Scholia

<!DOCTYPE html> <html> <head> <title>Scholia</title> <meta charset="UTF-8"> <meta name="robots" content="index, nofollow"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="og:url" content="https://scholia.toolforge.org/taxon/Q7623385" /> <meta name="og:site_name" content="Scholia" /> <meta name="og:image" content="/static/images/scholia_social_media.png" /> <meta name="twitter:card" content="summary" /> <meta name="twitter:site" content="@WDScholia" />  <link href="/static/css/bootstrap.min.css" rel="stylesheet"> <link rel="canonical" href="https://scholia.toolforge.org/taxon/Q7623385"> <link rel="stylesheet" type="text/css" href="/static/css/bootstrap.min.css"> <link rel="stylesheet" type="text/css" href="/static/jquery.dataTables.min.css"> <link rel="stylesheet" type="text/css" href="/static/css/scholia.css"> <link rel='stylesheet' type='text/css' href="/static/css/nightmode.css">  <link rel="apple-touch-icon" sizes="180x180" href="/static/favicon/apple-touch-icon.png"> <link rel="icon" type="image/png" sizes="32x32" href="/static/favicon/favicon-32x32.png"> <link rel="icon" type="image/png" sizes="16x16" href="/static/favicon/favicon-16x16.png"> <link rel="manifest" href="/static/favicon/site.webmanifest"> <link rel="mask-icon" href="/static/favicon/safari-pinned-tab.svg" color="#09af8a"> <link rel="shortcut icon" href="/static/favicon/favicon.ico"> <meta name="apple-mobile-web-app-title" content="Scholia"> <meta name="application-name" content="Scholia"> <meta name="msapplication-TileColor" content="#09af8a"> <meta name="theme-color" content="#09af8a"> </head> <body> <nav class="navbar navbar-expand-lg" style="max-width: 1200px;"> <a class="navbar-brand" href="/"><img src="/static/images/scholia_wordmark.svg" width="112px" height="24px" alt="Scholia"></a> <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div class="collapse navbar-collapse" id="navbarSupportedContent"> <ul class="navbar-nav mr-auto"> <li class="nav-item"><a class="nav-link" href="/author/">Author</a></li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="workDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Work </a> <div class="dropdown-menu" aria-labelledby="workDropdown"> <a class="dropdown-item" href="/work/">Work</a> <a class="dropdown-item" href="/venue/">Venue</a> <a class="dropdown-item" href="/series/">Series</a> <a class="dropdown-item" href="/catalogue/">Catalogue</a> <a class="dropdown-item" href="/publisher/">Publisher</a> <a class="dropdown-item" href="/printer/">Printer</a> </div> </li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="organisationDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Organization </a> <div class="dropdown-menu" aria-labelledby="organisationDropdown"> <a class="dropdown-item" href="/organization/">Organization</a> <a class="dropdown-item" href="/publisher/">Publisher</a> <a class="dropdown-item" href="/printer/">Printer</a> <a class="dropdown-item" href="/sponsor/">Sponsor</a> </div> </li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="locationDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Location </a> <div class="dropdown-menu" aria-labelledby="locationDropdown"> <a class="dropdown-item" href="/location/">Location</a> <a class="dropdown-item" href="/country/">Country</a> </div> </li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="eventDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Event </a> <div class="dropdown-menu" aria-labelledby="eventDropdown"> <a class="dropdown-item" href="/event/">Event</a> <a class="dropdown-item" href="/event-series/">Event series</a> </div> </li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="projectDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Project </a> <div class="dropdown-menu" aria-labelledby="projectDropdown"> <a class="dropdown-item" href="/clinical-trial/">Clinical trial</a> <a class="dropdown-item" href="/project/">Project</a> <a class="dropdown-item" href="/wikiproject/">WikiProject</a> </div> </li> <li class="nav-item"><a class="nav-link" href="/award/">Award</a></li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="topicDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Topic </a> <div class="dropdown-menu" aria-labelledby="projectDropdown"> <a class="dropdown-item" href="/topic/">General</a> <a class="dropdown-item" href="/disease/">Disease</a> <a class="dropdown-item" href="/taxon/">Taxon</a> <a class="dropdown-item" href="/gene/">Gene</a> <a class="dropdown-item" href="/protein/">Protein</a> <a class="dropdown-item" href="/pathway/">Pathway</a> <a class="dropdown-item" href="/chemical/">Chemical</a> <a class="dropdown-item" href="/chemical-element/">Chemical element</a> <a