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OMA orthology database: FAQ
<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>OMA orthology database: FAQ</title> <meta name="description" content="Our answers to questions we often get asked."> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="keywords" content="orthology,evolutionary gene relations,evolution,paralogy,inference"> <!-- Matomo --> <script> var _paq = window._paq = window._paq || []; /* tracker methods like "setCustomDimension" should be called before "trackPageView" */ _paq.push(["setCookieDomain", "*.omabrowser.org"]); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u="https://matomo.sib.swiss/"; _paq.push(['setTrackerUrl', u+'matomo.php']); _paq.push(['setSiteId', '6']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s); })(); </script> <noscript><p><img src="https://matomo.sib.swiss/matomo.php?idsite=6&rec=1" style="border:0;" alt="" /></p></noscript> <!-- End Matomo Code --> <link rel="shortcut icon" href="/static/image/favicon.ico" type="image/x-icon"> <!-- css includes --> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/css/bootstrap.min.css"> <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Dosis:400,800%7CNoto+Sans:400,700%7CRopa+Sans%7CMaterial+Icons"> <link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Material+Symbols+Outlined:opsz,wght,FILL,GRAD@48,400,0,0"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha256-eSi1q2PG6J7g7ib17yAaWMcrr5GrtohYChqibrV7PBE=" crossorigin="anonymous"> <link rel="stylesheet" href="/static/css/oma_styles.css"> <!-- js includes --> <script src="//cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.3/js/bootstrap.bundle.min.js" integrity="sha256-E/V4cWE4qvAeO5MOhjtGtqDzPndRO1LBk8lJ/PR7CA4=" crossorigin="anonymous"></script> <script>const static_root = "/static/";</script> <!-- AA: not sure which of those libs will still be needed. I suspect autocomplete.min.js for sure, rest probably not --> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.11.2/css/all.css"> <script src="/static/js/jquery.autocomplete.min.js"></script> <script id="release_char-data" type="application/json">"E"</script> </head> <body class=""> <nav class="navbar fixed-top navbar-expand-xl bg-light navbar-light topnav"> <div class="logos-navbar mr-auto"> <a href="https://www.sib.swiss/"><img src="/static/image/logo-SIB.png" alt="Logo SIB"/></a> <a href="/oma/home/"><img src="/static/image/logo-oma-mobile.svg" alt="Logo OMA small"/></a> </div> <span class="oma-main-search-header"> <script src="/static/js/vue.js"></script> <style> .button_search { cursor:pointer; align-self: center; height: 100%; background-color: transparent; border: none; margin-right: 4px; margin-left: auto; order: 2; } .button_search:disabled { cursor:not-allowed; } .help_icon { align-self: center; font-size: 1.5em; margin: 4px; cursor: pointer; } .prefix-dropdown { border: none; background-color: transparent; } .vl { border-left: 2px solid grey; margin-left: 4px; margin-right: 4px; } #search_nav_input_part { display: flex; border: 1px solid #eee; font-size: 0.9em; box-sizing: border-box; padding: 0 0 0 4px; border-radius: 500px; } .ml-input{} .sl-input{height: 50px;} .token-input__tag { height: 30px; display: inline-block; margin-right: 10px; background-color: #eee; margin-top: 10px; line-height: 30px; padding: 0 5px; border-radius: 5px; } .token-input__tag > span { cursor: pointer; opacity: 0.75; } .token-input__text { border: none; outline: none; font-size: 0.9em; line-height: 50px; flex-grow: 1; background: transparent; } .token-delete { margin-left: 4px; color: red; } #token-container_search_nav{ overflow: scroll; display: inline; } .ml-token-con{margin-bottom: 8px;} .sl-token-con{white-space: nowrap;} </style> <script type="module"> const {createApp} = Vue window.search_token_vue_search_nav = createApp({ data() { return { tokens: [], //{query: 'HUMAN', single_term: true, prefix: "Species", type: "Taxon"} prefixes: { 'Protein': ['proteinid','xref','go','ec','description','domain','sequence'], 'Taxon': ['species','taxid', 'taxon'], 'HOG': ['hog','sequence'], 'OMA_Group': ['og', 'fingerprint','sequence'], }, default_prefix : 'description', show_error: false, error_message : " Error.", post_query_search_nav: '', multiline: false, wild_card: 'sequence', placeholder: ' "Blue-light photoreceptor" | proteinid:P53_RAT | species:"Drosophila melanogaster" ', //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', placeholder_default: 'proteinid:P53_RAT | "Blue-light photoreceptor" | species:"Drosophila melanogaster" ' //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', } }, compilerOptions: { delimiters: ["$[", "]$"] }, methods: { get_list_prefixes(lowercase=false){ let lp = [].concat(...Object.values(this.prefixes)); if (lowercase){ lp = lp.map(element => {return element.toLowerCase();}); } return lp }, get_prefix_used(){ return this.tokens.map(x => this.get_type_prefix(x.prefix)); }, get_type_prefix(prefix){ for (var key in this.prefixes) { if (this.prefixes.hasOwnProperty(key)) { if (this.prefixes[key].includes(prefix.toLowerCase())){ return key } } } return null }, addToken(event) { event.preventDefault() let val = event.target.value.trim(); if (val.length === 0 && this.tokens.length > 0){ this.collect_token() // wanted to auto search if press and empty + token but post request miss post_query data } else { var sinle_term = val[0] !