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<!DOCTYPE html> <html class="client-nojs" lang="en" dir="ltr"> <head> <meta charset="UTF-8"/> <title>Identifiers: Difference between revisions - GO Wiki</title> <script>document.documentElement.className="client-js";RLCONF={"wgBreakFrames":false,"wgSeparatorTransformTable":["",""],"wgDigitTransformTable":["",""],"wgDefaultDateFormat":"dmy","wgMonthNames":["","January","February","March","April","May","June","July","August","September","October","November","December"],"wgRequestId":"Z79gr5TyCpDwuB3R8tq7TwAADaQ","wgCSPNonce":false,"wgCanonicalNamespace":"","wgCanonicalSpecialPageName":false,"wgNamespaceNumber":0,"wgPageName":"Identifiers","wgTitle":"Identifiers","wgCurRevisionId":82577,"wgRevisionId":55485,"wgArticleId":4447,"wgIsArticle":true,"wgIsRedirect":false,"wgAction":"view","wgUserName":null,"wgUserGroups":["*"],"wgCategories":["Curator 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href="/index.php?title=Special:RecentChanges&feed=atom"/> </head> <body class="skin-vector-legacy mediawiki ltr sitedir-ltr mw-hide-empty-elt ns-0 ns-subject page-Identifiers rootpage-Identifiers skin-vector action-view"><div id="mw-page-base" class="noprint"></div> <div id="mw-head-base" class="noprint"></div> <div id="content" class="mw-body" role="main"> <a id="top"></a> <div id="siteNotice"></div> <div class="mw-indicators"> <div id="mw-indicator-mw-helplink" class="mw-indicator"><a href="https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Diff" target="_blank" class="mw-helplink">Help</a></div> </div> <h1 id="firstHeading" class="firstHeading mw-first-heading">Identifiers: Difference between revisions</h1> <div id="bodyContent" class="vector-body"> <div id="siteSub" class="noprint">From GO Wiki</div> <div id="contentSub"><div id="mw-content-subtitle"></div></div> <div id="contentSub2"></div> <div id="jump-to-nav"></div> <a class="mw-jump-link" href="#mw-head">Jump to navigation</a> <a class="mw-jump-link" href="#searchInput">Jump to search</a> <div id="mw-content-text" class="mw-body-content mw-content-ltr" lang="en" dir="ltr"><table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" class="diff-otitle diff-side-deleted"><div id="mw-diff-otitle1"><strong><a href="/index.php?title=Identifiers&oldid=55484" title="Identifiers">Revision as of 15:23, 8 December 2014</a> <span class="mw-diff-edit">(<a href="/index.php?title=Identifiers&action=edit&oldid=55484" title="Identifiers">view source</a>)</span></strong></div><div id="mw-diff-otitle2"><a href="/User:Cjm" class="mw-userlink" title="User:Cjm" data-mw-revid="55484"><bdi>Cjm</bdi></a> <span class="mw-usertoollinks">(<a href="/index.php?title=User_talk:Cjm&action=edit&redlink=1" class="new mw-usertoollinks-talk" title="User talk:Cjm (page does not exist)">talk</a> | <a href="/Special:Contributions/Cjm" class="mw-usertoollinks-contribs" title="Special:Contributions/Cjm">contribs</a>)</span></div><div id="mw-diff-otitle3"> <span class="comment">(<span dir="auto"><span class="autocomment"><a href="#Prefix_Registry">→‎Prefix Registry</a></span></span>)</span></div><div id="mw-diff-otitle5"></div><div id="mw-diff-otitle4"><a href="/index.php?title=Identifiers&diff=prev&oldid=55484" title="Identifiers" id="differences-prevlink">← Older edit</a></div></td> <td colspan="2" class="diff-ntitle diff-side-added"><div id="mw-diff-ntitle1"><strong><a href="/index.php?title=Identifiers&oldid=55485" title="Identifiers">Revision as of 15:29, 8 December 2014</a> <span class="mw-diff-edit">(<a href="/index.php?title=Identifiers&action=edit&oldid=55485" title="Identifiers">view source</a>)</span> </strong></div><div id="mw-diff-ntitle2"><a href="/User:Cjm" class="mw-userlink" title="User:Cjm" data-mw-revid="55485"><bdi>Cjm</bdi></a> <span