2a:null 2b:["$","title",null,{"children":"EU-ToxRisk Data Browser | SaferWorldbyDesign | Observable"}] 30:[] 2e:{"id":"664c7f13d5e2477f","slug":"browse-through-eu-toxrisk-datsets","title":"EU-ToxRisk Data Browser","thumbnail":"a5896ba1864d80885cb1c0fdacf4994cdc7f924cba0702afa00093978519dbc3","access_level":"public","create_time":"$D2022-12-30T08:45:39.059Z","update_time":"$D2023-01-08T13:26:15.881Z","view_time":null,"first_public_time":"$D2022-12-30T09:11:35.830Z","fork":{"id":"ee9e4fb45c009de1","slug":"search-table","title":"Search + Table","owner":{"id":"f35c755083683fe5","login":"observablehq","name":"Observable"}},"stars":0,"starred":false,"owner":{"type":"team","id":"30ee3351e2ff67fe","login":"saferworldbydesign","name":"SaferWorldbyDesign","avatar_url":"https://avatars-next.observableusercontent.com/ae8ad54cbf1070f53313287fd09fe216fe7df3f89b64c74b80b5ead14bf1263b","tier":"starter_2024"},"version":408,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"acb80c7d769b3359","login":"tomazm","name":"Tomaz Mohoric","avatar_url":null,"tier":null}],"members":[{"type":"team","id":"30ee3351e2ff67fe","login":"saferworldbydesign","name":"SaferWorldbyDesign","avatar_url":"https://avatars-next.observableusercontent.com/ae8ad54cbf1070f53313287fd09fe216fe7df3f89b64c74b80b5ead14bf1263b","tier":"starter_2024","role":"editor"},{"type":"individual","id":"acb80c7d769b3359","login":"tomazm","name":"Tomaz Mohoric","avatar_url":null,"tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"EU-ToxRisk Data Browser","cells":[{"id":73,"value":"# EU-ToxRisk Data Browser\n\nYou can browse through EU-ToxRisk data by:\n1. (Optional) Entering your target compound structures (SMILES) and setting the chemical similarity threshold.\n2. Choosing assay properties\n3. Running additional free-text search\n\nTable with the results will contain all the EUToxRisk assays fulfilling the above criteria and their links to the Biostudies repository.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":4,"value":"## 1. Enter your target compound structure (SMILES) - optional\n\nDon't forget to **hit the *Confirm target compound* ** button and set the chemical similarity threshold below.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":47,"value":"viewof smiles = textarea({placeholder: \"Enter SMILES\", submit: \"Confirm target compound\", value: \"CC12CCC3C(C1CCC2O)CCC4=C3C=CC(=C4)O\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":53,"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":300,"value":"This is the structure of your target compound:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":83,"value":"compound_figure = html`${svg}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":28,"value":"## 2. Filter assays by choosing their properties","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":118,"value":"viewof selected_organisms = Inputs.select(organisms, {multiple: true, label: \"Organism\", value: organisms})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":123,"value":"viewof selected_organs = Inputs.select(organs, {multiple: true, label: \"Organ\", value: organs})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":129,"value":"viewof selected_celltypes = Inputs.select(celltypes, {multiple: true, label: \"Cell types\", value: celltypes})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":132,"value":"viewof selected_cellnames = Inputs.select(cellnames, {multiple: true, label: \"Cell name\", value: cellnames})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":135,"value":"viewof selected_organizations = Inputs.select(organizations, {multiple: true, label: \"Organization\", value: organizations})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":303,"value":"## 3. Free-text search\n\nYou can still perform a free-text search within the results filtered by the above criteria. You can e.g. search only for summary datasets by entering the keyword \"summary\".","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":57,"value":"viewof search = Inputs.search(data_unique_datasets)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":307,"value":"## 4.1 Results (assays)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":59,"value":"Inputs.table(search_prepared_for_display, {\n format: {\n Assay: links => htl.html`${links[0]} `\n },\n width: {\n Assay: 500\n },\n columns: ['Assay', 'Organism', 'Organ', 'Cell type', 'Cell name', 'Organization']})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":400,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined"},{"id":402,"value":"## 4.2 Results (similar compounds)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":339,"value":"plot_compounds = {\n var shtml;\n shtml = \"\";\n if (data_unique_compounds.length > 0) {\n var i;\n for (i = 0; i < data_unique_compounds.length; i++) {\n var this_svg = unique_svgs[i];\n var this_name = data_unique_compounds[i].name;\n shtml = shtml + \"\" + this_name + \" (Tanimoto similarity: \" + data_unique_compounds[i]['similarity'] +\")
