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Linking FAIR biodiversity data through publications: The BiCIKL approach

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <meta http-equiv="content-type" content="text/html; charset=UTF-8" /> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Linking FAIR biodiversity data through publications: The BiCIKL approach</title> <meta name="description" content="The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) supports free of charge* publications in a dedicated topical collection in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data. The criteria and requirements for publication are listed&nbsp;here. The authors need to acknowledge the&nbsp;BiCIKL project, Grant No 101007492 in the Acknowledgements section. BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc., to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles. Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem. In the Author&#39;s notes to the Editor,&nbsp;the authors will need to make a reference to the condition(s) their work complies with&nbsp;the requirements and expectations of the BiCIKL project, which are briefly outlined here. Likewise, they will need to abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics.&nbsp; The collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.&nbsp; The authors need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section. * The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at &euro; 650. Authors of larger manuscripts will need to cover the surplus charge (&euro;10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net." /> <meta name="keywords" content="" /> <base href="https://bdj.pensoft.net/" /> <meta name="author" content="authors"/> <meta name="distribution" content="global"/> <meta name="robots" content="index, follow, all"/> <meta name="description" content="The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) supports free of charge* publications in a dedicated topical collection in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data. The criteria and requirements for publication are listed&amp;nbsp;here. The authors need to acknowledge the&amp;nbsp;BiCIKL project, Grant No 101007492 in the Acknowledgements section. BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc., to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles. Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem. In the Author&amp;#39;s notes to the Editor,&amp;nbsp;the authors will need to make a reference to the condition(s) their work complies with&amp;nbsp;the requirements and expectations of the BiCIKL project, which are briefly outlined here. Likewise, they will need to abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics.&amp;nbsp; The collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.&amp;nbsp; The authors need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section. * The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at &amp;euro; 650. Authors of larger manuscripts will need to cover the surplus charge (&amp;euro;10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net."/> <meta name="keywords" content=""/> <meta name="distribution" content="global"/> <meta name="robots" content="index, follow, all"/> <meta property="og:image" content="https://bdj.pensoft.net/showimg/oo_819870.jpg"/> <meta property="og:title" content="Linking FAIR biodiversity data through publications: The BiCIKL approach"/> <meta property="og:description" content="The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) supports free of charge* publications in a dedicated topical collection in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data. The criteria and requirements for publication are listed&amp;nbsp;here. The authors need to acknowledge the&amp;nbsp;BiCIKL project, Grant No 101007492 in the Acknowledgements section. BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc., to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles. Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem. In the Author&amp;#39;s notes to the Editor,&amp;nbsp;the authors will need to make a reference to the condition(s) their work complies with&amp;nbsp;the requirements and expectations of the BiCIKL project, which are briefly outlined here. Likewise, they will need to abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics.&amp;nbsp; The collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.&amp;nbsp; The authors need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section. * The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at &amp;euro; 650. Authors of larger manuscripts will need to cover the surplus charge (&amp;euro;10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net."