== '"'; var multi_term_closed = (val.length > 1 && val[val.length - 1] === '"') var has_prefix = val.includes(':') var prefix_end = val[val.length - 1] === ':' var p = has_prefix ? val.split(':')[0].toLowerCase() : this.default_prefix; // If prefix but not valid if (has_prefix && !this.get_list_prefixes(true).includes(p.toLowerCase())) { this.show_error = true; this.error_message = "Error: Incorrect prefix." return; } else { this.show_error = false; } // If something typed if (val.length > 0) { // Multiple word query if (!sinle_term) { // STOP if multiple not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } // STOP if the prefix is fine and we are at : if (prefix_end) { return } // has a prefix if (has_prefix) { var tmp = val.split(':')[1].trim() sinle_term = tmp[0] !== '"'; multi_term_closed = (val.length > 1 && tmp[tmp.length - 1] === '"') // multiple term if (!sinle_term) { // STOP if not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } val = tmp } if (this.validate_token(val.replaceAll('"', ''), sinle_term, p)) { val = val.replaceAll('"', '') this.tokens.push({ query: val, single_term: sinle_term, prefix: p, type: this.get_type_prefix(p) }); event.target.value = ''; } } } document.getElementById("token-container_search_nav").scrollLeft += 200000; }, addToken_and_search(event){ this.addToken(event); if (this.tokens.length > 0){ this.collect_token() this.$refs.submit_button.click(); } }, removeToken(index) { this.tokens.splice(index, 1) }, removeLastToken(event) { if (event.target.value.length === 0) { this.removeToken(this.tokens.length - 1) } }, enter_from_input(event) { if (event.target.value.trim().length > 0) {this.addToken(event)} else{ event.target.nextElementSibling.focus().click() } }, collect_token(){ this.post_query_search_nav = JSON.stringify(this.tokens) }, detokenize(index){ var token = this.tokens.splice(index, 1)[0]; var input_token_search = document.getElementById('input_token_search_search_nav'); var token_str = token.prefix + ': ' token_str += token.single_term ? '' : '"' token_str += token.query token_str += token.single_term ? '' : '"' input_token_search.value = token_str }, on_change_prefix(target, t){ var prefix = target.value if (this.validate_token(t.query, t.single_term,prefix, true)){ t.prefix = prefix.toLowerCase() } else { target.value = t.prefix; } }, validate_token(val, sinle_term, p , OnChange=false){ if (this.wild_card.includes(p)){ return true } // todo Validate type val is valid for p // validate prefix not in conflict with other prefix var pu = this.get_prefix_used(); var current_prefix_type = this.get_type_prefix(p) if (current_prefix_type !== 'Taxon'){ var no_taxon = pu.filter(x => x !== 'Taxon'); if (no_taxon.length == 0){return true} else if (OnChange && no_taxon.length == 1){return true} else if (no_taxon.length > 0 && no_taxon.includes(current_prefix_type) ){return true} else if (no_taxon.length > 0 && !no_taxon.includes(current_prefix_type)) { this.show_error = true; this.error_message = "Warning: You are searching for " + no_taxon[0] + "; you can't add a token for " + current_prefix_type return false } } return true }, preload_token(tokens){ this.tokens = [] for (var i in tokens) { var token = tokens[i] if (this.validate_token(token.query, token.sinle_term, token.prefix )){ this.tokens.push({query: token.query, single_term: token.sinle_term, prefix: token.prefix, type:token.type}); } } this.placeholder = ''; this.$refs.input_handle.focus(); }, is_empty(){return this.tokens.length === 0}, modal_clicked(){ $('#exampleModal_search_nav').modal('show') }, format_token_string(str){ if (str.length < 20){return str} return str.slice(0, 20) + '...' } }, }).mount('#search_nav') var autocomplete_opts = { paramName: 'search', serviceUrl: '/api/xref/', minChars: 3, triggerSelectOnValidInput: false, deferRequestBy: 200, transformResult: function (response) { var json = JSON.parse(response); var xref_source_order = ['UniProtKB/SwissProt', 'UniProtKB/TrEMBL', 'Ensembl Protein', 'Ensembl Gene', 'Ensembl Transcript', 'RefSeq', 'EntrezGene', 'FlyBase', 'WormBase', 'EnsemblGenomes', 'NCBI', 'EMBL', 'SourceID', 'SourceAC', 'HGNC', 'Gene Name', 'Synonym', 'Protein Name', 'ORF Name', 'Ordered Locus Name', 'PDB', 'Swiss Model', 'STRING', 'neXtProt', 'Bgee', 'EPD', 'ChEMBL', 'GlyConnect', 'SwissPalm', 'DisGeNET', 'WikiGene', 'IPI', 'GI', 'n/a']; json.sort(function (a, b){ const idx_a = xref_source_order.indexOf(a.source), idx_b = xref_source_order.indexOf(b.source); if (idx_a === idx_b){ return a.xref > b.xref ? 