2a:null 2b:["$","title",null,{"children":"Chemical similarity search | Tomaz Mohoric | Observable"}] 30:T43c,plot_tox21_data_for_all_compounds = function(array) { var i; var vl_array = []; for (i = 0; i < array.length; i++) { var data = array[i]["Results"]; var compound_name = array[i]["Compound"]; vl_array.push( vl.markRect().data(data) .encode( vl.x({"grid": true}).fieldN("Dataset name"), vl.color().fieldN("Hit call") .legend({"orient": "left"}) .scale({ "type": "ordinal", "domain": ["active", "inactive", "ambiguous"], "range": ["#ff6f69", "#96ceb4", "#ffcc5c"]}), vl.tooltip([ vl.fieldN("Dataset name"), { "field": "IC50", "type": "quantitative", "format": ",.2f" }, vl.fieldN("Organism"), vl.fieldN("Biological process")]), ).title({"text": compound_name + " (Tanimoto similarity: " + tox21_hits.filter(function(item) {return item["Substance name"] == compound_name})[0].SMILES.similarity + ")", "anchor": "start"}) ); } return vl.vconcat(vl_array).render(); }31:T45f,plot_drugmatrix_tggates_data_for_all_compounds = function(array, assay_hits) { if (array.length < 1) { return "No data to display"; } else { var i; var vl_array = []; for (i = 0; i < array.length; i++) { var data = array[i]["Actual datasets with sample names"]; var compound_name = array[i]["Compound"]; vl_array.push( vl.markRect().data(data) .encode( vl.y().fieldN("Sample"), vl.x().fieldN("SYMBOL"), vl.color().fieldQ("logFC").legend({"orient": "left"}).scale({scheme: "lightmulti", reverse: false, zero: false}), vl.tooltip([ vl.fieldN("Sample"), { "field": "logFC", "type": "quantitative", "format": ",.2f" }, vl.fieldN("ENSEMBL"), vl.fieldN("ENTREZID")]), ).title({"text": compound_name + " (Tanimoto similarity: " + assay_hits.filter(function(item) {return item["Compound"] == compound_name})[0].SMILES.similarity + ")", "anchor": "start"}) ); } return vl.vconcat(vl_array).render(); } }32:T82d,reshape_tox21_datasets_for_all_compounds = function(array_of_datasets, array_of_compounds) { var i; var arr = []; var j; var hitcall; var ic50; for (i = 0; i < array_of_compounds.length; i++) { const compound = array_of_compounds[i]; var compound_datasets = array_of_datasets.filter(item => item["Substance name"] == compound); var unique_compound_datasets = Array.from(new Set(compound_datasets.map(item => item["Summary data"]))); var results = []; // loop over unique compound datasets and evaluate for (j = 0; j < unique_compound_datasets.length; j++) { const dataset_id = unique_compound_datasets[j]; const datasets = compound_datasets.filter(item => item["Summary data"] == dataset_id); const hitcalls = datasets.map(item => item["Hit call"]); const unique_hitcalls = Array.from(new Set(hitcalls)); const ic50_values = datasets.map(item => item["IC50"]); if (unique_hitcalls.length > 1) { hitcall = "ambiguous"; } else { hitcall = unique_hitcalls[0]; }; if (hitcall == "active") { const arrSum = ic50_values => ic50_values.reduce((a,b) => a + b, 0); ic50 = arrSum / (ic50_values.length); } else { ic50 = null; } const dataset_object = datasets[0]; if (colors.includes(hitcall)) { results.push({ "Hit call": hitcall, "Organism": dataset_object["Organism"], "Cell type": dataset_object["Cell type"], "Design type": dataset_object["Design Type"], "Target type": dataset_object["Target type"], "Target family": dataset_object["Target family"], "Biological process": dataset_object["Biolological process"], "Dataset name": dataset_object["Dataset name"].replace("EPA-InVitroDBV3.2-", "").replace("_", " "), "IC50": ic50, }); } }; var compound_object = { "Compound": compound, "Results": results, }; arr.push(compound_object); } return arr; }33:T452,reshape_datasets_for_all_compounds = function(array_of_compound_datasets, array_of_compounds) { var i; var arr = []; for (i = 0; i < array_of_compound_datasets.length; i++) { var compound_object = array_of_compound_datasets[i]; var compound = compound_object.Compound; if (array_of_compounds.includes(compound)) { var compound_samplenames = compound_object["Sample names"]; var compound_datasets = compound_object["Actual datasets"]; var compound_datasets_with_samplenames = []; // loop over datasets for this compound var j; for (j = 0; j < compound_datasets.length; j++) { var dataset = compound_datasets[j]; var dataset_with_samplename = dataset.map(item => { item["Sample"] = compound_samplenames[j]; return item }) compound_datasets_with_samplenames.push(dataset_with_samplename); } compound_object["Actual datasets with sample names"] = [].concat(...compound_datasets_with_samplenames); arr.push(compound_object); } } return arr; }34:[] 2e:{"id":"082fd5bde639423b","slug":"chemical-similarity-search","title":"Chemical similarity search","thumbnail":"a788aff992d4fbabd2af17288aff06cf832ed1e8b6a90daf92dc98bc8112b0ba","access_level":"public","create_time":"$D2021-02-09T17:03:24.721Z","update_time":"$D2022-04-02T12:28:34.687Z","view_time":null,"first_public_time":"$D2021-02-09T18:03:01.183Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"e418e540719406f7","login":"tomazm","name":"Tomaz Mohoric","avatar_url":null,"tier":"starter_2024"},"version":754,"publish_version":754,"role":null,"authored":false,"authors":[{"type":"individual","id":"acb80c7d769b3359","login":"tomazm","name":"Tomaz Mohoric","avatar_url":null,"tier":null}],"members":[{"type":"individual","id":"acb80c7d769b3359","login":"tomazm","name":"Tomaz Mohoric","avatar_url":null,"tier":null,"role":"editor"}],"comments":[{"id":"c6230ecd82b3d541","reply_to_id":null,"content":"C3H10T1/2 (Mouse mesenchymal cell line )\nCHO-K1 (Chinese Hamster Ovary cell line)\nDT40 (Chicken bursal lymphoma cell line)\nERR-HEK293T (Human embryonic kidney 293 cell line)\nGH3 (Rat pituitary tumor cell line )\nHCT-116 (Human colon carcinoma cell line)\nHEK293 (Human embryonic kidney 293 cell line)\nHEK293T (Human embryonic kidney 293 cell line)\nHeLa (Human epithelial cell line)\nHepG2 (Human hepatocellular carcinoma cell line)\nMCF-7 (Human breast cancer cell line)\nMDA-kb2 (Human breast cancer cell line)\nME-180 (Human epithelial cell line)\nNIH/3T3 (Mouse embryo fibroblast cell line)\nPGC/ERR HEK293T (Human embryonic kidney 293 cell line)\nPR-UAS-bla-HEK293T (Human embryonic kidney 293 cell line)\nVM7 (Human breast cancer cell line)","create_time":"$D2021-04-12T12:42:42.197Z","update_time":null,"resolved":false,"user":{"type":"individual","id":"13207340bd4ccbb7","login":"tadoktor","name":"Tatyana Doktorova","avatar_url":null,"tier":null}}],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Chemical similarity search","cells":[{"id":0,"value":"title = md`# Chemical similarity search`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":273,"value":"introduction = md`\n1. Enter SMILES structure of your compound. For example, zileuton: CC(c1cc2ccccc2s1)N(O)C(N)=O\n2. Set the logFC threshold that will be applied to filter out only significant fold changes in toxicogenomic databases (DrugMatrix, TG-GATES).\n3. Set Tanimoto similarity threhsold that will be used to filter out similar compounds in the databases.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":269,"value":"viewof smiles = textarea({placeholder: \"Enter SMILES\", submit: \"Confirm SMILES\", value: \"CC(=O)Oc1ccccc1C(O)=O\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":496,"value":"compound_figure = html`${svg}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":49,"value":"viewof logfc_threshold = slider({\n min: 0,\n max: 5,\n step: 0.1,\n value: 2,\n format: \",\",\n description:\n \"Select log fold change threshold. Only genes that have significant fold change are displayed below. \"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":71,"value":"viewof tanimoto_threshold = slider({\n min: 0,\n max: 1,\n step: 0.05,\n value: 0.8,\n format: \",\",\n description:\n \"Select Tanimoto similarity threshold. Compounds exceeding this threshold will be displayed below. \"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":343,"value":"subtitle_1 = md`### TG-GATES significantly differentially expressed genes`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":566,"value":"plot_tggates_compounds = {\n var shtml;\n shtml = \"\";\n if (tggates_unique_svg.length > 0) {\n var i;\n for (i = 0; i < tggates_unique_svg.length; i++) {\n var this_svg = tggates_unique_svg[i];\n var this_name = tggates_unique_compounds[i];\n shtml = shtml + \"\" + this_name + \" (Tanimoto similarity: \" + tggates_unique_compounds_similarities[i] +\")
\" + this_svg + \"