class="dropdown-item" href="/chemical-class/">Chemical class</a> <a class="dropdown-item" href="/lexeme/">Lexeme</a> <a class="dropdown-item" href="/ontology/">Ontology</a> <a class="dropdown-item" href="/software/">Software</a> <a class="dropdown-item" href="/use/">Use</a> </div> </li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="toolsDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Tools </a> <div class="dropdown-menu" aria-labelledby="toolsDropdown"> <a class="dropdown-item" href="/id-to-quickstatements">Identifier to Quickstatements</a> <a class="dropdown-item" href="/q-to-bibliography-templates">Q to Bibliography templates</a> <a class="dropdown-item" href="/text-to-topics">Text to topics</a> </div> </li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="helpDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Help </a> <div class="dropdown-menu" aria-labelledby="helpDropdown"> <a class="dropdown-item" href="/about">About</a> <a class="dropdown-item" href="/statistics">Statistics</a> <a class="dropdown-item" href="/faq">FAQ</a> </div> </li> </ul> <div class='nav nav-search'> <input class="form-control" type="text" id="searchterm" placeholder="Search..."/> </div> </div> </nav> <div class="content"> <div class="container d-flex justify-content-between"> <div class="dropdown" id="aspect-chooser"> </div> <div> <a id='curation-link' role="button" class="btn btn-outline-secondary d-none">Improve data</a> </div> </div> <div class="container"> <h1 id="h1">Taxon</h1> <script type="application/ld+json" id="bioschemas"></script> <div id="intro"></div> <div id="wembedder"></div> <h2 id="identifiers">Identifiers</h2> <table class="table table-hover" id="identifiers-table"></table> <h2 id="parent-taxa">Parent Taxa</h2> <table class="table table-hover" id="parent-taxa-table"></table> <div class="embed-responsive embed-responsive-16by9"> <iframe class="embed-responsive-item" id="tree-iframe" ></iframe> </div> <h2 id="co-occurring-taxa">Bibliographically co-occurring taxa</h2> Taxa that are mentioned in the same publications. This does not imply biological interactions (which are tracked by <a href="https://www.globalbioticinteractions.org/?sourceTaxon=WD%3AQ7623385">GloBI</a>), nor co-occurrence in ecological or biogeographical contexts. <table class="table table-hover" id="co-occurring-taxa-table"></table> <h2 id="genome">Genome</h2> <table class="table table-hover" id="genome-table"></table> <h2 id="proteome">Proteome</h2> <table class="table table-hover" id="proteome-table"></table> <h2 id="metabolome">Metabolome</h2> <table class="table table-hover" id="metabolome-table"></table> </div> </div> <div class="container footer"> <hr> Data from <a href="https://www.wikidata.org">Wikidata</a> and <a href="https://en.wikipedia.org">English Wikipedia</a> | Code from <a href="https://github.com/WDscholia/scholia">GitHub repository</a> | Hosted on <a href="https://toolforge.org/">Wikimedia Toolforge</a>, a <a href="https://wikimediafoundation.org">Wikimedia Foundation</a> service | License for content: CC0 for data, CC-BY-SA for text and media | Report technical problems at Scholia's <a href="https://github.com/WDscholia/scholia/issues">Issues</a> GitHub page. | Follow us on <a href="https://wikis.world/@wdscholia">Mastodon</a>. <hr> </div> <script src="/static/jquery.min.js"></script> <script src="/static/js/popper.min.js"></script> <script src="/static/js/bootstrap.min.js"></script> <script type="text/javascript" src="/static/d3.v5.min.js"></script> <script type="text/javascript" src="/static/d3-scale-chromatic.v1.min.js"></script> <script type="text/javascript" src="/static/jquery.dataTables.min.js"></script> <script type="text/javascript" src="/static/scholia.js"></script> <script type="text/javascript" src="/static/bootstrap-autocomplete.min.js"></script> <script type="text/javascript"> var url = 'https://www.wikidata.org/w/api.php?action=wbgetentities&ids=' + 'Q7623385' + '&format=json&callback=?'; const currentAspect = window.location.pathname.split("/")[1]; $.getJSON(url, function (data) { var item = data.entities["Q7623385"]; if ('en' in item.labels) { var title = item.labels.en.value; var wdtitle = item.labels.en.value; $("#h1").text(title); $(".self").text(title); $("title").text(title + " - Scholia"); var crossref_button = document.getElementById("check-crossref-button"); if (title && crossref_button) { crossref_button.onclick = () => {get_dois_from_crossref(wdtitle)} crossref_button.innerHTML = "Check Crossref" } } $("#h1").append(' (<a href="https://www.wikidata.org/wiki/Q7623385">Q7623385</a>)'); if ("P18" in item.claims) { // Find P18 claim which is not deprecated const p18Claim = item.claims.P18.find(function (claim) { return claim.rank !