\" + 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":141,"value":"

Supplementary code

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined"},{"id":198,"value":"search_prepared_for_display = search.map(item => {\n var newitem = item\n newitem.Assay = [item['Title'], item['Biostudies Link']]\n return newitem\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":116,"value":"cellnames = get_unique_elements(full_data, \"Cell name\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":114,"value":"organizations = get_unique_elements(full_data, \"Organization\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":32,"value":"organs = get_unique_elements(full_data, \"Organ\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":36,"value":"organisms = get_unique_elements(full_data, \"Organism\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":38,"value":"celltypes = get_unique_elements(full_data, \"Cell type\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":387,"value":"unique_svgs = Promise.all(promises_svgs)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":367,"value":"promises_svgs = data_unique_compounds.map(item => function_get_svg_from_smiles(item['SMILES']))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":362,"value":"data_unique_compounds = data_compounds.filter((v,i,a)=>a.findIndex(v2=>(v2.SMILES===v.SMILES))===i)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":357,"value":"data_compounds = data.map(item => {return {\n 'SMILES': item.SMILES.canonical,\n 'similarity': item.SMILES.similarity.toFixed(2),\n 'name': item[\"Compound name\"],\n \n}})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":277,"value":"data_unique_datasets = data.filter((v,i,a)=>a.findIndex(v2=>(v2.id===v.id))===i)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":347,"value":"similar_compounds_smiles = Array.from(new Set(data.map(item => item.SMILES.canonical)))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":25,"value":"data = fetch_dataset_to_array(dataset_url, query)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":157,"value":"full_data = fetch_dataset_to_array(dataset_url, query_full)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":251,"value":"query = {\n if (smiles == \"\") {\n return query_default\n } else {\n return query_similarity\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":168,"value":"query_full = {\n return {\n method: 'POST',\n body: JSON.stringify({\n columns: [\"Organization\", \"Organ\", \"Organism\", \"Cell type\", \"Cell name\"]\n })\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":40,"value":"query_similarity = {\n return {\n method: 'POST',\n body: JSON.stringify({\n condition: {\n and: [\n {gt: [{tanimotoSimilarity: [smiles, { column: [\"SMILES\"] }]}, tanimoto_threshold]},\n {containedIn: [{ column: [\"Organization\"] }, selected_organizations]},\n {containedIn: [{ column: [\"Organism\"] }, selected_organisms]},\n {containedIn: [{ column: [\"Organ\"] }, selected_organs]},\n {containedIn: [{ column: [\"Cell type\"] }, selected_celltypes]},\n {containedIn: [{ column: [\"Cell name\"] }, selected_cellnames]},\n ] \n },\n orderBy: [\n {expression: {tanimotoSimilarity: [smiles, { column: [\"SMILES\"] }]}, ordering: \"descending\"}\n ]\n })\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":61,"value":"query_default = {\n return {\n method: 'POST',\n body: JSON.stringify({\n condition: {\n and: [\n {containedIn: [{ column: [\"Organization\"] }, selected_organizations]},\n {containedIn: [{ column: [\"Organism\"] }, selected_organisms]},\n {containedIn: [{ column: [\"Organ\"] }, selected_organs]},\n {containedIn: [{ column: [\"Cell type\"] }, selected_celltypes]},\n {containedIn: [{ column: [\"Cell name\"] }, selected_cellnames]},\n\n ]\n },\n })\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":87,"value":"svg = function_get_svg_from_smiles(smiles)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":85,"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":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":30,"value":"get_unique_elements = function(array, parameter) {\n return Array.from(new Set(array.map(item => item[parameter])))\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":23,"value":"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":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":21,"value":"dataset_url = base_url_edelweiss + dataset_id + \"/versions/latest/data\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":19,"value":"dataset_id = \"319fdacd-4949-4bd2-a98a-e4ab63be02cb\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":17,"value":"base_url_edelweiss = 'https://api.edelweissdata.com/datasets/'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":49,"value":"import {select, textarea, text, slider} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W30","stdlib":"1","titling":"auto"}} 2f:"$2e:body"