/> <meta property="fb:app_id" content="1129013080805726"/> <meta property="og:url" content="https://bdj.pensoft.net/topical_collection/209/"/> <meta property="og:site_name" content="Biodiversity Data Journal"/> <meta property="og:type" content="collection"/> <meta name="twitter:card" content="summary"/> <meta name="twitter:site" content="@BioDataJournal"/> <meta name="twitter:title" content="Linking FAIR biodiversity data through publications: The BiCIKL approach"/> <meta name="twitter:description" content="The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) supports free of charge* publications in a dedicated topical collection in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data. The criteria and requirements for publication are listed&amp;nbsp;here. The authors need to acknowledge the&amp;nbsp;BiCIKL project, Grant No 101007492 in the Acknowledgements section. BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc., to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles. Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem. In the Author&amp;#39;s notes to the Editor,&amp;nbsp;the authors will need to make a reference to the condition(s) their work complies with&amp;nbsp;the requirements and expectations of the BiCIKL project, which are briefly outlined here. Likewise, they will need to abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics.&amp;nbsp; The collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.&amp;nbsp; The authors need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section. * The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at &amp;euro; 650. Authors of larger manuscripts will need to cover the surplus charge (&amp;euro;10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net."/> <meta name="twitter:image" content="https://bdj.pensoft.net/showimg/oo_819870.jpg"/> <meta name="twitter:url" content="https://bdj.pensoft.net/topical_collection/209/"/> <meta itemprop="image" content="https://bdj.pensoft.net/showimg/oo_819870.jpg"/> <link rel="SHORTCUT ICON" href="/i/ico/bdj.ico" /> <script type="text/javascript" src="/lib/js/build/output/cbase_en.bundle.js?v=1732105979"></script> <link type="text/css" rel="stylesheet" href="/lib/css/langs/en.css?v=1723472591" media="all" title="default" /> <link type="text/css" rel="stylesheet" href="/lib/css/journals/journal_1.css?v=1723472590" media="all" title="default" /> <script type="text/javascript" src="/lib/editors/ckeditor_4.4/ckeditor.js?v=1723472590"></script> <script type="text/javascript"> $(window).on("load", function(){ init_lang_switcher() gWindowIsLoaded = true; }); </script> <script src="https://www.google.com/recaptcha/api.js"></script> <link rel="preconnect" href="https://fonts.googleapis.com"> <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin> <link href="https://fonts.googleapis.com/css2?family=Inter:slnt,wght@-10..0,100..900&display=swap" rel="stylesheet"> <link href="https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic,300,300italic,600italic,700italic,800,800italic&subset=latin,greek,greek-ext,vietnamese,cyrillic-ext,latin-ext,cyrillic" rel="stylesheet"> <link href="https://fonts.googleapis.com/css?family=Lato:300,300i,400,400i,700,700i&amp;subset=latin-ext" rel="stylesheet" > </head> <body class="journal_1 no_logged_user pensoft lang_en "> <div id="container" class=""> <div class="wrapper100"> <div id="header"> <div id="nav"> <div class="constrained"> <a target="_blank" href="http://www.pensoft.net"><span class="logo"></span></a> <div id="menu" class=""> <a class="menu_btn" target="_blank" href="http://www.pensoft.net/about.php">About Pensoft</a><a class="menu_btn" target="_blank" href="http://www.pensoft.net/books/">Books</a><a class="menu_btn" target="_blank" href="http://journals.pensoft.net">Journals</a><a class="menu_btn" target="_blank" href="http://blog.pensoft.net">News &amp; 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width:100% !important;" onblur="delayFormSubmission(&#039;filter_articles&#039;);//$(&#039;#filter_articles&#039;).submit()" /> </div> <div class="row"> <div class="art_browse col-xs"> <label class="control control--radio"> <span title="To search for an exact phrase please put the search string in &quot;&quot;">Full Text</span> <input type="radio" id="search_in_" name="search_in_" value="0" onclick="var search_in_ = $(&quot;input[name=&#039;search_in_&#039;]:checked&quot;).val(); $(&quot;input[name=&#039;search_in_hidden&#039;]&quot;).val(search_in_); delayFormSubmission(&#039;filter_articles&#039;);//$(&#039;#filter_articles&#039;).submit();" checked="checked" /> <div class="control__indicator"></div> </label> </div> <div class="art_browse col-xs"> <label class="control control--radio"> Author <input type="radio" id="search_in_" name="search_in_" value="1" onclick="var search_in_ = $(&quot;input[name=&#039;search_in_&#039;]:checked&quot;).val(); $(&quot;input[name=&#039;search_in_hidden&#039;]&quot;).val(search_in_); delayFormSubmission(&#039;filter_articles&#039;);//$(&#039;#filter_articles&#039;).submit();" /> <div class="control__indicator"></div> </label> </div> <div class="art_browse col-xs"> <label class="control control--radio"> Title <input type="radio" id="search_in_" name="search_in_" value="2" onclick="var search_in_ = $(&quot;input[name=&#039;search_in_&#039;]:checked&quot;).val(); $(&quot;input[name=&#039;search_in_hidden&#039;]&quot;).val(search_in_); delayFormSubmission(&#039;filter_articles&#039;);//$(&#039;#filter_articles&#039;).submit();" /> <div class="control__indicator"></div> </label> </div> </div> </div> <input type="hidden" name="search_in_hidden" value="" id="search_in_hidden" /> </div> </div> <div class="class_wrapper"> <div class="filterBlock category articles_filter"> <div class="filterBlockTitle"> by Taxon <a id="taxon_arrow" class="blockUpArrow tree" href="javascript:void(0);" onclick="toggleBlock('taxon_arrow', 'taxon_tree')"></a> </div> <div class="filterBlockContent" id="taxon_tree"> <div class="P-Input-Full-Width P-W390 spacer10t"> <input type="text" name="alerts_taxon_cats" value="" id="alerts_taxon_cats_autocomplete" class="" /> </div> <!