot.rst ├── kg_covid_19.transform_utils.scibite_cord.rst ├── kg_covid_19.transform_utils.string_ppi.rst ├── kg_covid_19.transform_utils.ttd.rst ├── kg_covid_19.transform_utils.zhou_host_proteins.rst ├── kg_covid_19.utils.rst ├── make.bat ├── run.rst └── tests.rst ├── templates ├── README.build └── README.toplevel ├── tests ├── __init__.py ├── resources │ ├── 31315999_weird_chebi_id.xml │ ├── P0DTC1.edges.tsv │ ├── P0DTC1.nodes.tsv │ ├── P1-01-TTD_target_download_SNIPPET.txt │ ├── chembl │ │ ├── chembl_activities.snippet.txt │ │ ├── chembl_activity_records.json │ │ ├── chembl_assay_records.json │ │ ├── chembl_document_records.json │ │ └── chembl_molecule_records.json │ ├── download │ │ ├── download.yaml │ │ ├── download_api.yaml │ │ └── download_diff_local_name.yaml │ ├── drug_central │ │ ├── drug.target.interaction_SNIPPET.tsv │ │ ├── drug.target.interaction_SNIPPET.tsv.gz │ │ ├── tchem_SNIPPET.tsv │ │ ├── tclin_SNIPPET.tsv │ │ └── test.zip │ ├── drugs.tsv │ ├── gene2ensembl.gz │ ├── gene_info.gz │ ├── gocams │ │ └── lifted-go-cams-20200619_SNIPPET.nt │ ├── holdouts │ │ ├── bigger_graph_degree_info.txt │ │ ├── bigger_graph_edges.tsv │ │ ├── bigger_graph_edges_HIGHER_DEGREE_NODES.tsv │ │ ├── bigger_graph_nodes.tsv │ │ ├── bigger_graph_nodes_EXTRA_IDS.tsv │ │ ├── bigger_graph_nodes_MISSING_IDS.tsv │ │ ├── small_graph_edges.tsv │ │ ├── small_graph_nodes.tsv │ │ ├── small_graph_nodes_EXTRA_IDS.tsv │ │ └── small_graph_nodes_MISSING_IDS.tsv │ ├── intact_3_participants.xml │ ├── intact_test.xml │ ├── merge_MISSING_FILE.yaml │ ├── merge_valid.yaml │ ├── mock_download.py │ ├── pharmgkb_gene_SNIPPET.tsv │ ├── query │ │ ├── test_result_dict.pkl │ │ └── test_template.yaml │ ├── relationships_SNIPPET.tsv │ ├── sars_cov_2_gene_annot_SNIPPET.tsv │ ├── scibite_cord │ │ ├── cv19_scc_1_2.zip │ │ ├── gene_info.gz │ │ ├── pdf_json_part_1.zip │ │ ├── pdf_json_part_2.zip │ │ ├── pmc_json.zip │ │ └── wikidata_country_codes.tsv │ ├── string │ │ ├── 9606.protein.links.full.v11.0.txt.gz │ │ ├── 9606.protein.links.full.v11.5.txt.gz │ │ ├── HUMAN_9606_idmapping.dat.gz │ │ ├── gene2ensembl.gz │ │ └── gene_info.gz │ ├── test_sars_cov2_intact_nodes.tsv │ ├── test_sars_cov2_pro_candidates_nodes_SNIPPET.tsv │ ├── uniprot_sars-cov-2_SNIPPET.gpa │ └── uniprot_sars-cov-2_SNIPPET.gpi ├── test_chembl.py ├── test_drug_central.py ├── test_gocams.py ├── test_gpi_file.py ├── test_holdouts.py ├── test_intact.py ├── test_pharmgkb.py ├── test_query.py ├── test_run.py ├── test_sars_cov_2_gene_annot.py ├── test_scibite_cord.py ├── test_string.py ├── test_transform_class.py ├── test_transform_utils.py ├── test_ttd_transform.py └── tmp │ └── GOCAMs │ ├── GOCAMs_edges.tsv │ └── GOCAMs_nodes.tsv └── tox.ini /.github/ISSUE_TEMPLATE/bug-report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Knowledge-Graph-Hub/kg-covid-19/HEAD/.github/ISSUE_TEMPLATE/bug-report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/dataset-request.md: 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