1 : -1; } return idx_a - idx_b; }); return { suggestions: $.map(json, function (dataItem) { return {value: dataItem.xref, data: dataItem}; }) }; }, groupBy: 'source', formatResult: function(suggestion, currentValue) { // Do not replace anything if there current value is empty if (!currentValue) { return suggestion.value; } // escape any special char var pattern = '(' + currentValue.replace(/[|\\{}()[\]^$+*?.]/g, "\\$&") + ')'; var highlight_and_escape = function(val){ return val.replace(new RegExp(pattern, 'gi'), '<strong>$1<\/strong>') .replace(/&/g, '&') .replace(/</g, '<') .replace(/>/g, '>') .replace(/"/g, '"') .replace(/<(\/?strong)>/g, '<$1>'); }; return '<span class="auto-xref">' + highlight_and_escape(suggestion.data.xref) + '</span> ' + '<span class="auto-omaid">' + suggestion.data.omaid + '</span>' + '<span class="auto-species">' + highlight_and_escape(suggestion.data.genome.species) + '</span>'; }, onSelect: function(item){ window.location.href = "/oma/vps/" + item.data.entry_nr; return false; }, response: function( event, ui ) {console.log('HOG')} }; $('#input_token_search_search_nav').autocomplete(autocomplete_opts); </script> <!-- Modal --> <div class="modal fade" data-backdrop="false" id="exampleModal_search_nav" tabindex="-1" aria-labelledby="exampleModalLabelsearch_nav" aria-hidden="true"> <div class="modal-dialog modal-lg modal-dialog-centered" > <div class="modal-content"> <div class="modal-header"> <h4 class="modal-title" id="exampleModalLabelsearch_nav">How to use the search in OMA Browser ?</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body" style="text-align: justify"> <strong>How does the search work?</strong> <p>Input a query in the search field. Everytime you press Space or Enter after a word, a <b>token</b> will be created. The token is composed of a <b>prefix</b> describing how the query should be treated and the actual <b>query</b> itself.</p> <strong>What are the different types of tokens?</strong> <p>Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term. </p> <table class="table table-bordered"> <thead> <tr> <th scope="col">Category</th> <th scope="col">Prefixes</th> </tr> </thead> <tbody> <tr> <th scope="row">Genes</th> <td>id, go, ec, description, domain, sequence</td> </tr> <tr> <th scope="row">HOGs</th> <td>hog, sequence</td> </tr> <tr> <th scope="row">OMA Groups</th> <td>omagroup, fingerprint, sequence</td> </tr> <tr> <th scope="row">Taxon</th> <td>species, taxid, taxon</td> </tr> </tbody> </table> <small>For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term. </small> <br> <strong>How to search for a multi-word query?</strong> <p>If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it. </p> <strong>How many tokens can I have?</strong> <p>There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207. </p> <strong>How to edit/delete a token?</strong> <p>To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.</p> <strong>Autosuggest</strong> <p>Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.</p> </div> <div class="modal-footer"> <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button> </div> </div> </div> </div> <form method="POST" id='form_' action="/oma/search-token/" > <input type="hidden" name="csrfmiddlewaretoken" value="Huukwnczkn1uXSEnv3EqOajolz1IHTYbSSxSXf1fc8vJqqXuqEUXXNUOpdvisASQ"> <div id="search_nav"> <div id="search_nav_input_part" :class="multiline ? 'ml-input' : 'sl-input'"> <span class="material-symbols-outlined help_icon" @click="modal_clicked"> help </span> <div id="token-container_search_nav" :class="multiline ? 'ml-token-con' : 'sl-token-con'" > <span v-for="token, index in tokens" :key="token" class="token-input__tag"> <select class="prefix-dropdown" @change="on_change_prefix($event.target, token)"> <template v-for="(prefixes_list, prefix_type) in prefixes"> <optgroup :label="prefix_type" > <option v-for="prefix in prefixes_list" :key="prefix" :selected="prefix == token.prefix"> $[ prefix ]$ </option> </optgroup> </template> </select> <span class="vl"></span> <p style="display: inline" @click='detokenize(index)'> $[ format_token_string(token.query) ]$ </p> <span @click='removeToken(index)' class="token-delete">X</span> </select> </span> </div> <input type="hidden" name="hidden_query" :value="post_query_search_nav"> <input