-- Tree alerts_taxon_cats --> <div id="treealerts_taxon_cats" class="filterBy"> <ul> <li id="t8" class="lazy folder" data="pos: 'AG'"> Animalia </li> <li id="t1" class="lazy folder" data="pos: 'AA'"> Archaea </li> <li id="t4" class="lazy folder" data="pos: 'AB'"> Bacteria </li> <li id="t364" class="lazy folder" data="pos: 'AC'"> Chromista </li> <li id="t6" class="lazy folder" data="pos: 'AE'"> Fungi </li> <li id="t7" class="lazy folder" data="pos: 'AF'"> Plantae </li> <li id="t5" class="lazy folder" data="pos: 'AD'"> Protozoa </li> </ul> </div> <script type="text/javascript"> //<![CDATA[ var gAdded = -1; $("#treealerts_taxon_cats").dynatree({ checkbox: true, selectMode: 2, debugLevel: 0, onLazyRead: function(node){ node.appendAjax({url: "/lib/ajax_srv/autocomplete_srv.php", data: {"key": node.data.pos, // Optional url arguments "action": "get_tree_autocomplete", "table_name": "taxon_categories", "filter_by_document_journal" : 1 }, success: function(node) { // Called after nodes have been created and the waiting icon was removed. var lInputVals = $("#alerts_taxon_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if($("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id)) $("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id).select(); } }, error: function(node, XMLHttpRequest, textStatus, errorThrown) { // Called on error, after error icon was created. }, cache: false }); }, onSelect: function(flag, node) { if (!flag) { // Deselected item //$("#treealerts_taxon_cats").dynatree("getTree").visit(function(node){ if( !node.bSelected ) { var lInputVals = $("#alerts_taxon_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ $("#alerts_taxon_cats_autocomplete").tokenInput("remove", { id: lInputVals[i].id }); break; } } } //}); }else{ if( gAdded == node.data.key ){ }else{ var lDontAdd = 0; var lInputVals = $("#alerts_taxon_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ lDontAdd = 1; break; } } if(!lDontAdd){ $("#alerts_taxon_cats_autocomplete").tokenInput("add", { id: node.data.key, name: node.data.title }); } } gAdded = -1; } }, onDblClick: function(node, event) { node.toggleSelect(); }, onKeydown: function(node, event) { if( event.which == 32 ) { node.toggleSelect(); return false; } }, onActivate: function(node) { }, onDeactivate: function(node) { }, // The following options are only required, if we have more than one tree on one page: //initId: "treeData", cookieId: "dynatree-Cb-alerts_taxon_cats", idPrefix: "dynatree-Cb-alerts_taxon_cats" }); $("#alerts_taxon_cats_autocomplete").tokenInput( "/lib/ajax_srv/autocomplete_srv.php" + "?action=get_reg_autocomplete&filter_by_document_journal=1&table_name=taxon_categories", { theme: "facebook", queryParam: "term", preventDuplicates: true, minChars: 3, onResult: function(data){ return data; }, onAdd: function(item){ var input = '<input id="alerts_taxon_cats' + item.id + '_hiddenInp" name="alerts_taxon_cats[]" value="' + item.id + '" type="hidden"></input>'; $(input).insertBefore( "#alerts_taxon_cats_autocomplete" ); gAdded = item.id; if( $("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(item.id).activate(); $("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(item.id).select(); } else { console.log(item.id + " was not found in the currently loaded part of the tree"); } if (typeof initComplete == "boolean" && initComplete) { //console.log("Init is complete; this is a user add"); delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } }, onDelete: function(item){ $( "#alerts_taxon_cats" + item.id + "_hiddenInp" ).remove(); if( $("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(item.id).select(false); $("#treealerts_taxon_cats").dynatree("getTree").getNodeByKey(item.id).deactivate(); } delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } } ); //]]> </script> <script type="text/javascript"> //<![CDATA[ // Тук популираме първоначално инпута със селектнатите стойности или ако има грешка при сейв със селектнатите + новоселектнатите преди сейв var lSelectedCats = []; /*if(!lSelectedCats.length) toggleBlock('taxon_arrow', 'taxon_tree');*/ for ( var i = 0; i < lSelectedCats.length; i++) { $("#alerts_taxon_cats_autocomplete").tokenInput("add", lSelectedCats[i]); } //]]> </script> <!-- Tree #3 END --> <div class="P-Clear"></div> </div> </div> <div class="filterBlock category articles_filter"> <div class="filterBlockTitle"> by Subject <a id="subject_arrow" class="blockUpArrow tree" href="javascript:void(0);" onclick="toggleBlock('subject_arrow', 'subject_tree')"></a> </div> <div class="filterBlockContent" id="subject_tree"> <div class="P-Input-Full-Width P-W390"> <input type="text" name="alerts_subject_cats" value="" id="alerts_subject_cats_autocomplete" class="" /> </div> <!