class="mw-usertoollinks">(<a href="/index.php?title=User_talk:Cjm&action=edit&redlink=1" class="new mw-usertoollinks-talk" title="User talk:Cjm (page does not exist)">talk</a> | <a href="/Special:Contributions/Cjm" class="mw-usertoollinks-contribs" title="Special:Contributions/Cjm">contribs</a>)</span> </div><div id="mw-diff-ntitle3"> <span class="comment">(<span dir="auto"><span class="autocomment"><a href="#MGI">→‎MGI</a></span></span>)</span></div><div id="mw-diff-ntitle5"></div><div id="mw-diff-ntitle4"><a href="/index.php?title=Identifiers&diff=next&oldid=55485" title="Identifiers" id="differences-nextlink">Newer edit →</a></div></td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l52">Line 52:</td> <td colspan="2" class="diff-lineno">Line 52:</td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div>Josh has been alerted, bringing this up with FlyBase</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div>Josh has been alerted, bringing this up with FlyBase</div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div>=== MGI ===</div></td><td class="diff-marker" data-marker="+"></td><td class="diff-addedline diff-side-added"><div>=== MGI <ins class="diffchange diffchange-inline">and prefix doubling </ins> ===</div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div>MGI IDs are a major problem</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div>MGI IDs are a major problem</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l64">Line 64:</td> <td colspan="2" class="diff-lineno">Line 64:</td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div>* MGI:MGI:98297</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div>* MGI:MGI:98297</div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div>Here we have a doubling up of the MGI prefix. <del class="diffchange diffchange-inline">Note that this is inconsistent with NCBI xrefs, which use MGI:98297 - '''this inconsistency has yet to be resolved with NCBI'''</del></div></td><td class="diff-marker" data-marker="+"></td><td class="diff-addedline diff-side-added"><div>Here we have a doubling up of the MGI prefix.</div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div>Note <del class="diffchange diffchange-inline">also </del>that <del class="diffchange diffchange-inline">typically people </del>used the <del class="diffchange diffchange-inline">local ID in their WITH columns; eg rat has</del>:</div></td><td class="diff-marker" data-marker="+"></td><td class="diff-addedline diff-side-added"><div>Note that <ins class="diffchange diffchange-inline">NCBI previously </ins>used <ins class="diffchange diffchange-inline">'non-doubled- global identifiers of </ins>the <ins class="diffchange diffchange-inline">form MGI</ins>:<ins class="diffchange diffchange-inline">nnn, but they are now switching to the doubled form MGI</ins>:MGI:<ins class="diffchange diffchange-inline">nnn - see http</ins>:<ins class="diffchange diffchange-inline">//www.ncbi.nlm.nih.gov/feed/rss</ins>.<ins class="diffchange diffchange-inline">cgi?ChanKey=genenews article from Wed, 06 Aug 2014 "Important change coming for HGNC and MGI database identifiers"</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div><del class="diffchange diffchange-inline"> RGD RGD:3673 Shh GO</del>:<del class="diffchange diffchange-inline">0001525 RGD:1580654 ISS </del>MGI:<del class="diffchange diffchange-inline">98297 P sonic hedgehog homolog (Drosophila) gene taxon</del>:<del class="diffchange diffchange-inline">10116 20060820 RGD </del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div><del class="diffchange diffchange-inline">(NOTE: RGD have fixed this</del>. <del class="diffchange diffchange-inline">Thanks RGD!)