type='text' :placeholder='placeholder' ref="input_handle" class='token-input__text' id="input_token_search_search_nav" @keydown.enter='enter_from_input' @keydown.space='addToken' @keydown.delete='removeLastToken' /> <button class=" button_search float-right" id="button_submit" ref="submit_button" :disabled="is_empty()" @click='collect_token()' type="submit"> <img style='width: 24px;' src="/static/image/logo-oma-o.svg" alt="Logo OMA icon"/> </button> </div> <div style="display: flex" v-show="show_error"> <small style="color: red; margin-right: auto;" > $[this.error_message]$ </small> </div> </div> </form> </span> <button type="button" class="navbar-toggler ml-auto collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1"> <span></span> <span></span> <span></span> </button> <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1"> <div class="navbar-nav ml-auto"> <div class="search"> <h3>Search</h3> <script src="/static/js/vue.js"></script> <style> .button_search { cursor:pointer; align-self: center; height: 100%; background-color: transparent; border: none; margin-right: 4px; margin-left: auto; order: 2; } .button_search:disabled { cursor:not-allowed; } .help_icon { align-self: center; font-size: 1.5em; margin: 4px; cursor: pointer; } .prefix-dropdown { border: none; background-color: transparent; } .vl { border-left: 2px solid grey; margin-left: 4px; margin-right: 4px; } #search_min_input_part { display: flex; border: 1px solid #eee; font-size: 0.9em; box-sizing: border-box; padding: 0 0 0 4px; border-radius: 500px; } .ml-input{} .sl-input{height: 50px;} .token-input__tag { height: 30px; display: inline-block; margin-right: 10px; background-color: #eee; margin-top: 10px; line-height: 30px; padding: 0 5px; border-radius: 5px; } .token-input__tag > span { cursor: pointer; opacity: 0.75; } .token-input__text { border: none; outline: none; font-size: 0.9em; line-height: 50px; flex-grow: 1; background: transparent; } .token-delete { margin-left: 4px; color: red; } #token-container_search_min{ overflow: scroll; display: inline; } .ml-token-con{margin-bottom: 8px;} .sl-token-con{white-space: nowrap;} </style> <script type="module"> const {createApp} = Vue window.search_token_vue_search_min = createApp({ data() { return { tokens: [], //{query: 'HUMAN', single_term: true, prefix: "Species", type: "Taxon"} prefixes: { 'Protein': ['proteinid','xref','go','ec','description','domain','sequence'], 'Taxon': ['species','taxid', 'taxon'], 'HOG': ['hog','sequence'], 'OMA_Group': ['og', 'fingerprint','sequence'], }, default_prefix : 'description', show_error: false, error_message : " Error.", post_query_search_min: '', multiline: false, wild_card: 'sequence', placeholder: ' "Blue-light photoreceptor" | proteinid:P53_RAT | species:"Drosophila melanogaster" ', //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', placeholder_default: 'proteinid:P53_RAT | "Blue-light photoreceptor" | species:"Drosophila melanogaster" ' //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', } }, compilerOptions: { delimiters: ["$[", "]$"] }, methods: { get_list_prefixes(lowercase=false){ let lp = [].concat(...Object.values(this.prefixes)); if (lowercase){ lp = lp.map(element => {return element.toLowerCase();}); } return lp }, get_prefix_used(){ return this.tokens.map(x => this.get_type_prefix(x.prefix)); }, get_type_prefix(prefix){ for (var key in this.prefixes) { if (this.prefixes.hasOwnProperty(key)) { if (this.prefixes[key].includes(prefix.toLowerCase())){ return key } } } return null }, addToken(event) { event.preventDefault() let val = event.target.value.trim(); if (val.length === 0 && this.tokens.length > 0){ this.collect_token() // wanted to auto search if press and empty + token but post request miss post_query data } else { var sinle_term = val[0] !== '"'; var multi_term_closed = (val.length > 1 && val[val.length - 1] === '"') var has_prefix = val.includes(':') var prefix_end = val[val.length - 1] === ':' var p = has_prefix ? val.split(':')[0].toLowerCase() : this.default_prefix; // If prefix but not valid if (has_prefix && !this.get_list_prefixes(true).includes(p.toLowerCase())) { this.show_error = true; this.error_message = "Error: Incorrect prefix." return; } else { this.show_error = false; } // If something typed if (val.length > 0) { // Multiple word query if (!sinle_term) { // STOP if multiple not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } // STOP if the prefix is fine and we are at : if (prefix_end) { return } // has a prefix if (has_prefix) { var tmp = val.split(':')[1].trim() sinle_term = tmp[0] !