-- Tree alerts_subject_cats --> <div id="treealerts_subject_cats" class="filterBy"> <ul> <li id="s1" class="lazy folder" data="pos: 'AA'"> Agriculture and Forestry </li> <li id="s20" class="lazy folder" data="pos: 'AM'"> Aquatic biology </li> <li id="s332" class="lazy folder" data="pos: 'AB'"> Bioacoustics </li> <li id="s51" class="lazy folder" data="pos: 'AN'"> Biodiversity &amp; Conservation </li> <li id="s297" class="lazy folder" data="pos: 'AC'"> Biogeography </li> <li id="s285" class="lazy folder" data="pos: 'AD'"> Bioinformatics </li> <li id="s495" class="lazy folder" data="pos: 'AO'"> Biotechnology </li> <li id="s7" class="lazy folder" data="pos: 'AS'"> Data analysis &amp; Modelling </li> <li id="s398" class="lazy folder" data="pos: 'AR'"> Databases </li> <li id="s9" class="lazy folder" data="pos: 'AT'"> Ecology &amp; Environmental sciences </li> <li id="s10" class="lazy folder" data="pos: 'AE'"> Evolutionary biology </li> <li id="s42" class="lazy folder" data="pos: 'AJ'"> Genetics </li> <li id="s2390" class="lazy folder" data="pos: 'AU'"> Microbiology </li> <li id="s43" class="lazy folder" data="pos: 'AI'"> Microbiology &amp; Virology </li> <li id="s326" class="lazy folder" data="pos: 'AF'"> Molecular biology </li> <li id="s24" class="lazy folder" data="pos: 'AG'"> Palaeontology </li> <li id="s312" class="lazy folder" data="pos: 'AH'"> Parasitology </li> <li id="s514" class="lazy folder" data="pos: 'AQ'"> Physiology </li> <li id="s263" class="lazy folder" data="pos: 'AL'"> Systematics </li> <li id="s508" class="lazy folder" data="pos: 'AP'"> Toxicology </li> <li id="s34" class="lazy folder" data="pos: 'AK'"> Zoology &amp; Animal Biology </li> </ul> </div> <!-- Tree #1 END --> <script type="text/javascript"> //<![CDATA[ var gAdded = -1; $("#treealerts_subject_cats").dynatree({ checkbox: true, selectMode: 2, debugLevel: 0, onLazyRead: function(node){ node.appendAjax({url: "/lib/ajax_srv/autocomplete_srv.php", data: {"key": node.data.pos, // Optional url arguments "action": "get_tree_autocomplete", "table_name": "subject_categories", "filter_by_document_journal" : 1 }, success: function(node) { // Called after nodes have been created and the waiting icon was removed. var lInputVals = $("#alerts_subject_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if($("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id)) $("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id).select(); } }, error: function(node, XMLHttpRequest, textStatus, errorThrown) { // Called on error, after error icon was created. }, cache: false }); }, onSelect: function(flag, node) { if (!flag) { // Deselected item //$("#treealerts_subject_cats").dynatree("getTree").visit(function(node){ if( !node.bSelected ) { var lInputVals = $("#alerts_subject_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ $("#alerts_subject_cats_autocomplete").tokenInput("remove", { id: lInputVals[i].id }); break; } } } //}); }else{ if( gAdded == node.data.key ){ }else{ var lDontAdd = 0; var lInputVals = $("#alerts_subject_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ lDontAdd = 1; break; } } if(!lDontAdd){ $("#alerts_subject_cats_autocomplete").tokenInput("add", { id: node.data.key, name: node.data.title }); } } gAdded = -1; } }, onDblClick: function(node, event) { node.toggleSelect(); }, onKeydown: function(node, event) { if( event.which == 32 ) { node.toggleSelect(); return false; } }, onActivate: function(node) { }, onDeactivate: function(node) { }, // The following options are only required, if we have more than one tree on one page: //initId: "treeData", cookieId: "dynatree-Cb-alerts_subject_cats", idPrefix: "dynatree-Cb-alerts_subject_cats" }); $("#alerts_subject_cats_autocomplete").tokenInput( "/lib/ajax_srv/autocomplete_srv.php" + "?action=get_reg_autocomplete&filter_by_document_journal=1&table_name=subject_categories", { theme: "facebook", queryParam: "term", preventDuplicates: true, minChars: 3, onResult: function(data){ return data; }, onAdd: function(item){ var input = '<input id="alerts_subject_cats' + item.id + '_hiddenInp" name="alerts_subject_cats[]" value="' + item.id + '" type="hidden"></input>'; $(input).insertBefore( "#alerts_subject_cats_autocomplete" ); gAdded = item.id; if( $("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(item.id).activate(); $("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(item.id).select(); } else { console.log(item.id + " was not found in the currently loaded part of the tree"); } if (typeof initComplete == "boolean" && initComplete) { //console.log("Init is complete; this is a user add"); delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } }, onDelete: function(item){ $( "#alerts_subject_cats" + item.id + "_hiddenInp" ).remove(); if( $("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(item.id).select(false); $("#treealerts_subject_cats").dynatree("getTree").getNodeByKey(item.id).deactivate(); } delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } } ); //]]> </script> <script