</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div>Compare with the (well-behaved) ZFIN GAFs and IDs:</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div>Compare with the (well-behaved) ZFIN GAFs and IDs:</div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div> ZFIN ZDB-GENE-980526-166 shha</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div> ZFIN ZDB-GENE-980526-166 shha</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td class="diff-addedline diff-side-added"><div><ins class="diffchange"></ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td class="diff-addedline diff-side-added"><div><ins class="diffchange">(example col1,2,3 in GAF)</ins></div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div>col1:col2 =</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div>col1:col2 =</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l82">Line 82:</td> <td colspan="2" class="diff-lineno">Line 80:</td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div>This is identical to what NCBI uses in their xref</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div>This is identical to what NCBI uses in their xref</div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td class="diff-deletedline diff-side-deleted"><div>MGI <del class="diffchange diffchange-inline">has </del>confirmed that the global ID is MGI:MGI:nnnnn, and the local internal ID is MGI:nnnn</div></td><td class="diff-marker" data-marker="+"></td><td class="diff-addedline diff-side-added"><div>MGI <ins class="diffchange diffchange-inline">previously </ins>confirmed that the global ID is MGI:MGI:nnnnn, and the local internal ID is MGI:nnnn</div></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><br/></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><br/></td></tr> <tr><td class="diff-marker"></td><td class="diff-context diff-side-deleted"><div>=== RGD ===</div></td><td class="diff-marker"></td><td class="diff-context diff-side-added"><div>=== RGD ===</div></td></tr> </table><hr class='diff-hr' id='mw-oldid' /> <h2 class='diff-currentversion-title'>Revision as of 15:29, 8 December 2014</h2> <div class="mw-parser-output"><p><br /> All identifiers in GO (e.g. referenced in GAF, ontology or associated documents) should be conform to the following format: </p> <pre> GlobalID = Prefix ':' LocalID </pre> <p>We use the term 'identifier' as synonymous with GlobalID, although confusingly some use 'identifier' to refer to what we call LocalID. </p> <ul><li>Prefixes: Each prefix must be registered in the GO xrfs registry file. It should correspond to some known authority. The characters must all be alphanumeric (a-z, A-Z, 0-9), underscores or dashes.</li> <li>The LocalID scheme is under the control of the Database/authorit. It should include no whitespace or non-ascii characters. The characters must all be printable ascii characters, excluding spaces.</li></ul> <div id="toc" class="toc" role="navigation" aria-labelledby="mw-toc-heading"><input type="checkbox" role="button" id="toctogglecheckbox" class="toctogglecheckbox" style="display:none" /><div class="toctitle" lang="en" dir="ltr"><h2 id="mw-toc-heading">Contents</h2><span class="toctogglespan"><label class="toctogglelabel" for="toctogglecheckbox"></label></span></div> <ul> <li class="toclevel-1 tocsection-1"><a href="#Examples"><span class="tocnumber">1</span> <span class="toctext">Examples</span></a></li> <li class="toclevel-1 tocsection-2"><a href="#Identifiers_in_GAFs"><span class="tocnumber">2</span> <span class="toctext">Identifiers in GAFs</span></a></li> <li class="toclevel-1 tocsection-3"><a href="#Prefix_Registry"><span class="tocnumber">3</span> <span class="toctext">Prefix Registry</span></a></li> <li class="toclevel-1 tocsection-4"><a href="#Problems_with_existing_usage"><span class="tocnumber">4</span> <span class="toctext">Problems with existing usage</span></a> <ul> <li class="toclevel-2 