== "deprecated"; }); if (undefined !== p18Claim) { var imageName = p18Claim.mainsnak.datavalue.value; // spaces must be replaced by underscores in the file name imageName = imageName.replaceAll(" ", "_") var imageNameMd5 = md5(imageName); var imageURL = "https://upload.wikimedia.org/wikipedia/commons/thumb/" imageURL += imageNameMd5[0] + "/" + imageNameMd5.slice(0,2) + "/" var filetype = imageName.match(/\.(\w+)$/); var extension = filetype[1].toLowerCase() if (extension === "tif" || extension === "tiff") { imageURL += encodeURIComponent(imageName) + "/lossy-page1-500px-" + encodeURIComponent(imageName) + ".jpg"; } else if (extension === "svg") { imageURL += encodeURIComponent(imageName) + "/500px-" + encodeURIComponent(imageName) + ".png"; } else { imageURL += encodeURIComponent(imageName) + "/500px-" + encodeURIComponent(imageName); } var itemImage = document.getElementById("item-image"); if (itemImage) { itemImage.src = imageURL; itemImage.title = imageName.slice(0, imageName.lastIndexOf('.')); itemImage.setAttribute('alt', imageName); var link = document.createElement('a'); link.href = "https://commons.wikimedia.org/wiki/File:" + encodeURIComponent(imageName); link.style = "max-width: 50%" var parent = itemImage.parentNode; parent.replaceChild(link, itemImage); link.appendChild(itemImage); } } } if ("P10286" in item.claims) { var imageURL = item.claims.P10286[0].mainsnak.datavalue.value; var itemImage = document.getElementById("item-image"); if (itemImage) { itemImage.src = imageURL; } } function socialMediaLink(detailsList, user, site, logo = '') { var html = ''; if (logo) { html += '<a href="' + site.url + '"><img alt="' + site.name + ' logo" src="'; html += logo.src + '" width="16" height="16" hspace="4" /></a> '; } html += '<a href="' + site.url + encodeURI(user.name) + '">'; html += user.prefix + escapeHTML(user.name) + '</a>'; detailsList.push(html); } function sortRank(a, b) { const aRank = a["rank"]; const bRank = b["rank"]; if (aRank == bRank) { return 0; } if (aRank == "preferred" || bRank == "deprecated") { return -1; } if (bRank == "preferred" || aRank == "deprecated") { return 1; } return 0; } var detailsList = Array(); if ("P496" in item.claims) { var user = {name: item.claims.P496[0].mainsnak.datavalue.value, prefix: 'https://orcid.org/'}; var site = {name: "ORCID", url: "https://orcid.org/"}; var logo = {src: "/static/images/orcid.svg"}; socialMediaLink(detailsList, user, site, logo); } if ("P4033" in item.claims) { var mastodonAccount = item.claims.P4033[0].mainsnak.datavalue.value; var mastodonComponents = mastodonAccount.split("@"); if (mastodonComponents.length == 2) { // Mastodon user URLs start with @ var user = { name: '@' + mastodonComponents[0], prefix: '' }; var site = { name: "Mastodon", url: 'https://' + mastodonComponents[1] + '/' }; var logo = { src: "/static/images/mastodon.svg" }; socialMediaLink(detailsList, user, site, logo); } } if ("P2037" in item.claims) { var user = {name: item.claims.P2037[0].mainsnak.datavalue.value, prefix: "@"}; var site = { name: "GitHub", url: "https://github.com/" }; var logo = { src: "/static/images/github.svg" }; socialMediaLink(detailsList, user, site, logo); } if ("P6782" in item.claims) { var user = { name: item.claims.P6782[0].mainsnak.datavalue.value, prefix: 'https://ror.org/' }; var site = { name: "Research Organization Registry", url: 'https://ror.org/' }; var logo = { src: "/static/images/ror.svg" }; socialMediaLink(detailsList, user, site, logo); } if ("P2572" in item.claims) { var user = { name: item.claims.P2572[0].mainsnak.datavalue.value, prefix: '#' }; var site = { name: "Hashtag hub", url: 'https://hashtags-hub.toolforge.org/' }; socialMediaLink(detailsList, user, site); } /* Official homepage */ if ("P856" in item.claims) { var homepage = item.claims.P856.sort(sortRank)[0] var homepageURL = homepage.mainsnak.datavalue.value detailsList.push(' <a href="' + homepageURL + '">' + homepageURL + '</a>'); } if (detailsList.length > 0) { $('#details').append(detailsList.join(" | ")); } try { var doi = item.claims.P356[0].mainsnak.datavalue.value; $("head").append( '<meta name="citation_doi" content="' + doi + '"/>' ); } catch(e) {} /* BioSchemas annotation */ if (item.claims.P31 && ((item.claims.P31[0].mainsnak.datavalue.value.id == 'Q5'))) { try { /* Person */ bioschemasAnnotation = { "@context" : "https://schema.org", "@type" : "Person" , "http://purl.org/dc/terms/conformsTo": { "@type": "CreativeWork", "@id": "https://bioschemas.org/profiles/Person/0.2-DRAFT-2019_07_19/" }, "description" : "A person" , "identifier" : "Q7623385" , "mainEntityOfPage" : "http://www.wikidata.org/entity/Q7623385" } if ('en' in item.labels) { bioschemasAnnotation.name = item.labels.en.value; } $( '#bioschemas' ).append( JSON.stringify(bioschemasAnnotation) ); } catch(e) {} } else if (item.claims.P31 && ((item.claims.P31[0].mainsnak.datavalue.value.id == 'Q47461491') || (item.claims.P31[0].mainsnak.datavalue.value.id == 'Q967847'))) { try { /* ChemicalSubstance */ bioschemasAnnotation = { "@context" : "https://schema.org", "@type" : "ChemicalSubstance" , "http://purl.org/dc/terms/conformsTo": { "@type": "CreativeWork", "@id": "https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE/" }, "identifier" : "Q7623385" , "url" : "http://www.wikidata.org/entity/Q7623385" } if ('en' in item.labels) { bioschemasAnnotation.name = item.labels.en.value; } $( '#bioschemas' ).append( JSON.stringify(bioschemasAnnotation) ); } catch(e) {} } else if (item.claims.P225) { try { /* Taxon */ var taxonName = item.claims.P225[0].mainsnak.datavalue.value; bioschemasAnnotation = { "@context" : "https://schema.org", "@type" : "Taxon" , "http://purl.org/dc/terms/conformsTo": { "@type": "CreativeWork", "@id": "https://bioschemas.org/profiles/Taxon/0.6-RELEASE/" }, "name" : taxonName , "url" : "http://www.wikidata.org/entity/Q7623385" } if (item.claims.P105) { var taxonRank = item.claims.P105[0].mainsnak.datavalue.value.id; bioschemasAnnotation.taxonRank = "http://www.wikidata.org/entity/" + taxonRank ; } if (item.claims.P171) { var parent = item.claims.P171[0].mainsnak.datavalue.value.id; bioschemasAnnotation.parentTaxon = "http://www.wikidata.org/entity/" + parent ; } $( '#bioschemas' ).append( JSON.stringify(bioschemasAnnotation) ); // console.log(JSON.stringify(bioschemasAnnotation, "", 2)) } catch(e) {} } else if (item.claims.P235) { try { /* Chemical Compound */ var inchiKey = item.claims.P235[0].mainsnak.datavalue.value; bioschemasAnnotation = { "@context" : "https://schema.org", "@type" : "MolecularEntity" , "http://purl.org/dc/terms/conformsTo": { "@type": "CreativeWork", "@id": "https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE/" }, "identifier" : "Q7623385" , "inChIKey" : inchiKey , "url" : "http://www.wikidata.org/entity/Q7623385" } if ('en' in item.labels) { bioschemasAnnotation.name = item.labels.en.value; } if (item.claims.P234 && item.claims.P234[0].mainsnak.datavalue) { var inchi = item.claims.P234[0].mainsnak.datavalue.value; bioschemasAnnotation.inChI = inchi ; } if (item.claims.P274 && item.claims.P274[0].mainsnak.datavalue) { var chemformula = item.claims.P274[0].mainsnak.datavalue.value; bioschemasAnnotation.molecularFormula = chemformula ; } if (item.claims.P2017 && item.claims.P2017[0].mainsnak.datavalue) { var smiles = item.claims.P2017[0].mainsnak.datavalue.value; bioschemasAnnotation.molecularFormula = smiles.replace("\"", "\'\'") ; } else if (item.claims.P233 && item.claims.P233[0].mainsnak.datavalue) { var smiles = item.claims.P233[0].mainsnak.datavalue.value; bioschemasAnnotation.smiles = smiles.replace("\"", "\'\'") ; } $( '#bioschemas' ).append( JSON.stringify(bioschemasAnnotation) ); } catch(e) { console.error("Exception: " + e) } } else if (item.claims.P352) { // UniProt ID try { /* Protein */ var uniprot = item.claims.P352[0].mainsnak.datavalue.value; bioschemasAnnotation = { "@context" : "https://schema.org", "@type" : "Protein" , "http://purl.org/dc/terms/conformsTo": { "@type": "CreativeWork", "@id": "https://bioschemas.org/profiles/Protein/0.11-RELEASE/" }, "identifier" : "Q7623385" , "url" : "http://www.wikidata.org/entity/Q7623385" , "sameAs": "https://www.uniprot.org/uniprot/" + uniprot } if ('en' in item.labels) { bioschemasAnnotation.name = item.labels.en.value; } $( '#bioschemas' ).append( JSON.stringify(bioschemasAnnotation) ); } catch(e) { console.error("Exception: " + e) } } else if (item.claims.P351 || item.claims.P594) { // NCBI Gene or Ensembl try { /* Gene */ bioschemasAnnotation = { "@context" : "https://schema.org", "@type" : "Gene" , "http://purl.org/dc/terms/conformsTo": { "@type": "CreativeWork", "@id": "https://bioschemas.org/profiles/Gene/0.7-RELEASE/" }, "identifier" : "Q7623385" , "url" : "http://www.wikidata.org/entity/Q7623385" } if ('en' in item.labels) { bioschemasAnnotation.name = item.labels.en.value; } counter = 0 bioschemasAnnotation.sameAs = [] if (item.claims.P351 && item.claims.P351[0].mainsnak.datavalue) { var ncbi = item.claims.P351[0].mainsnak.datavalue.value; bioschemasAnnotation.sameAs[counter] = "https://www.ncbi.nlm.nih.gov/gene/" + ncbi; counter++ } if (item.claims.P594 && item.claims.P594[0].mainsnak.datavalue) { var ensembl = item.claims.P594[0].mainsnak.datavalue.value; bioschemasAnnotation.sameAs[counter] = "http://identifiers.org/ensembl/" + ensembl; } $( '#bioschemas' ).append( JSON.stringify(bioschemasAnnotation) ); } catch(e) { console.error("Exception: " + e) } } /* English Wikipedia */ if ('enwiki' in item.sitelinks) { var title = item.sitelinks.enwiki.title; var wikipediaApiUrl = 'https://en.wikipedia.org/api/rest_v1/page/summary/' + encodeURIComponent(title); var wikipediaUrl = 'https://en.wikipedia.org/wiki/' + encodeURIComponent(title) var headers = new Headers({"Api-User-Agent": "https://github.com/WDscholia/scholia"}); fetch(wikipediaApiUrl, {method: 'GET', headers: headers}) .then(response => response.json()) .then(data => { var html = " (<a href=\"" + wikipediaUrl + "\">Read more on English Wikipedia</a>)"; $("#intro").text(data.extract).append(html); }).catch(error => { var html = "<a href=\"" + wikipediaUrl + "\">View on English Wikipedia</a>"; $("#intro").append(html); console.error('Could not get summary from enwiki: ', error); }); } /* English Wikiversity */ if ('enwikiversity' in item.sitelinks) { var enwikiversityTitle = item.sitelinks.enwikiversity.title; var wikiversityApiUrl = 'https://en.wikiversity.org/w/api.php?' + 'action=query&prop=extracts&exsentences=3&exlimit=1&exintro=1&' + 'explaintext=1&callback=?&format=json&titles=' + encodeURIComponent(enwikiversityTitle); var wikiversityUrl = 'https://en.wikiversity.org/wiki/' + encodeURIComponent(enwikiversityTitle) $.getJSON(wikiversityApiUrl, function(data) { var pages = data.query.pages; var text = pages[Object.keys(pages)[0]].extract; if (text) { var html = "... (from the <a href=\"" + wikiversityUrl + "\">English Wikiversity</a>)"; } else { var html = "Read on the <a href=\"" + wikiversityUrl + "\">English Wikiversity</a>"; } $("#wikiversity-extract").text(text).append(html); }).fail(function(d, textStatus, error) { var html = "Read on the <a href=\"" + wikiversityUrl + "\">English Wikiversity</a>"; $("#wikiversity-extract").append(html); console.error("getJSON failed, status: " + textStatus + ", error: "+error) }); } }); var curationElement = document.getElementById("curation-link"); curationElement.href = "/" + currentAspect + "/Q7623385/curation"; curationElement.classList.remove("d-none"); // this query opens the Wikidata item as a different aspect var endpointUrl = 'https://query.wikidata.org/sparql'; if ("".length) { var query = ` SELECT DISTINCT ?aspect WHERE { { [] wdt:P17 wd:Q7623385 . BIND("country" AS ?aspect) } UNION { wd:Q7623385 wdt:P159? / wdt:P625 [] . BIND("location" AS ?aspect) } UNION { [] wdt:P1416 | wdt:P108 wd:Q7623385 . BIND("organization" AS ?aspect) } } `; } else { var query = ` SELECT DISTINCT ?aspect WHERE { { [] wdt:P50 wd:Q7623385 . BIND("author" AS ?aspect) } UNION { [] wdt:P166 wd:Q7623385 . BIND("award" AS ?aspect) } UNION { wd:Q7623385 wdt:P31 / wdt:P279? wd:Q22325163 . BIND("complex" AS ?aspect) } UNION { [] wdt:P17 wd:Q7623385 . BIND("country" AS ?aspect) } UNION { [] wdt:P972 wd:Q7623385 . BIND("catalogue" AS ?aspect) } UNION { wd:Q7623385 wdt:P235 [] . BIND("chemical" AS ?aspect) } UNION { wd:Q7623385 ^wdt:P31/wdt:P235 [] . BIND("chemical-class" AS ?aspect) } UNION { wd:Q7623385 wdt:P644 [] . BIND("gene" AS ?aspect) } UNION { wd:Q7623385 wdt:P159? / wdt:P625 [] . BIND("location" AS ?aspect) } UNION { [] wdt:P1416 | wdt:P108 wd:Q7623385 . BIND("organization" AS ?aspect) } UNION { wd:Q7623385 wdt:P31 wd:Q2996394 . BIND("pathway" AS ?aspect) } UNION { wd:Q7623385 wdt:P31 wd:Q4915012 . BIND("pathway" AS ?aspect) } UNION { [] wdt:P872 wd:Q7623385 . BIND("printer" AS ?aspect) } UNION { wd:Q7623385 wdt:P31 wd:Q8054 . BIND("protein" AS ?aspect) } UNION { [] wdt:P123 wd:Q7623385 . BIND("publisher" AS ?aspect) } UNION { [] wdt:P179 wd:Q7623385 . BIND("series" AS ?aspect) } UNION { wd:Q7623385 wdt:P31 / wdt:P279* wd:Q7397 . BIND("software" AS ?aspect) } UNION { [] wdt:P859 wd:Q7623385 . BIND("sponsor" AS ?aspect) } UNION { wd:Q7623385 wdt:P225 [] . BIND("taxon" AS ?aspect) } UNION { [] wdt:P921 wd:Q7623385 . BIND("topic" AS ?aspect) } UNION { [] wdt:P4510 wd:Q7623385 . BIND("use" AS ?aspect) } UNION { [] wdt:P1433 wd:Q7623385 . BIND("venue" AS ?aspect) } UNION { wd:Q7623385 wdt:P50 | wdt:P2093 [] . BIND("work" AS ?aspect) } } `; } settings = { headers: { Accept: 'application/sparql-results+json' }, data: { query: query } }; $.ajax(endpointUrl, settings).then(function (data) { createDropdownButton("aspect-chooser", 'aspectMenuButton', currentAspect, data, "Q7623385") if (data.results.bindings.length > 1) { addDropdownList("aspect-chooser", 'aspectMenuList', currentAspect, data) } }).then(function () { if ("".length) { var endpointUrl = 'https://query.wikidata.org/sparql'; var query = "SELECT DISTINCT ?aspect WHERE {" query += '{ [] wdt:P921 wd:Q7623385 . BIND("topic" AS ?aspect) } }'; settings = { headers: { Accept: 'application/sparql-results+json' }, data: { query: query } }; $.ajax(endpointUrl, settings).then(function (data) { var aspectLabel = " / <a href='/" + currentAspect + "/Q7623385'>Q7623385</a> / " document.getElementById("aspect-chooser-label").innerHTML = aspectLabel; var currentSubAspect = window.location.pathname.split("/")[3]; document.querySelectorAll("#aspectMenuList a").forEach((link) => link.href += "/" + currentSubAspect + "/") createDropdownButton("aspect-chooser", 'aspectMenuButton', currentSubAspect, data, "") if (data.results.bindings.length > 1) { addDropdownList("aspect-chooser", 'aspectMenuList', currentSubAspect, data) } }).fail(function (jqXHR, textStatus, errorThrown) { console.error("Subaspect chooser failed to generate. " + textStatus + " " + errorThrown) }); } }).fail(function (jqXHR, textStatus, errorThrown) { console.error("Aspect chooser failed to generate. " + textStatus + " " + errorThrown) }); function createDropdownButton(parent, id, currentAspect, data, q) { var aspectDropdown = document.createElement('button'); aspectDropdown.type = 'button'; aspectDropdown.id = id; aspectDropdown.classList = 'btn btn-outline-secondary'; // only show aspects which have a curation page with author-disambig or wikidata links var validCurationPages = ["author", "award", "organization", "topic", "venue"] if (data.results.bindings.length > 1) { aspectDropdown.classList.add('dropdown-toggle'); aspectDropdown.setAttribute('data-toggle', 'dropdown'); aspectDropdown.setAttribute('aria-haspopup', 'true'); aspectDropdown.setAttribute('aria-expanded', 'false'); } aspectDropdown.innerText = currentAspect; document.getElementById(parent).append(aspectDropdown); aspectDropdown.insertAdjacentHTML("afterend", '<span id="aspect-chooser-label" style="color: #6C757D; vertical-align: middle;margin: 2px;"> / '+ q + '</span>') } function addDropdownList(parent, id, currentAspect, data) { var aspectDropdownMenu = document.createElement('div'); aspectDropdownMenu.classList = 'dropdown-menu'; aspectDropdownMenu.setAttribute('aria-labelledby', 'aspectMenuButton'); aspectDropdownMenu.id = id data.results.bindings.forEach(function (entry) { var aspect = entry.aspect.value; if (aspect != currentAspect) { var dropdownItem = document.createElement('a'); dropdownItem.classList = 'dropdown-item'; dropdownItem.href = "/" + aspect + '/Q7623385'; dropdownItem.innerText = aspect; aspectDropdownMenu.append(dropdownItem); } }); document.getElementById(parent).append(aspectDropdownMenu); } /* Wembedder */ var wembedderUrl = "https://wembedder.toolforge.org/api/most-similar/Q7623385"; $.ajax({ url: wembedderUrl, success: function (data) { var html = `<hr>` + `<span data-toogle="tooltip" ` + `title="Related items from Wembedder knowledge graph embedding.">` + `<a alt="Wembedder about page" ` + `href="https://wembedder.toolforge.org/about">Related</a>:</span> `; $( '#wembedder' ).append(html); // Make list with results data.most_similar.forEach(function(entry, idx, array) { var listed_q = entry.item; var language = 'en'; if (idx !== 0) { $( '#wembedder' ).append( ' · '); } var html = '<a href="../' + listed_q + '"><span id="wembedder-result-' + listed_q + '">' + listed_q + '</span></a> ' $( '#wembedder' ).append( html ); // Convert Q identifier to labels $.getJSON("https://www.wikidata.org/w/api.php?callback=?", { action: "wbgetentities", ids: listed_q, language: language, uselang: language, format: "json", strictlanguage: true, }, function (data) { if (listed_q in data.entities) { label = entityToLabel(data.entities[listed_q], language=language); $('#wembedder-result-' + listed_q).empty(); $('#wembedder-result-' + listed_q).text(label); } }); }); $( '#wembedder' ).append( '<hr>' ); }, error: function (jqXHR, textStatus, errorThrown) { console.error("Wembedder failed. " + textStatus + " " + errorThrown) }, }); $(document).ready(function () { $('#searchterm').autoComplete({ minLength: 2, resolver: 'custom', events: { search: debounce((searchTerm, callback) => { var url = "https://www.wikidata.org/w/api.php?callback=?"; var settings = { dataType: 'jsonp', data: { search: searchTerm, action: "wbsearchentities", language: "en", uselang: "en", format: "json", strictlanguage: true } }; $.ajax(url, settings).then(function (data) { if (data.search.length) { let results = ['Show all results for "' + searchTerm + '"'] for (let item of data.search) { results.push(item.label + " - " + item.description + " (" + item.title + ")"); } callback(results) } else { callback([]) } }).fail(function (jqXHR, textStatus, errorThrown) { callback(["Search