== '"'; multi_term_closed = (val.length > 1 && tmp[tmp.length - 1] === '"') // multiple term if (!sinle_term) { // STOP if not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } val = tmp } if (this.validate_token(val.replaceAll('"', ''), sinle_term, p)) { val = val.replaceAll('"', '') this.tokens.push({ query: val, single_term: sinle_term, prefix: p, type: this.get_type_prefix(p) }); event.target.value = ''; } } } document.getElementById("token-container_search_nav").scrollLeft += 200000; }, addToken_and_search(event){ this.addToken(event); if (this.tokens.length > 0){ this.collect_token() this.$refs.submit_button.click(); } }, removeToken(index) { this.tokens.splice(index, 1) }, removeLastToken(event) { if (event.target.value.length === 0) { this.removeToken(this.tokens.length - 1) } }, enter_from_input(event) { if (event.target.value.trim().length > 0) {this.addToken(event)} else{ event.target.nextElementSibling.focus().click() } }, collect_token(){ this.post_query_search_min = JSON.stringify(this.tokens) }, detokenize(index){ var token = this.tokens.splice(index, 1)[0]; var input_token_search = document.getElementById('input_token_search_search_min'); var token_str = token.prefix + ': ' token_str += token.single_term ? '' : '"' token_str += token.query token_str += token.single_term ? '' : '"' input_token_search.value = token_str }, on_change_prefix(target, t){ var prefix = target.value if (this.validate_token(t.query, t.single_term,prefix, true)){ t.prefix = prefix.toLowerCase() } else { target.value = t.prefix; } }, validate_token(val, sinle_term, p , OnChange=false){ if (this.wild_card.includes(p)){ return true } // todo Validate type val is valid for p // validate prefix not in conflict with other prefix var pu = this.get_prefix_used(); var current_prefix_type = this.get_type_prefix(p) if (current_prefix_type !== 'Taxon'){ var no_taxon = pu.filter(x => x !== 'Taxon'); if (no_taxon.length == 0){return true} else if (OnChange && no_taxon.length == 1){return true} else if (no_taxon.length > 0 && no_taxon.includes(current_prefix_type) ){return true} else if (no_taxon.length > 0 && !no_taxon.includes(current_prefix_type)) { this.show_error = true; this.error_message = "Warning: You are searching for " + no_taxon[0] + "; you can't add a token for " + current_prefix_type return false } } return true }, preload_token(tokens){ this.tokens = [] for (var i in tokens) { var token = tokens[i] if (this.validate_token(token.query, token.sinle_term, token.prefix )){ this.tokens.push({query: token.query, single_term: token.sinle_term, prefix: token.prefix, type:token.type}); } } this.placeholder = ''; this.$refs.input_handle.focus(); }, is_empty(){return this.tokens.length === 0}, modal_clicked(){ $('#exampleModal_search_min').modal('show') }, format_token_string(str){ if (str.length < 20){return str} return str.slice(0, 20) + '...' } }, }).mount('#search_min') var autocomplete_opts = { paramName: 'search', serviceUrl: '/api/xref/', minChars: 3, triggerSelectOnValidInput: false, deferRequestBy: 200, transformResult: function (response) { var json = JSON.parse(response); var xref_source_order = ['UniProtKB/SwissProt', 'UniProtKB/TrEMBL', 'Ensembl Protein', 'Ensembl Gene', 'Ensembl Transcript', 'RefSeq', 'EntrezGene', 'FlyBase', 'WormBase', 'EnsemblGenomes', 'NCBI', 'EMBL', 'SourceID', 'SourceAC', 'HGNC', 'Gene Name', 'Synonym', 'Protein Name', 'ORF Name', 'Ordered Locus Name', 'PDB', 'Swiss Model', 'STRING', 'neXtProt', 'Bgee', 'EPD', 'ChEMBL', 'GlyConnect', 'SwissPalm', 'DisGeNET', 'WikiGene', 'IPI', 'GI', 'n/a']; json.sort(function (a, b){ const idx_a = xref_source_order.indexOf(a.source), idx_b = xref_source_order.indexOf(b.source); if (idx_a === idx_b){ return a.xref > b.xref ? 1 : -1; } return idx_a - idx_b; }); return { suggestions: $.map(json, function (dataItem) { return {value: dataItem.xref, data: dataItem}; }) }; }, groupBy: 'source', formatResult: function(suggestion, currentValue) { // Do not replace anything if there current value is empty if (!currentValue) { return suggestion.value; } // escape any special char var pattern = '(' + currentValue.replace(/[|\\{}()[\]^$+*?.]/g, "\\$&") + ')'; var highlight_and_escape = function(val){ return val.replace(new RegExp(pattern, 'gi'), '<strong>$1<\/strong>') .replace(/&/g, '&') .replace(/</g, '<') .replace(/>/g, '>') .replace(/"/g, '"') .replace(/<(\/?strong)>/g, '<$1>'); }; return '<span class="auto-xref">' + highlight_and_escape(suggestion.data.xref) + '</span> ' + '<span class="auto-omaid">' + suggestion.data.omaid + '</span>' + '<span class="auto-species">' + highlight_and_escape(suggestion.data.genome.species) + '</span>'; }, onSelect: function(item){ window.location.href = "/oma/vps/" + item.data.entry_nr; return false; }, response: function( event, ui ) {console.log('HOG')} }; $('#input_token_search_search_min').autocomplete(autocomplete_opts); </script> <!