tocsection-5"><a href="#FLYBASE_vs_FB"><span class="tocnumber">4.1</span> <span class="toctext">FLYBASE vs FB</span></a></li> <li class="toclevel-2 tocsection-6"><a href="#MGI_and_prefix_doubling"><span class="tocnumber">4.2</span> <span class="toctext">MGI and prefix doubling</span></a></li> <li class="toclevel-2 tocsection-7"><a href="#RGD"><span class="tocnumber">4.3</span> <span class="toctext">RGD</span></a> <ul> <li class="toclevel-3 tocsection-8"><a href="#recommendation"><span class="tocnumber">4.3.1</span> <span class="toctext">recommendation</span></a></li> </ul> </li> </ul> </li> <li class="toclevel-1 tocsection-9"><a href="#See_Also"><span class="tocnumber">5</span> <span class="toctext">See Also</span></a></li> </ul> </div> <h2><span class="mw-headline" id="Examples">Examples</span></h2> <p>Examples of well behaved IDs: </p> <ul><li>GO:0008152 <ul><li>Database=GO LocalID=0008152</li></ul></li> <li>SGD:S000006435 <ul><li>Database=SGD LocalID=S000006435</li></ul></li> <li>ZFIN:ZDB-GENE-980526-166 <ul><li>Database=ZFIN LocalID=ZDB-GENE-980526-166</li></ul></li></ul> <h2><span class="mw-headline" id="Identifiers_in_GAFs">Identifiers in GAFs</span></h2> <p>In the gene association files, Database goes in column 1, LocalID goes in column 2 </p><p>For filling in the WITH column, the <i>Global</i> ID should be used. This has to be the case, otherwise it would be difficult to tell where the ID came from </p> <h2><span class="mw-headline" id="Prefix_Registry">Prefix Registry</span></h2> <p>The Database <b>should</b> be registered in GO.xrf_abbs, available here: </p> <ul><li><a rel="nofollow" class="external free" href="http://www.geneontology.org/doc/GO.xrf_abbs">http://www.geneontology.org/doc/GO.xrf_abbs</a></li> <li><a rel="nofollow" class="external free" href="http://www.geneontology.org/cgi-bin/xrefs.cgi">http://www.geneontology.org/cgi-bin/xrefs.cgi</a></li></ul> <p>Spec: </p> <ul><li><a rel="nofollow" class="external free" href="http://www.geneontology.org/doc/GO.xrf_abbs_spec">http://www.geneontology.org/doc/GO.xrf_abbs_spec</a></li></ul> <p>We are in the process of moving the primary version of this file to a yaml file with primary location in a github repo: </p> <ul><li><a rel="nofollow" class="external free" href="https://github.com/kltm/go-site/blob/master/metadata/go-db-xrefs.yaml">https://github.com/kltm/go-site/blob/master/metadata/go-db-xrefs.yaml</a></li></ul> <h2><span class="mw-headline" id="Problems_with_existing_usage">Problems with existing usage</span></h2> <h3><span class="mw-headline" id="FLYBASE_vs_FB">FLYBASE vs FB</span></h3> <p>We have both FB and FlyBase registered here Also in the fb gene_association files, the col1 is FB but the assigned_by column is FlyBase. NCBI seem to use FLYBASE </p><p>Josh has been alerted, bringing this up with FlyBase </p> <h3><span class="mw-headline" id="MGI_and_prefix_doubling">MGI and prefix doubling</span></h3> <p>MGI IDs are a major problem </p><p>GAF (cols 1-3): </p> <pre> MGI MGI:98297 Shh </pre> <p>Using the concatenation rule, this composez to the global ID </p> <ul><li>MGI:MGI:98297</li></ul> <p>Here we have a doubling up of the MGI prefix. </p><p>Note that NCBI previously used 'non-doubled- global identifiers of the form MGI:nnn, but they are now switching to the doubled form MGI:MGI:nnn - see <a rel="nofollow" class="external free" href="http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=genenews">http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=genenews</a> article from Wed, 06 Aug 2014 "Important change coming for HGNC and MGI database identifiers" </p><p>Compare with the (well-behaved) ZFIN GAFs and IDs: </p> <pre> ZFIN ZDB-GENE-980526-166 shha </pre> <p>(example col1,2,3 in GAF) </p><p>col1:col2 = </p> <ul><li>ZFIN:ZDB-GENE-980526-166</li></ul> <p>This