type="text/javascript"> //<![CDATA[ // Тук популираме първоначално инпута със селектнатите стойности или ако има грешка при сейв със селектнатите + новоселектнатите преди сейв var lSelectedCats = []; /*if(!lSelectedCats.length) toggleBlock('subject_arrow', 'subject_tree');*/ for ( var i = 0; i < lSelectedCats.length; i++) { $("#alerts_subject_cats_autocomplete").tokenInput("add", lSelectedCats[i]); } //]]> </script> </div> </div> </div><div class="class_wrapper"> <div class="filterBlock category articles_filter"> <div class="filterBlockTitle"> by Geographical Region <a id="geographical_arrow" class="blockUpArrow tree" href="javascript:void(0);" onclick="toggleBlock('geographical_arrow', 'geographical_tree')"></a> </div> <div class="filterBlockContent" id="geographical_tree"> <div class="P-Input-Full-Width P-W390"> <input type="text" name="alerts_geographical_cats" value="" id="alerts_geographical_cats_autocomplete" class="" /> </div> <!-- Tree alerts_geographical_cats --> <div id="treealerts_geographical_cats" class="filterBy"> <ul> <li id="g7" class="lazy folder" data="pos: 'AJ'"> Africa </li> <li id="g4" class="lazy folder" data="pos: 'AL'"> Americas </li> <li id="g5" class="lazy folder" data="pos: 'AF'"> Asia </li> <li id="g6" class="lazy folder" data="pos: 'AH'"> Australasia </li> <li id="g1" class="lazy folder" data="pos: 'AD'"> Europe </li> <li id="g10" class="lazy folder" data="pos: 'AR'"> Oceans </li> <li id="g8" class="lazy folder" data="pos: 'AN'"> Pacific </li> <li id="g9" class="lazy folder" data="pos: 'AP'"> Polar </li> <li id="g3" class="lazy folder" data="pos: 'AB'"> World </li> </ul> </div> <script type="text/javascript"> //<![CDATA[ var gAdded = -1; $("#treealerts_geographical_cats").dynatree({ checkbox: true, selectMode: 2, debugLevel: 0, onLazyRead: function(node){ node.appendAjax({url: "/lib/ajax_srv/autocomplete_srv.php", data: {"key": node.data.pos, // Optional url arguments "action": "get_tree_autocomplete", "table_name": "geographical_categories", "filter_by_document_journal" : 1 }, success: function(node) { // Called after nodes have been created and the waiting icon was removed. var lInputVals = $("#alerts_geographical_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if($("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id)) $("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id).select(); } }, error: function(node, XMLHttpRequest, textStatus, errorThrown) { // Called on error, after error icon was created. }, cache: false }); }, onSelect: function(flag, node) { if (!flag) { // Deselected item //$("#treealerts_geographical_cats").dynatree("getTree").visit(function(node){ if( !node.bSelected ) { var lInputVals = $("#alerts_geographical_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ $("#alerts_geographical_cats_autocomplete").tokenInput("remove", { id: lInputVals[i].id }); break; } } } //}); }else{ if( gAdded == node.data.key ){ }else{ var lDontAdd = 0; var lInputVals = $("#alerts_geographical_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ lDontAdd = 1; break; } } if(!lDontAdd){ $("#alerts_geographical_cats_autocomplete").tokenInput("add", { id: node.data.key, name: node.data.title }); } } gAdded = -1; } }, onDblClick: function(node, event) { node.toggleSelect(); }, onKeydown: function(node, event) { if( event.which == 32 ) { node.toggleSelect(); return false; } }, onActivate: function(node) { }, onDeactivate: function(node) { }, // The following options are only required, if we have more than one tree on one page: //initId: "treeData", cookieId: "dynatree-Cb-alerts_geographical_cats", idPrefix: "dynatree-Cb-alerts_geographical_cats" }); $("#alerts_geographical_cats_autocomplete").tokenInput( "/lib/ajax_srv/autocomplete_srv.php" + "?action=get_reg_autocomplete&filter_by_document_journal=1&table_name=geographical_categories", { theme: "facebook", queryParam: "term", preventDuplicates: true, minChars: 3, onResult: function(data){ return data; }, onAdd: function(item){ var input = '<input id="alerts_geographical_cats' + item.id + '_hiddenInp" name="alerts_geographical_cats[]" value="' + item.id + '" type="hidden"></input>'; $(input).insertBefore( "#alerts_geographical_cats_autocomplete" ); gAdded = item.id; if( $("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(item.id).activate(); $("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(item.id).select(); } else { console.log(item.id + " was not found in the currently loaded part of the tree"); } if (typeof initComplete == "boolean" && initComplete) { //console.log("Init is complete; this is a user add"); delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } }, onDelete: function(item){ $( "#alerts_geographical_cats" + item.id + "_hiddenInp" ).remove(); if( $("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(item.id).select(false); $("#treealerts_geographical_cats").dynatree("getTree").getNodeByKey(item.id).deactivate(); } delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } } ); //]]> </script> <script type="text/javascript"> //<![CDATA[ // Тук популираме първоначално инпута със селектнатите стойности или ако има грешка при сейв със селектнатите + новоселектнатите преди сейв var lSelectedCats = []; if(!lSelectedCats.length) toggleBlock('geographical_arrow', 'geographical_tree'); for ( var i = 0; i < lSelectedCats.length; i++) { $("#alerts_geographical_cats_autocomplete").tokenInput("add", lSelectedCats[i]); } //]]> </script> <!