\";\n }\n } else {\n return \"No similar compounds found\";\n }\n return html`${shtml}`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":602,"value":"viewof selected_tggates_compounds = Select(tggates_unique_compounds, {multiple: true, label: \"Select compounds to be displayed:\", value: tggates_unique_compounds})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":341,"value":"tggates_results_display = plot_drugmatrix_tggates_data_for_all_compounds(reshaped_tggates_datasets_for_all_compounds, tggates_hits)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":286,"value":"subtitle_2 = md`### DrugMatrix significantly differentially expressed genes`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":556,"value":"plot_drugmatrix_compounds = {\n var shtml;\n shtml = \"\";\n if (drugmatrix_unique_svg.length > 0) {\n var i;\n for (i = 0; i < drugmatrix_unique_svg.length; i++) {\n var this_svg = drugmatrix_unique_svg[i];\n var this_name = drugmatrix_unique_compounds[i];\n shtml = shtml + \"\" + this_name + \" (Tanimoto similarity: \" + drugmatrix_unique_compounds_similarities[i] + \")
\" + this_svg + \"
\";\n }\n } else {\n return \"No similar compounds found\";\n }\n return html`${shtml}`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":596,"value":"viewof selected_drugmatrix_compounds = Select(drugmatrix_unique_compounds, {multiple: true, label: \"Select compounds to be displayed:\", value: drugmatrix_unique_compounds})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":255,"value":"drugmatrix_results_display = plot_drugmatrix_tggates_data_for_all_compounds(reshaped_drugmatrix_datasets_for_all_compounds, drugmatrix_hits)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":443,"value":"subtitle_3 = md`### EPA Tox21/ToxCat activities`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":578,"value":"plot_tox21_compounds = {\n var shtml;\n shtml = \"\";\n if (tox21_unique_svg.length > 0) {\n var i;\n for (i = 0; i < tox21_unique_svg.length; i++) {\n var this_svg = tox21_unique_svg[i];\n var this_name = tox21_unique_compounds[i];\n shtml = shtml + \"\" + this_name + \" (Tanimoto similarity: \" + tox21_unique_compounds_similarities[i] + \")
\" + this_svg + \"
\";\n }\n } else {\n return \"No similar compounds found\";\n }\n return html`${shtml}`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":465,"value":"viewof selected_cell_types_with_descriptions = Select(cell_types_with_descriptions, {multiple: true, label: \"Select cell types to be displayed:\", value:cell_types_with_descriptions})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":468,"value":"viewof selected_target_types = Select(target_types, {multiple: true, label: \"Select target types to be displayed:\", value:target_types})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":470,"value":"viewof selected_target_families = Select(target_families, {multiple: true, label: \"Select target families to be displayed:\", value: target_families})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":591,"value":"viewof selected_tox21_compounds = Select(tox21_unique_compounds, {multiple: true, label: \"Select compounds be displayed:\", value: tox21_unique_compounds})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":690,"value":"viewof colors = Checkbox([\"active\", \"inactive\", \"ambiguous\"], {label: \"Choose activity types to be displayed:\", value: [\"active\", \"inactive\", \"ambiguous\"]})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":441,"value":"tox21_results_display = plot_tox21_data_for_all_compounds(reshaped_tox21_datasets_for_all_compounds)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":348,"value":"subtitle_4 = md`## Supplementary code`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":415,"value":"$30","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":208,"value":"$31","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":405,"value":"reshaped_tox21_datasets_for_all_compounds = reshape_tox21_datasets_for_all_compounds(filtered_tox21_hits, selected_tox21_compounds)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":396,"value":"tox21_similar_compounds= Array.from(new Set(filtered_tox21_hits.map(item => item[\"Substance name\"])))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":383,"value":"$32","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":476,"value":"filtered_tox21_hits = tox21_hits\n .filter(item => selected_cell_types.includes(item[\"Cell type\"]))\n .filter(item => selected_target_types.includes(item[\"Target type\"]))\n .filter(item => selected_target_families.includes(item[\"Target