-- Modal --> <div class="modal fade" data-backdrop="false" id="exampleModal_search_min" tabindex="-1" aria-labelledby="exampleModalLabelsearch_min" aria-hidden="true"> <div class="modal-dialog modal-lg modal-dialog-centered" > <div class="modal-content"> <div class="modal-header"> <h4 class="modal-title" id="exampleModalLabelsearch_min">How to use the search in OMA Browser ?</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body" style="text-align: justify"> <strong>How does the search work?</strong> <p>Input a query in the search field. Everytime you press Space or Enter after a word, a <b>token</b> will be created. The token is composed of a <b>prefix</b> describing how the query should be treated and the actual <b>query</b> itself.</p> <strong>What are the different types of tokens?</strong> <p>Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term. </p> <table class="table table-bordered"> <thead> <tr> <th scope="col">Category</th> <th scope="col">Prefixes</th> </tr> </thead> <tbody> <tr> <th scope="row">Genes</th> <td>id, go, ec, description, domain, sequence</td> </tr> <tr> <th scope="row">HOGs</th> <td>hog, sequence</td> </tr> <tr> <th scope="row">OMA Groups</th> <td>omagroup, fingerprint, sequence</td> </tr> <tr> <th scope="row">Taxon</th> <td>species, taxid, taxon</td> </tr> </tbody> </table> <small>For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term. </small> <br> <strong>How to search for a multi-word query?</strong> <p>If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it. </p> <strong>How many tokens can I have?</strong> <p>There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207. </p> <strong>How to edit/delete a token?</strong> <p>To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.</p> <strong>Autosuggest</strong> <p>Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.</p> </div> <div class="modal-footer"> <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button> </div> </div> </div> </div> <form method="POST" id='form_' action="/oma/search-token/" > <input type="hidden" name="csrfmiddlewaretoken" value="Huukwnczkn1uXSEnv3EqOajolz1IHTYbSSxSXf1fc8vJqqXuqEUXXNUOpdvisASQ"> <div id="search_min"> <div id="search_min_input_part" :class="multiline ? 'ml-input' : 'sl-input'"> <span class="material-symbols-outlined help_icon" @click="modal_clicked"> help </span> <div id="token-container_search_min" :class="multiline ? 'ml-token-con' : 'sl-token-con'" > <span v-for="token, index in tokens" :key="token" class="token-input__tag"> <select class="prefix-dropdown" @change="on_change_prefix($event.target, token)"> <template v-for="(prefixes_list, prefix_type) in prefixes"> <optgroup :label="prefix_type" > <option v-for="prefix in prefixes_list" :key="prefix" :selected="prefix == token.prefix"> $[ prefix ]$ </option> </optgroup> </template> </select> <span class="vl"></span> <p style="display: inline" @click='detokenize(index)'> $[ format_token_string(token.query) ]$ </p> <span @click='removeToken(index)' class="token-delete">X</span> </select> </span> </div> <input type="hidden" name="hidden_query" :value="post_query_search_min"> <input type='text' :placeholder='placeholder' ref="input_handle" class='token-input__text' id="input_token_search_search_min" @keydown.enter='enter_from_input' @keydown.space='addToken' @keydown.delete='removeLastToken' /> <button class=" button_search float-right" id="button_submit" ref="submit_button" :disabled="is_empty()" @click='collect_token()' type="submit"> <img style='width: 24px;' src="/static/image/logo-oma-o.svg" alt="Logo OMA icon"/> </button> </div> <div style="display: flex" v-show="show_error"> <small style="color: red; margin-right: auto;" > $[this.error_message]$ </small> </div> </div> </form> </div> <ul class="navbar-nav"> <!-- explore dropdown --> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle text-nowrap" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Explore <span class="caret"></span></a> <div class="dropdown-menu" role="menu"> <a class="dropdown-item" href="/oma/release/">Species/release information</a> <a class="dropdown-item" href="/oma/phylostratigraphy/">Phylostratigraphy</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Quick access to</div> <a class="dropdown-item" href="/oma/genome/">Extant and Ancestral genomes</a> <a class="dropdown-item" href="/oma/landOMA/">OMA groups</a> <a class="dropdown-item" href="/oma/hogs/">Hierarchical orthologous groups (HOGs)</a> <a class="dropdown-item" href="/oma/landAnnotation/">Functional annotations</a> <a class="dropdown-item" href="/oma/synteny/">Local synteny</a> </div> </li> <!