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The Open Protein Structure Annotation Network
PDB Keyword
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Template:Uniprot

    Table of contents
    No headers

    {{note.import( 'UNIPROT:'..args.uniprot) }}

    {{ var key = 'FILTER regex(str(?keyword), "key")'; var compProt = 'FILTER (?keyLabel != "Complete proteome")'; var queryReturn=note.query("PREFIX protein: <http://purl.uniprot.org/uniprot/> PREFIX core: <http://purl.uniprot.org/core/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#>PREFIX rdf: <http://www.w3.org/2000/01/rdf-schema#> SELECT DISTINCT ?mnemonic ?recName ?altName ?subAnn ?funcAnn ?geneName ?altGeneName ?ptm ?keyLabel ?goLabel ?goTerm WHERE { { protein:"..args.uniprot.." core:mnemonic ?mnemonic . } UNION { protein:"..args.uniprot.." core:recommendedName ?tempRecName. ?tempRecName core:fullName ?recName. } UNION { protein:"..args.uniprot.." core:alternativeName ?tempAltName. ?tempAltName core:fullName ?altName. } UNION { protein:"..args.uniprot.." core:annotation ?val. ?val a core:Subunit_Annotation. ?val rdfs:comment ?subAnn. }  UNION { protein:"..args.uniprot.." core:annotation ?val. ?val a core:Function_Annotation. ?val rdfs:comment ?funcAnn. } UNION { protein:"..args.uniprot.." core:encodedBy ?tempGene. ?tempGene a core:Gene. { ?tempGene skos:prefLabel ?geneName. } UNION { OPTIONAL { ?tempGene skos:altLabel ?altGeneName. } } } UNION { protein:"..args.uniprot.." core:annotation ?val. ?val a core:PTM_Annotation. ?val rdfs:comment ?ptm. } UNION { protein:"..args.uniprot.." core:classifiedWith ?tempKeyword. ?tempKeyword rdf:seeAlso ?goTerm. ?goTerm a core:Concept. ?goTerm rdf:label ?goLabel. } UNION { protein:"..args.uniprot.." core:classifiedWith ?keyword. ?keyword rdf:label ?keyLabel."..key.." "..compProt.."} }");  }}

    {{var ebiQuery=note.query("PREFIX protein: <http://purl.uniprot.org/uniprot/> PREFIX core: <http://purl.uniprot.org/core/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#>PREFIX rdf: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?reactions WHERE { protein:"..args.uniprot.." core:interaction ?interactions. ?interactions core:participant ?reactions. } LIMIT 1")}}

    if (#list.collect(queryReturn, 'recName') > 0) {
    <b> "Recommended Name: " </b>;
    foreach(var line in queryReturn){ line['recName'] }
    } <br />;
    if (#list.collect(queryReturn, 'altName') > 0) {
    <b> "Alternate Name(s):" </b>;
    <ul style="list-style:none">;
    foreach(var line in queryReturn) {
    if (line['altName'] && line['altName'] != '') {
    <li> line['altName'] </li>;
    }
    }
    </ul>;
    }
    
    if (#list.collect(queryReturn, 'geneName') > 0) {
    <b> "Gene Name: " </b>;
    foreach(var line in queryReturn){ line['geneName'] }
    } <br />;
    if (#list.collect(queryReturn, 'altGeneName') > 0) {
    <b> "Synonyms:" </b>;
    <ul style="list-style:none">;
    foreach(var line in queryReturn) {
    if (line['altGeneName'] && line['altGeneName'] != '') {
    <li> line['altGeneName'] </li>;
    }
    }
    </ul>;
    }
    if (#list.collect(queryReturn, 'keyLabel') > 0){
    var keywords = list.reduce(list.collect(queryReturn, 'keyLabel'),"$value .. ', ' .. $item ");
    <b>"Keywords: "</b>; string.substr(keywords, 2);
    }
    if (#list.collect(ebiQuery, 'reactions') > 0) {
    "Interaction partners, experimental conditions, and related publications can be found ";
    foreach(var line in ebiQuery) {
    web.link(line['reactions'], "here", "List of interactions provided by IntAct", "_blank");
    }
    }
    if (#list.collect(queryReturn, 'goLabel') > 0) {
    var goList = [' '];
    foreach(var line in queryReturn) {
    if (line['goLabel'] && line['goLabel'] != '') {
    let goList ..= [ web.link(line['goTerm'], line['goLabel'], line['goLabel'], "_blank") ];
    }
    }
    var goTerms = list.reduce(goList,"$value .. ', ' .. $item ");
    <b> CollapseItem{id:"goTerms",effect:"fade"};
    "Gene Ontology" </b>;
    <p id="goTerms"> web.html(string.substr(goTerms, 4)) </p>;
    }
    var ptmContent = "";
    if (#list.collect(queryReturn, 'ptm') > 0) {
    let ptmContent = "<ul id='content1'><hr />";
    foreach (var line in queryReturn) {
    if (line['ptm'] && line['ptm'] != '') {
    let ptmContent ..= "<li>"..line['ptm'].."</li>";}
    }
    let ptmContent ..= "<hr /></ul>";
    <b> CollapseItem{id:"content1",effect:"slide"};
    "Post-Translational Modifications"</b>;
    web.html(ptmContent);
    }
    
    var subAnn = "";
    if (#list.collect(queryReturn, 'subAnn') > 0) {
    let subAnn = "<ul id='content2'><hr />";
    foreach (var line in queryReturn) {
    if (line['subAnn'] && line['subAnn'] != '') {
    let subAnn ..= line['subAnn'];}
    }
    let subAnn ..= "<hr /></ul>";
    <b> CollapseItem{id:"subunitContent",effect:"slide"};
    "Subunit Annotations" </b>; 
    web.html(subAnn);
    }
    
    var funcAnn = "";
    if (#list.collect(queryReturn, 'funcAnn') > 0) {
    let funcAnn = "<ul id='content3'><hr />";
    foreach (var line in queryReturn) {
    if (line['funcAnn'] && line['funcAnn'] != '') {
    let funcAnn ..= line['funcAnn'];}
    }
    let funcAnn ..= "<hr /></ul>";
    <b> CollapseItem{id:"content3",effect:"slide"};
    "Functional Annotations" </b>;
    web.html(funcAnn);
    }
    

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