-- Tree #4 END --> </div> </div> <div class="filterBlock category articles_filter"> <div class="filterBlockTitle"> by Chronological Period <a id="chronological_arrow" class="blockUpArrow tree" href="javascript:void(0);" onclick="toggleBlock('chronological_arrow', 'chronological_tree')"></a> </div> <div class="filterBlockContent" id="chronological_tree"> <div class="P-Input-Full-Width P-W390"> <input type="text" name="alerts_chronical_cats" value="" id="alerts_chronical_cats_autocomplete" class="" /> </div> <!-- Tree alerts_chronical_cats --> <div id="treealerts_chronical_cats" class="filterBy"> <ul> <li id="c2" class="lazy folder" data="pos: 'AH'"> Cenozoic </li> <li id="c1" class="lazy folder" data="pos: 'AF'"> Mesozoic </li> <li id="c9" class="lazy folder" data="pos: 'AD'"> Paleozoic </li> <li id="c7" class="lazy folder" data="pos: 'AB'"> Precambrian </li> </ul> </div> <!-- Tree #2 END --> <script type="text/javascript"> //<![CDATA[ var gAdded = -1; $("#treealerts_chronical_cats").dynatree({ checkbox: true, selectMode: 2, debugLevel: 0, onLazyRead: function(node){ node.appendAjax({url: "/lib/ajax_srv/autocomplete_srv.php", data: {"key": node.data.pos, // Optional url arguments "action": "get_tree_autocomplete", "table_name": "chronological_categories", "filter_by_document_journal" : 1 }, success: function(node) { // Called after nodes have been created and the waiting icon was removed. var lInputVals = $("#alerts_chronical_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if($("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id)) $("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(lInputVals[i].id).select(); } }, error: function(node, XMLHttpRequest, textStatus, errorThrown) { // Called on error, after error icon was created. }, cache: false }); }, onSelect: function(flag, node) { if (!flag) { // Deselected item //$("#treealerts_chronical_cats").dynatree("getTree").visit(function(node){ if( !node.bSelected ) { var lInputVals = $("#alerts_chronical_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ $("#alerts_chronical_cats_autocomplete").tokenInput("remove", { id: lInputVals[i].id }); break; } } } //}); }else{ if( gAdded == node.data.key ){ }else{ var lDontAdd = 0; var lInputVals = $("#alerts_chronical_cats_autocomplete").tokenInput("get"); for ( var i = 0; i < lInputVals.length; ++i) { if(lInputVals[i].id == node.data.key){ lDontAdd = 1; break; } } if(!lDontAdd){ $("#alerts_chronical_cats_autocomplete").tokenInput("add", { id: node.data.key, name: node.data.title }); } } gAdded = -1; } }, onDblClick: function(node, event) { node.toggleSelect(); }, onKeydown: function(node, event) { if( event.which == 32 ) { node.toggleSelect(); return false; } }, onActivate: function(node) { }, onDeactivate: function(node) { }, // The following options are only required, if we have more than one tree on one page: //initId: "treeData", cookieId: "dynatree-Cb-alerts_chronical_cats", idPrefix: "dynatree-Cb-alerts_chronical_cats" }); $("#alerts_chronical_cats_autocomplete").tokenInput( "/lib/ajax_srv/autocomplete_srv.php" + "?action=get_reg_autocomplete&filter_by_document_journal=1&table_name=chronological_categories", { theme: "facebook", queryParam: "term", preventDuplicates: true, minChars: 3, onResult: function(data){ return data; }, onAdd: function(item){ var input = '<input id="alerts_chronical_cats' + item.id + '_hiddenInp" name="alerts_chronical_cats[]" value="' + item.id + '" type="hidden"></input>'; $(input).insertBefore( "#alerts_chronical_cats_autocomplete" ); gAdded = item.id; if( $("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(item.id).activate(); $("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(item.id).select(); } else { console.log(item.id + " was not found in the currently loaded part of the tree"); } if (typeof initComplete == "boolean" && initComplete) { //console.log("Init is complete; this is a user add"); delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } }, onDelete: function(item){ $( "#alerts_chronical_cats" + item.id + "_hiddenInp" ).remove(); if( $("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(item.id) ) { $("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(item.id).select(false); $("#treealerts_chronical_cats").dynatree("getTree").getNodeByKey(item.id).deactivate(); } delayFormSubmission(gFormToSubmit, 0); //$('#' + gFormToSubmit).submit(); } } ); //]]> </script> <script type="text/javascript"> //<![CDATA[ // Тук популираме първоначално инпута със селектнатите стойности или ако има грешка при сейв със селектнатите + новоселектнатите преди сейв var lSelectedCats = []; if(!lSelectedCats.length) toggleBlock('chronological_arrow', 'chronological_tree'); for ( var i = 0; i < lSelectedCats.length; i++) { $("#alerts_chronical_cats_autocomplete").tokenInput("add", lSelectedCats[i]); } //]]> </script> </div> </div> </div> <script type="text/javascript"> //<![CDATA[ initComplete = true; gFormToSubmit = "filter_articles"; lRadioSetCheckedByAttrFunction("#search_in_hidden", "name", "search_in_"); lRadioSetCheckedByAttrFunction("#search_in_hidden", "name", "search_in"); lInputCloneValueFunction("#hidden_search_text", "#stext"); //]]> </script> <div class="filterBlock category"> <div class="filterBlockTitle"> by Publication Date (dd/mm/yyyy) </div> <div class="filterBlockContent"> <div class="dateHolder"> <div style="float: left; margin-right: 5px;">from</div> <div class="fieldHolder date"> <input type="text" name="from_date" value="" class="" id="from_date" /> </div> </div> <div class="dateHolder"> <div style="float: left; margin-right: 5px; margin-left: 10px;">to</div> <div class="fieldHolder date"> <input type="text" name="to_date" value="" class="" id="to_date" /> </div> </div> <div class="P-Clear"></div> <script type="text/javascript"> $(function() { $( "#from_date, #to_date" ).datepicker({ showOn: "button", buttonImage: "/i/icons_calendar.svg", buttonImageOnly: true, dateFormat: 'dd/mm/yy', onSelect: function(dateStr) { delayFormSubmission('filter_articles'); //$('#filter_articles').submit(); } }); }); </script> </div> </div> <div class="filterBlock category" style=""> <div class="filterBlockTitle" style="margin-bottom: 10px;"> by Publication Type </div> <div class="filterBlockContent sec_type row"> <div class="label_section_types col-xs-6 no-col-padding"> <label class="control control--checkbox"> Research Article <span class="sec_type_counts">(3)</span> <input type="checkbox" id="chk_358" name="section_type[]" value="358" class="producttypes " class="producttypes " onclick="delayFormSubmission(&#039;filter_articles&#039;);" /> <div class="control__indicator"></div> </label> </div> <div class="label_section_types col-xs-6 no-col-padding"> <label class="control control--checkbox"> Short Communication <span class="sec_type_counts">(1)</span> <input type="checkbox" id="chk_477" name="section_type[]" value="477" class="producttypes " class="producttypes " onclick="delayFormSubmission(&#039;filter_articles&#039;);" /> <div class="control__indicator"></div> </label> </div> <div class="label_section_types col-xs-6 no-col-padding"> <label class="control control--checkbox"> Methods <span class="sec_type_counts">(2)</span> <input type="checkbox" id="chk_331" name="section_type[]" value="331" class="producttypes " class="producttypes " onclick="delayFormSubmission(&#039;filter_articles&#039;);" /> <div class="control__indicator"></div> </label> </div> <div class="label_section_types col-xs-6 no-col-padding"> <label class="control control--checkbox"> Taxonomy & Inventories <span class="sec_type_counts">(7)</span> <input type="checkbox" id="chk_128" name="section_type[]" value="128" class="producttypes " class="producttypes " onclick="delayFormSubmission(&#039;filter_articles&#039;);" /> <div class="control__indicator"></div> </label> </div> <div class="label_section_types col-xs-6 no-col-padding"> <label class="control control--checkbox"> Data Paper <span class="sec_type_counts">(5)</span> <input type="checkbox" id="chk_131" name="section_type[]" value="131" class="producttypes " class="producttypes " onclick="delayFormSubmission(&#039;filter_articles&#039;);" /> <div class="control__indicator"></div> </label> </div> <div class="label_section_types col-xs-6 no-col-padding"> <label class="control control--checkbox"> Data Paper <span class="sec_type_counts">(1)</span> <input type="checkbox" id="chk_741" name="section_type[]" value="741" class="producttypes " class="producttypes " onclick="delayFormSubmission(&#039;filter_articles&#039;);" /> <div class="control__indicator"></div> </label> </div> </div> </div> <div class="filterBlock category" style="display:none;"> <div class="filterBlockTitle" style="margin-bottom: 10px;"> by Journal </div> <div class="filterBlockContent sec_type row"> </div> </div> <div class="filterBlock category"> <div class="filterBlockTitle"> by Funding Agency </div> <div class="filterBlockContent"> <div class="fieldHolder bigColField fund_ag"> <input type="text" name="funding_agency" value="" onblur="delayFormSubmission(&#039;filter_articles&#039;);//$(&#039;#filter_articles&#039;).submit()" style="width:100% !important" class="fund_ag " /> </div> <div class="P-Clear"></div> </div> </div> <script type="text/javascript"> $(document).ready(function(){ $("#filter_articles").submit(function(){ $("input").each(function(index, obj){ this.disabled = !