-- compute dropdown --> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle text-nowrap" data-toggle="dropdown">Tools <span class="caret"></span></a> <div class="dropdown-menu" role="menu"> <div role="presentation" class="dropdown-header">Online tools</div> <a class="dropdown-item" href="/oma/fastmapping/">Fast mapping</a> <a class="dropdown-item" href="/oma/functions/">Functional prediction</a> <a class="dropdown-item" href="/oma/dotplot/">Synteny dotplot</a> <a class="dropdown-item" href="/oma/genomePW/">Genome pair orthology</a> <a class="dropdown-item" href="/oma/go_enrichment/">GO enrichment analysis</a> <a class="dropdown-item" href="/oma/omamo/search/">OMA-MO: Find model organism</a> <a class="dropdown-item" href="https://omark.omabrowser.org">OMArk: Assess proteome quality</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Software</div> <a class="dropdown-item" href="https://omabrowser.org/standalone/">OMA StandAlone</a> <a class="dropdown-item" href="https://github.com/dessimozlab/read2tree">read2tree</a> <a class="dropdown-item" href="https://github.com/dessimozlab/FastOMA">FastOMA</a> <a class="dropdown-item" href="https://github.com/dessimozlab/pyham">pyHam</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Visualisation tools</div> <a class="dropdown-item" href="https://phylo.io/">Phylo.io</a> <a class="dropdown-item" href="https://github.com/dessimozlab/iham">IHam</a> <div class="dropdown-divider"></div> <a class="dropdown-item text-center" href="/oma/tools/"><b> <i class="fas fa-toolbox"></i> See all OMA tools</b></a> </div> </li> <!-- Download dropdown --> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle text-nowrap" data-toggle="dropdown">Download <span class="caret"></span></a> <ul class="dropdown-menu" role="menu"> <div role="presentation" class="dropdown-header">OMA database files</div> <a class="dropdown-item" href="/oma/current/">Current release</a> <a class="dropdown-item" href="/oma/export/">Export All/All</a> <a class="dropdown-item" href="/oma/export_markers">Export marker genes</a> <a class="dropdown-item" href="/oma/archives/">Archives</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">API</div> <a class="dropdown-item" href="/api/docs">OMA API</a> <a class="dropdown-item" href="/oma/APISOAP/">SOAP</a> <a class="dropdown-item" href="https://bioconductor.org/packages/release/bioc/html/OmaDB.html">R API binding</a> <a class="dropdown-item" href="https://github.com/DessimozLab/pyomadb">Python API binding</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Semantic web</div> <a class="dropdown-item" href="https://sparql.omabrowser.org/">SPARQL endpoint</a> <div class="dropdown-divider"></div> <a class="dropdown-item text-center" href="/oma/uses/"><b> <i class="fas fa-keyboard"></i> Access the OMA data</b></a> </ul> </li> <!-- Help dropdown --> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle text-nowrap" data-toggle="dropdown">Help <span class="caret"></span></a> <ul class="dropdown-menu dropdown-menu-right" role="menu"> <a class="dropdown-item" href="/oma/about/">Introduction</a> <a class="dropdown-item" href="/oma/type/">Orthology Basics</a> <a class="dropdown-item" href="/oma/homologs/">Type of homologs</a> <a class="dropdown-item" href="/oma/uses/">Access the OMA data</a> <a class="dropdown-item" href="/oma/tools/">Catalog of tools</a> <a class="dropdown-item" href="/oma/suggestion/genome/">Suggesting a genome</a> <a class="dropdown-item" href="/oma/FAQ/">FAQ</a> <a class="dropdown-item" href="https://www.biostars.org/tag/oma/">Q&A on BioStars</a> <a class="dropdown-item " href="/oma/glossary/"> Glossary</a> <div class="dropdown-divider"></div> <a class="dropdown-item text-center" href="/oma/academy/"><b> <i class="fas fa-book"></i> OMA Academy</b></a> </ul> </li> <!-- about dropdown --> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle text-nowrap" href="#" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">About <span class="caret"></span></a> <div class="dropdown-menu dropdown-menu-right" role="menu"> <a class="dropdown-item" href="/oma/about/">OMA</a> <a class="dropdown-item" href="/oma/team/">Team</a> <a class="dropdown-item" href="/oma/sab/">SAB</a> <a class="dropdown-item" href="/oma/funding/">Funding</a> <a class="dropdown-item" href="/oma/terms_of_use/">Terms of use</a> <div class="dropdown-divider"></div> <a class="dropdown-item" href="mailto:contact@omabrowser.org"><span class="glyphicon glyphicon-envelope"></span> Contact</a> </div> </li> </ul> </div> </div> </nav> <style> #accordion .card .card-header:hover { cursor: pointer; color: #307C3B; font-weight: bolder; } </style> <div id="oma-generic-container"> <div class="container"> <div class="jumbotron"> <h1>FAQ</h1><h5 class="text-muted text-center">You have questions, we have answers.