failed"]) console.error("Search failed. " + textStatus + " " + errorThrown) }); }, 200) } }); $("#searchterm").on("autocomplete.select", (event, item) => { handleSearch(item) }); $("#searchterm").on("keydown", function (event) { switch (event.key) { case "Enter": handleSearch(this.value); break; default: } }); $("#searchbutton").on("click", () => { handleSearch(document.getElementById("searchterm").value) }) function handleSearch(item) { // headerSearch and authorIndexAutocomplete reference where the two formats come from let headerSearch = item.match(/ $(Q\d+)$$/); if (headerSearch) { window.location.href = "/" + headerSearch[1]; } else { let authorIndexAutocomplete = item.match(/\/\w+\/Q\d+$/); if (authorIndexAutocomplete) { window.location.href = item; } else { let search_text = item.match(/Show all results for "(.+)"$/) if (search_text) { window.location.href = "/search?q=" + search_text[1]; } else { window.location.href = "/search?q=" + item; } } } } function debounce(callback, wait) { let timeout; return (...args) => { clearTimeout(timeout); timeout = setTimeout(function () { callback.apply(this, args); }, wait); }; } // Add table of content var headings = document.querySelectorAll("h2,h3"); if (headings.length >= 3) { var tocParent = document.createElement("div"); tocParent.className = "table-of-contents" var toc = document.createElement("div"); tocTitle = document.createElement("b"); tocTitle.innerText = "Table of Contents" toc.appendChild(tocTitle) var tocList = document.createElement("ul"); var sublist = ""; for (let i = 0; i < headings.length; i++) { const element = headings[i]; if (!element.id) { element.id = element.innerText.replaceAll(" ", "-"); } if (element.tagName === "H3" && !sublist) { var sublist = document.createElement("ul"); } tocListItem = document.createElement("li"); tocEntry = document.createElement("a"); tocEntry.setAttribute("href", "#" + element.id); tocEntry.innerText = headings[i].innerText; tocListItem.appendChild(tocEntry); if (element.tagName === "H3") { sublist.appendChild(tocListItem); if (i == headings.length - 1) { tocList.appendChild(sublist); } } else { if (sublist) { tocList.appendChild(sublist); sublist = ""; } tocList.appendChild(tocListItem); } } toc.appendChild(tocList) var itemImage = document.createElement("img"); itemImage.id = "item-image"; itemImage.alt = ""; itemImage.href = ""; itemImage.onclick = function () { window.location.href = itemImage.href; }; tocParent.appendChild(toc); tocParent.appendChild(itemImage); document.querySelector("h2").insertAdjacentElement("beforebegin", tocParent) itemImage.height = toc.clientHeight } // Add anchor links to all headings var headers = document.querySelectorAll('h2[id], h3[id]') if (headers) { headers.forEach(element => { var title = element.innerText; element.removeChild(element.childNodes[0]) element.insertAdjacentHTML('afterbegin', `<a href="#${element.id}" class="hlink" ariaLabel="Anchor">${title}</a>`) }) } // identifiers table sparqlToDataTable2("https://query.wikidata.org/sparql", "https://query.wikidata.org/#", `# tool: scholia PREFIX target: <http://www.wikidata.org/entity/Q7623385> SELECT ?Identifier ?IdentifierLabel ?id (SAMPLE(?idUrls) as ?idUrl) ?IdentifierDescription WITH { SELECT ?Identifier ?id ?formatterurl WHERE { target: ?IDdir ?id . ?Identifier wikibase:directClaim ?IDdir ; wdt:P31/wdt:P279* wd:Q42396390 . OPTIONAL { ?Identifier wdt:P1630 ?formatterurl . } FILTER (?Identifier != wd:P233) FILTER (?Identifier != wd:P234) FILTER (?Identifier != wd:P2017) } LIMIT 500 } AS %RESULTS { { SELECT * WHERE { INCLUDE %RESULTS FILTER (?Identifier = wd:P234) BIND(IRI(REPLACE(?formatterurl, '\\\\$1', ENCODE_FOR_URI(str(?id)))) AS ?idUrls). } } UNION { SELECT * WHERE { INCLUDE %RESULTS FILTER (?Identifier != wd:P234) BIND(IRI(REPLACE(?formatterurl, '\\\\$1', str(?id))) AS ?idUrls). } } SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". } } GROUP BY ?Identifier ?IdentifierLabel ?IdentifierDescription ?id ORDER BY ASC(?IdentifierLabel) `, "#identifiers-table", "taxon_identifiers.sparql", options={}); // parent-taxa table sparqlToDataTable2("https://query.wikidata.org/sparql", "https://query.wikidata.org/#", `# tool: scholia PREFIX target: <http://www.wikidata.org/entity/Q7623385> SELECT (COUNT(?middle) AS ?distance) (GROUP_CONCAT(DISTINCT ?rank_label_; separator=", ") AS ?rank) ?parent ?parentLabel ?parentDescription { target: wdt:P171* ?middle . ?middle wdt:P171+ ?parent . ?parent wdt:P105 ?rank . OPTIONAL { ?rank rdfs:label ?rank_label_ . FILTER (LANG(?rank_label_) = 'en') } SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". } } GROUP BY ?parent ?parentLabel ?parentDescription ORDER BY ?distance `, "#parent-taxa-table", "taxon_parent-taxa.sparql", options={}); // tree iframe sparqlToIframe2("https://query.wikidata.org/sparql", "https://query.wikidata.org/#", "https://query.wikidata.org/embed.html#", `# tool: scholia #defaultView:Graph PREFIX target: <http://www.wikidata.org/entity/Q7623385> SELECT ?child ?childLabel ?rgb ?parent ?parentLabel WITH { SELECT ?child ?rgb ?parent WHERE { { # Parent taxa SELECT ?child ?rgb ?parent WHERE { SERVICE gas:service { gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" ; gas:in target: ; # We should not do undirected here because this could result # in very big graphs. gas:traversalDirection "Forward" ; gas:out ?child ; gas:out1 ?depth ; gas:out2 ?parent1 ; gas:linkType wdt:P171 ; } ?child wdt:P171 ?parent . BIND(IF(?child = target:, "FF0000", "FFFFFF") AS ?rgb) } } UNION { # Child taxa SELECT ?child ?rgb ?parent WHERE { BIND(target: AS ?parent) ?child wdt:P171 ?parent . BIND("DDDDDD" AS ?rgb) } LIMIT 100 } } } AS %results WHERE { INCLUDE %results ?child rdfs:label ?child_label . FILTER(LANG(?child_label) = 'en') ?parent rdfs:label ?parent_label . FILTER(LANG(?parent_label) = 'en') OPTIONAL { ?child wdt:P105 / rdfs:label ?child_rank_label . FILTER (LANG(?child_rank_label) = 'en') } OPTIONAL { ?parent wdt:P105 / rdfs:label ?parent_rank_label . FILTER (LANG(?parent_rank_label) = 'en') } BIND(CONCAT(?child_label, " - ", COALESCE(?child_rank_label, "???")) AS ?childLabel) BIND(CONCAT(?parent_label, " - ", COALESCE(?parent_rank_label, "???")) AS ?parentLabel) }`, "#tree-iframe", "taxon_tree.sparql"); // co-occurring-taxa table sparqlToDataTable2("https://query.wikidata.org/sparql", "https://query.wikidata.org/#", `# tool: scholia #title: Taxa that co-occur with the target taxon in the literature PREFIX target: <http://www.wikidata.org/entity/Q7623385> SELECT ?count (CONCAT("/topics/",SUBSTR(STR(target:), 32), ",", SUBSTR(STR(?taxon), 32)) AS ?countUrl) ?taxon ?taxonLabel (CONCAT("/taxon/", SUBSTR(STR(?taxon), 32)) AS ?taxonUrl) ?example_work ?example_workLabel (CONCAT("/work/", SUBSTR(STR(?example_work), 32)) AS ?example_workUrl) WITH { SELECT (COUNT(?work) AS ?count) ?taxon (SAMPLE(?work) AS ?example_work) WHERE { # Find works for the specific queried topic ?work wdt:P921 target: . # Find co-occuring topics ?work wdt:P921 ?taxon . # Filter for taxa ?taxon wdt:P105 ?taxonrank . # Avoid listing the queried topic itself FILTER (target: != ?taxon) } GROUP BY ?taxon } AS %result WHERE { # Label the results INCLUDE %result SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en" . } } ORDER BY DESC(?count) LIMIT 200 `, "#co-occurring-taxa-table", "taxon_co-occurring-taxa.sparql", options={}); // genome table sparqlToDataTable2("https://query.wikidata.org/sparql", "https://query.wikidata.org/#", `# tool: scholia PREFIX target: <http://www.wikidata.org/entity/Q7623385> SELECT ?gene ?geneLabel ?geneDescription ?chromosome ?chromosomeLabel ?chromosomeDescription WITH { SELECT ?gene ?chromosome WHERE { ?gene wdt:P31 wd:Q7187 ; wdt:P703 target: ; wdt:P1057 ?chromosome . } } AS %results { INCLUDE %results SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". } } `, "#genome-table", "taxon_genome.sparql", options={}); // proteome table sparqlToDataTable2("https://query.wikidata.org/sparql", "https://query.wikidata.org/#", `# tool: scholia PREFIX target: <http://www.wikidata.org/entity/Q7623385> SELECT ?protein ?proteinLabel ?proteinDescription ?gene ?geneLabel WITH { SELECT ?protein ?gene ?chromosome WHERE { ?protein wdt:P31 wd:Q8054 ; wdt:P703 target: . } } AS %results { INCLUDE %results ?protein wdt:P702 ?gene . SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". } } `, "#proteome-table", "taxon_proteome.sparql", options={}); // metabolome table sparqlToDataTable2("https://query.wikidata.org/sparql", "https://query.wikidata.org/#", `# tool: scholia PREFIX target: <http://www.wikidata.org/entity/Q7623385> SELECT DISTINCT ?metabolite ?metaboliteLabel ?metaboliteChemicalStructure ?metaboliteDescription WITH { SELECT DISTINCT ?children WHERE { ?children (wdt:P171*) target:. } } AS %taxa WITH { SELECT DISTINCT ?metabolite ?metaboliteChemicalStructure WHERE { INCLUDE %taxa { ?metabolite wdt:P703 ?children } VALUES ?chemical { wd:Q113145171 wd:Q59199015 } ?metabolite wdt:P31 ?chemical . OPTIONAL { ?metabolite wdt:P233 ?canSmiles } OPTIONAL { ?metabolite wdt:P2017 ?isoSmiles } BIND(COALESCE(?isoSmiles, ?canSmiles) AS ?metaboliteChemicalStructure) } } AS %results { INCLUDE %results SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". } } `, "#metabolome-table", "taxon_metabolome.sparql", options={}); }); </script> </body> </html>

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