CINXE.COM
OMA Scientific Advisory Board
<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>OMA Scientific Advisory Board</title> <meta name="description" content="OMA is a method and database for the inference of orthologs among complete genomes. Since 2004 it has been continuesly maintained and improved. We provide browsable orthology predictions, APIs, flat file downloads and a standalone version of the inference algorithm."> <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="J2uZLITJcg1fC8lMDaaTOJOO9e9VilAT6S2LLyMlN82DiVpFfcUtMTCpq0AMWhSG"> <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="J2uZLITJcg1fC8lMDaaTOJOO9e9VilAT6S2LLyMlN82DiVpFfcUtMTCpq0AMWhSG"> <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> <div id="oma-generic-container"> <div class="container"> <div class="jumbotron"> <h1>OMA Scientific Advisory Board</h1> <div class="oma-seperator"> <span class="colour1"></span> <span class="colour2"></span> <span class="colour3"></span> </div> <p>To complement advice provided by the <a href="https://www.sib.swiss/about/organization">SIB scientific advisory board</a>, which reviews the progress of OMA every other year, the dedicated OMA SAB plays a vital role in guiding the direction and development of the Orthologous Matrix (OMA), our comprehensive database and method for orthology inference, available at <a href="https://omabrowser.org">https://omabrowser.org</a>. It comprises esteemed experts in comparative genomics, agricultural research/biotechnology, and big database management, and provide invaluable insights to ensure that OMA remains a cutting-edge resource with high usability and impact for biologists.</p> <p>The dedicated OMA SAB meets every year, with odd years being a half-day event online and even years being a full day event in-person in Lausanne, Switzerland.</p> <h2>Current members</h2> <div class="card card-header-oma border-0"> <h3>Dr Claire Yanhui Hu</h3> <div class="card-body"> <div class="mx-2"> <img alt="Claire Yanhui Hu" src="/static/image/sab/claire_yanhui_hu.jpg" class="rounded d-block w-50" style="max-width: 256px;"> <div class="small">Director of Bioinformatics, Harvard Medical School</div> </div> <p>As an accomplished leader in bioinformatics of mammalian and Drosophila systems, Dr. Hu's expertise and perspective will help shape the future direction of OMA. With a focus on creating bioinformatics tools that are not only relevant but also highly usable and impactful, Dr. Hu's contributions will significantly enhance OMA's functionality and value for our users.</p> </div> </div> <div class="card card-header-oma border-0"> <h3>Dr. Elspeth Bruford</h3> <div class="card-body"> <div class="mx-2"> <img alt="Dr. Elspeth Bruford" src="/static/image/sab/bruford_elspeth_web.jpg" class="rounded d-block w-50" style="max-width: 256px;"> <div class="small">HGNC Group Coordinator, EMBL-EBI & University of Cambridge</div> </div> <p>Dr. Bruford is a PI at the European Molecular Biology Laboratory, European Bioinformatics Institute, as well as the Group Coordinator for the HUGO Gene Nomenclature Committee. She is an expert in genome annotation, gene family curation, comparative genomics, and evolutionary biology, in addition to playing a critical role in the ortholog community鈥檚 benchmarking efforts. Her experience and advice will help to improve not only the OMA methodology, but also its applications.</p> </div> </div> <div class="card card-header-oma border-0"> <h3>Dr. Aoife McLysaght</h3> <div class="card-body"> <div class="mx-2"> <a title="Lensmen Photoshelter https://lensmen.photoshelter.com/about/index, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons" href="https://commons.wikimedia.org/wiki/File:Aoife_McLysaght.jpg"><img class="rounded d-block w-50" style="max-width: 256px;" alt="Dr Aoife McLysaght" src="https://upload.wikimedia.org/wikipedia/commons/thumb/8/8a/Aoife_McLysaght.jpg/256px-Aoife_McLysaght.jpg"></a> <div class="small">Smurfit Institute of Genetics, Trinity College Dublin</div> </div> <p>Dr. Aoife McLysaght, an Irish geneticist and professor at the Smurfit Institute of Genetics at Trinity College Dublin, specializes in the field of molecular evolution. Her research focuses on topics such as horizontal gene transfer, the reconstruction of ancestral genomes, and synteny. With her expertise, she will offer valuable insights and guidance to OMA in these areas.</p> </div> </div> <h3>SAB Meeting 22. March 2024</h3> <p>On March 23, 2024, a first virtual SAB meeting took place. The OMA team and the Scientific Advisory Board member discussed together the ongoing projects and the possible future directions.</p> <p>There will be more information about the OMA Scientific Advisory Board coming soon. As the board takes shape, we will provide updates on their expertise and background, highlighting the diverse perspectives that will enrich the OMA project. Keep an eye on this page for announcements, introductions, and insights from our esteemed Scientific Advisory Board members.</p> <p style="font-weight: bold;">Together with our members, we are committed to advancing OMA, ensuring it remains a cutting-edge resource at the forefront of orthology inference.</p> </div> </div> </div> </body> </html>