</h5> <div class="oma-seperator"> <span class="colour1"></span> <span class="colour2"></span> <span class="colour3"></span> </div> <div id="accordion"> <div class="card mb-1"> <div class="card-header" id="headingOne" data-toggle="collapse" data-target="#collapseOne" aria-expanded="true" aria-controls="collapseOne"> I have a question or need help to perform an analysis. Can I contact you to get any help? </div> <div id="collapseOne" class="collapse show" aria-labelledby="headingOne" data-parent="#accordion"> <div class="card-body"> <p>Yes, we are reachable by email at contact@omabrowser.org. However, for general questions about OMA, our preferred way of answering questions is through <a href="https://www.biostars.org/">BioStars</a>. Please consider asking your question there, <b>including the tags "OMA" and "orthologs"</b>. We monitor BioStars for such questions and will answer them directly on that platform.</p> </div> </div> </div> <div class="card mb-1"> <div class="card-header collapsed" id="headingTwo" data-toggle="collapse" data-target="#collapseTwo" aria-expanded="true" aria-controls="collapseTwo"> Why is my favorite genome not present in OMA? </div> <div id="collapseTwo" class="collapse" aria-labelledby="headingOne" data-parent="#accordion"> <div class="card-body"> <p>We strive to include as many complete genomes as possible, provided they are released publicly and meet reasonable quality standards. We are open for suggestions and are willing to adapt our priority queue based on user requests. The best way is to fill a request for a <a href="/oma/suggestion/genome/">new or updated genome</a>. For more informal information or batch suggestions drop us an <a href="mailto:contact@omabrowser.org">email</a>.</p> <p>If you want to analyze your "own" genomes, you can use the <a href="http://omabrowser.org/standalone/">OMA standalone pipeline</a> to do so and even make use of already analyzed genomes using the export function. OMA standalone is licenced under the Mozilla Public License Version 2.0. In a nutshell, OMA standalone is open source and free for commercial and non-commercial use.</p> </div> </div> </div> <div class="card mb-1"> <div class="card-header collapsed" id="headingThree" data-toggle="collapse" data-target="#collapseThree" aria-expanded="true" aria-controls="collapseThree"> What is the difference between OMA Groups and Hierarchical Groups? </div> <div id="collapseThree" class="collapse" aria-labelledby="headingOne" data-parent="#accordion"> <div class="card-body"> <p>OMA Groups are sets of genes which are all orthologous to each other according to the definition of Fitch (1970). In presence of a duplication in certain gene familly, this grouping strategy will pick only one of the two lineages resulting from the duplication event. The hierarchical orthologous groups (HOGs) are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest, i.e. they correspond to the member of a clade in a gene tree rooted at the speciation node of interest. Which type of groups you should choose depends highly on the type of your analysis. For more specific information, consult the <a href="/oma/uses">page on typical uses</a>.</p> </div> </div> </div> <div class="card mb-1"> <div class="card-header collapsed" id="headingFour" data-toggle="collapse" data-target="#collapseFour" aria-expanded="true" aria-controls="collapseFour"> Why are OMA Groups often relatively small? Covering so many genomes, I expected them to be much bigger. </div> <div id="collapseFour" class="collapse" aria-labelledby="headingOne" data-parent="#accordion"> <div class="card-body"> <p>For the OMA Groups, we apply a very stringent grouping strategy. All the members of a group need to be bona fide orthologs to each other, i.e. the form a clique in graph-theoretic terms. This grouping strategy is mainly intended for applications which require orthologs of high confidence, e.g. for reconstructing species trees. A gene tree built from the members of an OMA Group should - in absence of LGT are incomplete lineage sorting - be congruent with the underlying species tree. If you are interested in larger groups, consider using the OMA HOGs. These hierarchical orthologous groups are defined as set of genes that all started diverging from a single ancestral gene at a given time point of reference.</p> </div> </div> </div> <div class="card mb-1"> <div class="card-header collapsed" id="headingFive" data-toggle="collapse" data-target="#collapseFive" aria-expanded="false" aria-controls="collapseFive"> Under what licence is OMA distributed </div> <div id="collapseFive" class="collapse" aria-labelledby="headingFive" data-parent="#accordion"> <div class="card-body"> <p>The OMA Browser is available under the Creative Commons Attribution-Share Alike 2.5 License, and the OMA standalone package under the MPL 2.0 (open source) licence.</p> </div> </div> </div> </div> </div> </div> </div> </body> </html>