($(this).val()); }); }); }); </script> <div class="buttonsHolder"> <input type="submit" name="tAction" value="Filter" style="display:none" class="notranslate" /> <div class="P-Grey-Btn-Holder"> <a class="P-Grey-Btn-Middle" href="/topical_collection/209">Clear filters</a> </div> <div class="P-Clear"></div> </div> <div class="P-Clear"></div> </div> </form> </div> </div> <div class="P-Clear"></div> </div> <div class="flex_wrapper3"> <div id="contentSmallHolder"> <div id="contentSmall"> <div class="sp_issue_wrapper"> <div class="issue_title_identifier no_up_down_padding article_title_with_sort collection_documents_sort"> <div class="zag">Linking FAIR biodiversity data through publications: The BiCIKL approach</div> <div class="P-Input-Full-Width fieldHolder P-SelectHolder P-Articles-Sort-Select w270 article_sort_text_wrapper"> <div class="article_sort_text_wrapper">Sort by:</div> <div class="article_sort_select_wrapper"> <select name="country" onchange="SortArticleResults(this, 'filter_articles')" id="countries"> <option value="3" style="padding-left: 10px;" >Publication date newest</option> <option value="4" style="padding-left: 10px;" >Publication date oldest</option> <option value="1" style="padding-left: 10px;" >Total views</option> <option value="2" style="padding-left: 10px;" >Unique views</option> <option value="6" style="padding-left: 10px;" >Best match</option> <option value="8" style="padding-left: 10px;" >Citations count</option><option value="10001" style="padding-left: 10px;" >Highly accessed (last month)</option><option value="10002" style="padding-left: 10px;" >Highly accessed (last 3 months)</option><option value="10003" style="padding-left: 10px;" >Highly accessed (last 6 months)</option><option value="10004" style="padding-left: 10px;" >Highly accessed (last year)</option> </select> </div> <form name="filter_topical_documents" enctype="multipart/form-data" method="get" action="browse_topical_collection_documents.php" id="filter_topical_documents"> <input type="hidden" name="collection_id" value="209"/> <input type="hidden" name="journal_id" value="1"/> <input type="hidden" name="sortby" id="filter_topical_documents_sortby" value=""/> <input type="hidden" name="form_name" value="filter_topical_documents"/> </form> </div> </div> <div class="right"></div> <div class="issue_editors"><i>Edited by</i> Anne Thessen, J. Adilson Pinedo-Escatel, Jader Oliveira, Renan Barbosa, Krizler Tanalgo, Paulo A. V. Borges, Panakkool Thamban Aneesh, Hanieh Saeedi, Vincent Smith, Lyubomir Penev</div> <div class="issue_description issue_info_fields"><p>The EU-funded project <a href="https://bicikl-project.eu/">BiCIKL</a> (Biodiversity Community Integrated Knowledge Library) supports free of charge* publications in a dedicated topical collection in the <a href="https://bdj.pensoft.net/">Biodiversity Data Journal</a>, demonstrating advanced publishing methods of <strong>linked biodiversity data</strong>.</p> <p><strong>The criteria and requirements for publication are listed&nbsp;<u><a href="https://blog.pensoft.net/2023/03/06/bicikl-project-supports-article-collection-in-biodiversity-data-journal-about-use-of-linked-data/">here</a></u>. The authors need to acknowledge the&nbsp;<a href="https://bicikl-project.eu/">BiCIKL project</a>, Grant No 101007492 in the Acknowledgements section.</strong></p> <p>BiCIKL is dedicated to building a new community of key <u><a href="https://bicikl-project.eu/research-infrastructures">research infrastructures</a></u>, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc., to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles. Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem.</p> <p>In the <strong>Author&#39;s notes to the Editor,&nbsp;</strong>the authors will need to make a reference to the condition(s) their work complies with&nbsp;the requirements and expectations of the BiCIKL project, which are briefly outlined <strong><a href="https://blog.pensoft.net/2023/03/06/bicikl-project-supports-article-collection-in-biodiversity-data-journal-about-use-of-linked-data/">here</a></strong>. Likewise, they will need to abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics.&nbsp;</p> <p>The collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.&nbsp;</p> <p>The authors need to acknowledge the <a href="https://bicikl-project.eu/">BiCIKL project</a>, Grant No 101007492 in the Acknowledgements section.</p> <p>* The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at &euro; 650. Authors of larger manuscripts will need to cover the surplus charge (&euro;10 for each 1,000 characters above 40,000). See more about the <a href="https://bdj.pensoft.net/about#ArticleProcessingCharges" rel="noopener noreferrer" target="_blank">APC policy</a> at Biodiversity Data Journal, or contact the journal editorial team at: <a href="mailto:bdj@pensoft.net" rel="noreferrer">bdj@pensoft.net</a>.</p> </div> <div> <div class="parent_collection_doi" style="margin-left: 16px; display: inline-block;"><a class="coll_doi_link" href="https://doi.org/10.3897/bdj.coll.209"><span class="col_doi"></span> 10.3897/bdj.coll.209</a></div> </div> <div class="clear"></div> <div class="nav_border row end-xs browse_select_articles in_issue"> <div class="col-xs-6 end-xs browse_select_articles"> <div class="browse_articles_download hidden-sm-down"> <div class="row middle-xs end-xs"> <div class="col-xs-6 end-xs"> Select: &nbsp; <a href="javascript:void(0)" title="Select all visible articles" onclick="selectAllItems('itemCheckBox')">All</a> &nbsp; <a href="javascript:void(0)" title="Reset selection" 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