family\"]))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":462,"value":"target_families = Array.from(new Set(tox21_hits.map(item => item[\"Target family\"])))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":460,"value":"target_types = Array.from(new Set(tox21_hits.map(item => item[\"Target type\"])))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":653,"value":"selected_cell_types = selected_cell_types_with_descriptions.map(item => item.split(\" \")[0])","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":635,"value":"cell_types_with_descriptions = [\n\"C3H10T1/2 (Mouse mesenchymal cell line)\",\n\"CHO-K1 (Chinese Hamster Ovary cell line)\",\n\"DT40 (Chicken bursal lymphoma cell line)\",\n\"ERR-HEK293T (Human embryonic kidney 293 cell line)\",\n\"GH3 (Rat pituitary tumor cell line)\",\n\"HCT-116 (Human colon carcinoma cell line)\",\n\"HEK293 (Human embryonic kidney 293 cell line)\",\n\"HEK293T (Human embryonic kidney 293 cell line)\",\n\"HeLa (Human epithelial cell line)\",\n\"HepG2 (Human hepatocellular carcinoma cell line)\",\n\"MCF-7 (Human breast cancer cell line)\",\n\"MDA-kb2 (Human breast cancer cell line)\",\n\"ME-180 (Human epithelial cell line)\",\n\"NIH/3T3 (Mouse embryo fibroblast cell line)\",\n\"PGC/ERR HEK293T (Human embryonic kidney 293 cell line)\",\n\"PR-UAS-bla-HEK293T (Human embryonic kidney 293 cell line)\",\n\"VM7 (Human breast cancer cell line)\",\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":459,"value":"cell_types = cell_types_with_null.filter(item => item != null).sort()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":454,"value":"cell_types_with_null = Array.from(new Set(tox21_hits.map(item => item[\"Cell type\"])))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":333,"value":"reshaped_tggates_datasets_for_all_compounds = reshape_datasets_for_all_compounds(tggates_datasets_for_all_compounds, selected_tggates_compounds)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":229,"value":"reshaped_drugmatrix_datasets_for_all_compounds = reshape_datasets_for_all_compounds(drugmatrix_datasets_for_all_compounds, selected_drugmatrix_compounds)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":227,"value":"$33","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":331,"value":"tggates_datasets_for_all_compounds = get_promised_fold_changes_datasets_for_all_compounds(reshaped_tggates_hits)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":115,"value":"drugmatrix_datasets_for_all_compounds = get_promised_fold_changes_datasets_for_all_compounds(reshaped_drugmatrix_hits)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":52,"value":"get_datasets_from_promises = function(array_of_promises) {\n return Promise.all(array_of_promises).then(item => item.map(dataset => dataset.results.map(row => row.data)))\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":181,"value":"get_promised_fold_changes_datasets_for_all_compounds = async function(array) {\n var i;\n var new_array = [];\n \n for (i = 0; i < array.length; i++) {\n var object = array[i];\n const promised_datasets = get_promised_fold_changes_datasets(object[\"Fold changes datasets\"]); \n object[\"Promised datasets\"] = promised_datasets;\n object[\"Actual datasets\"] = await get_datasets_from_promises(promised_datasets);\n new_array.push(object);\n }\n \n return new_array;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":37,"value":"get_promised_fold_changes_datasets = function(array_of_datasets) {\n return array_of_datasets.map(dataset => {\n return fetch(base_url_edelweiss + dataset + \"/versions/latest/data\", query_options_for_fold_changes).then(response_dataset => {\n if (!response_dataset.ok) throw new Error(response_dataset.status);\n return response_dataset.json();\n }) \n })\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":41,"value":"query_options_for_fold_changes = {\n return {\n method: 'POST',\n body: JSON.stringify({\n condition: {\n or: [\n {lt: [{column: [\"logFC\"]}, -logfc_threshold]},\n {gt: [{column: [\"logFC\"]}, logfc_threshold]},\n ]\n },\n columns: [\"logFC\", \"SYMBOL\", \"ENSEMBL\", \"ENTREZID\"] \n })\n }\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":329,"value":"reshaped_tggates_hits = reshape_tggates_hits(tggates_hits, tggates_unique_compounds)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":324,"value":"reshape_tggates_hits = function(array_of_datasets, compounds) {\n var arr = [];\n \n compounds.forEach(compound => {\n var compound_datasets = array_of_datasets.filter(object => object[\"Compound\"] == compound);\n var unique_compound_datasets = function_get_unique_fold_changes_datasets(compound_datasets);\n \n var i;\n var sample_names = [];\n for (i = 0; i < unique_compound_datasets.length; i++) {\n var dataset_id = unique_compound_datasets[i];\n var obj = array_of_datasets.filter(item => item[\"Dataset ID\"] == dataset_id)[0];\n var sample_name = obj[\"Organism\"] + \" / \" + obj[\"Study type\"] + \" / \" + obj[\"Organ\"] + \" / \" + obj[\"Dosing\"] + \" / \" + obj[\"Dose\"] + \" / \" + obj[\"Duration\"] + \" \" + obj[\"Duration unit\"];\n sample_names.push(sample_name);\n }\n \n arr.push({\n \"Compound\": compound,\n \"Fold changes datasets\": unique_compound_datasets,\n \"Sample names\": sample_names\n })\n });\n return arr;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":98,"value":"reshaped_drugmatrix_hits = reshape_drugmatrix_hits(drugmatrix_hits, drugmatrix_unique_compounds)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":90,"value":"reshape_drugmatrix_hits = function(array_of_datasets, compounds) {\n var arr = [];\n \n compounds.forEach(compound => {\n var compound_datasets = array_of_datasets.filter(object => object[\"Compound\"] == compound);\n var unique_compound_datasets = function_get_unique_fold_changes_datasets(compound_datasets);\n \n var i;\n var sample_names = [];\n for (i = 0; i < unique_compound_datasets.length; i++) {\n var dataset_id = unique_compound_datasets[i];\n var obj = array_of_datasets.filter(item => item[\"Dataset ID\"] == dataset_id)[0];\n var sample_name = obj[\"Strain\"] + \" / \" + obj[\"Route\"] + \" / \" + obj[\"Organ or cell type\"] + \" / \" + obj[\"Dose\"] + \" \" + obj[\"Dose unit\"] + \" / \" + obj[\"Duration\"] + \" \" + obj[\"Duration unit\"];\n sample_names.push(sample_name);\n }\n \n arr.push({\n \"Compound\": compound,\n \"Fold changes datasets\": unique_compound_datasets,\n \"Sample names\": sample_names\n })\n });\n return arr;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":712,"value":"tox21_unique_compounds_similarities = tox21_unique_compounds.map(compound => {\n return tox21_hits.filter(item => item[\"Substance name\"] == compound).map(item => item.SMILES.similarity)[0]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":549,"value":"tox21_unique_svg = Promise.all(tox21_unique_smiles.map(smiles => function_get_svg_from_smiles(smiles)))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":544,"value":"tox21_unique_smiles = tox21_unique_compounds.map(compound => {\n return tox21_hits.filter(item => item[\"Substance name\"] == compound).map(item => item.SMILES.canonical)[0]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":361,"value":"tox21_unique_compounds = get_unique_compounds(tox21_hits, \"Substance name\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":709,"value":"tggates_unique_compounds_similarities = tggates_unique_compounds.map(compound => {\n return tggates_hits.filter(item => item.Compound == compound).map(item => item.SMILES.similarity)[0]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":547,"value":"tggates_unique_svg = Promise.all(tggates_unique_smiles.map(smiles => function_get_svg_from_smiles(smiles)))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":541,"value":"tggates_unique_smiles = tggates_unique_compounds.map(compound => {\n return tggates_hits.filter(item => item.Compound == compound).map(item => item.SMILES.canonical)[0]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":319,"value":"tggates_unique_compounds = get_unique_compounds(tggates_hits, \"Compound\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":553,"value":"drugmatrix_unique_svg = Promise.all(drugmatrix_unique_smiles.map(smiles => function_get_svg_from_smiles(smiles)))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":534,"value":"drugmatrix_unique_smiles = drugmatrix_unique_compounds.map(compound => {\n return drugmatrix_hits.filter(item => item.Compound == compound).map(item => item.SMILES.canonical)[0]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":705,"value":"drugmatrix_unique_compounds_similarities = drugmatrix_unique_compounds.map(compound => {\n return drugmatrix_hits.filter(item => item.Compound == compound).map(item => item.SMILES.similarity)[0]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":526,"value":"drugmatrix_hits.filter(item => item.Compound == drugmatrix_unique_compounds[0]).map(item => item.SMILES.canonical)[0]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":88,"value":"drugmatrix_unique_compounds = get_unique_compounds(drugmatrix_hits, \"Compound\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":54,"value":"function_get_unique_fold_changes_datasets = function get_unique_fold_changes_datasets(array_of_datasets) {\n var set_of_datasets = new Set(array_of_datasets.map(x => x[\"Dataset ID\"]));\n return Array.from(set_of_datasets).filter(function(item) {return item != null;})\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":83,"value":"get_unique_compounds = function(array_of_datasets, compound_name_column) {\n var set_of_datasets = new Set(array_of_datasets.map(x => x[compound_name_column]));\n return Array.from(set_of_datasets).filter(function(item) {return item != null;})\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":726,"value":"tox21_hits.filter(function(item) {return item[\"Substance name\"] == \"Zileuton\"})[0].SMILES.similarity","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":359,"value":"tox21_hits = function_fetch_dataset_to_array(tox21_summary_url, query_options)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":313,"value":"tggates_hits = function_fetch_dataset_to_array(tggates_summary_url, query_options)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":13,"value":"drugmatrix_hits = function_fetch_dataset_to_array(drugmatrix_summary_url, query_options)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":9,"value":"function_fetch_dataset_to_array = function fetch_dataset_to_array(dataset_url, query_options) {\n return fetch(dataset_url, query_options).then(response_dataset => {\n if (!response_dataset.ok) throw new Error(response_dataset.status);\n return response_dataset.json();}).then(json => json.results.map(x => x.data));\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":356,"value":"tox21_summary_url = base_url_edelweiss + tox21_summary_id + \"/versions/latest/data\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":309,"value":"tggates_summary_url = base_url_edelweiss + tggates_summary_id + \"/versions/latest/data\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":10,"value":"drugmatrix_summary_url = base_url_edelweiss + drugmatrix_summary_id + \"/versions/latest/data\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":355,"value":"tox21_summary_id = \"8cc0534a-5e52-4253-a736-40f616b84a41\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":308,"value":"tggates_summary_id = '16a4418e-01ff-4dcd-9b2d-90ef00565655'","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":45,"value":"drugmatrix_summary_id = '9c1c25e0-2943-4c36-9123-ccbb1f4ef2ae'","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":44,"value":"base_url_edelweiss = 'https://api.kit.edelweissconnect.com/datasets/'","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":4,"value":"query_options = {\n return {\n method: 'POST',\n body: JSON.stringify({\n condition: {\n gt: [{tanimotoSimilarity: [smiles, { column: [\"SMILES\"] }]}, tanimoto_threshold]\n },\n orderBy: [\n {expression: {tanimotoSimilarity: [smiles, { column: [\"SMILES\"] }]}, ordering: \"descending\"}\n ]\n })\n }\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":497,"value":"svg = function_get_svg_from_smiles(smiles)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":368,"value":"function_get_svg_from_smiles = function get_svg_from_smiles(smiles) {\n const safeSmiles = encodeURIComponent(smiles);\n const svg_url = \"https://chemidconvert.cloud.douglasconnect.com/v1/asSvg?width=200&height=200&smiles=\" + safeSmiles;\n return fetch(svg_url).then(response => response.text());\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":212,"value":"import {vl} from \"@vega/vega-lite-api\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":262,"value":"import {select, textarea, text, slider} from \"@jashkenas/inputs\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":451,"value":"import {Select, Checkbox} from \"@observablehq/inputs\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W34","stdlib":"1","titling":"auto"}} 2f:"$2e:body"