is identical to what NCBI uses in their xref </p><p>MGI previously confirmed that the global ID is MGI:MGI:nnnnn, and the local internal ID is MGI:nnnn </p> <h3><span class="mw-headline" id="RGD">RGD</span></h3> <p>RGD previously used the same pattern as MGI. As of 2008/06/23 they have confirmed their policy and fixed their files. RGD:nnnn is the global ID. The local ID is purely a number (for both genes and references) </p> <h4><span class="mw-headline" id="recommendation">recommendation</span></h4> <p>MGI should either </p> <ul><li>change their col2 in their GAFs such that only the number is used (PREFERRED)</li> <li>coordinate with other databases, including NCBI to make it clear that the global ID is MGI:MGI:nnnnn</li></ul> <h2><span class="mw-headline" id="See_Also">See Also</span></h2> <ul><li><a rel="nofollow" class="external text" href="http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#2.5">OBO Format ID syntax</a></li> <li><a rel="nofollow" class="external text" href="http://www.obofoundry.org/id-policy.shtml">OBO Foundry ID policy</a></li></ul></div> <div class="printfooter" data-nosnippet="">Retrieved from "<a dir="ltr" href="https://wiki.geneontology.org/index.php?title=Identifiers&oldid=55485">https://wiki.geneontology.org/index.php?title=Identifiers&oldid=55485</a>"</div></div> <div id="catlinks" class="catlinks" data-mw="interface"><div id="mw-normal-catlinks" class="mw-normal-catlinks"><a href="/Special:Categories" title="Special:Categories">Categories</a>: <ul><li><a href="/index.php?title=Category:Curator_Guides&action=edit&redlink=1" class="new" title="Category:Curator Guides (page does not exist)">Curator Guides</a></li><li><a href="/Category:Annotation" title="Category:Annotation">Annotation</a></li><li><a href="/index.php?title=Category:Formats&action=edit&redlink=1" class="new" title="Category:Formats (page does not exist)">Formats</a></li></ul></div></div> </div> </div> <div id="mw-navigation"> <h2>Navigation menu</h2> <div id="mw-head"> <nav id="p-personal" class="vector-menu mw-portlet mw-portlet-personal vector-user-menu-legacy" aria-labelledby="p-personal-label" role="navigation" > <h3 id="p-personal-label" class="vector-menu-heading " > <span class="vector-menu-heading-label">Personal tools</span> </h3> <div class="vector-menu-content"> <ul class="vector-menu-content-list"><li id="pt-login" class="mw-list-item"><a href="/index.php?title=Special:UserLogin&returnto=Identifiers&returntoquery=diff%3Dnext%26oldid%3D55484" title="You are encouraged to log in; however, it is not mandatory [o]" accesskey="o"><span>Log in</span></a></li></ul> </div> </nav> <div id="left-navigation"> <nav id="p-namespaces" class="vector-menu mw-portlet mw-portlet-namespaces vector-menu-tabs vector-menu-tabs-legacy" aria-labelledby="p-namespaces-label" role="navigation" > <h3 id="p-namespaces-label" class="vector-menu-heading " > <span class="vector-menu-heading-label">Namespaces</span> </h3> <div class="vector-menu-content"> <ul class="vector-menu-content-list"><li id="ca-nstab-main" class="selected mw-list-item"><a href="/Identifiers" title="View the content page [c]" accesskey="c"><span>Page</span></a></li><li id="ca-talk" class="new mw-list-item"><a href="/index.php?title=Talk:Identifiers&action=edit&redlink=1" rel="discussion" title="Discussion about the content page (page does not exist) [t]" accesskey="t"><span>Discussion</span></a></li></ul> </div> </nav> <nav id="p-variants" class="vector-menu mw-portlet mw-portlet-variants emptyPortlet vector-menu-dropdown" aria-labelledby="p-variants-label" role="navigation" > <input type="checkbox" id="p-variants-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-p-variants" class="vector-menu-checkbox" aria-labelledby="p-variants-label" /> <label id="p-variants-label" aria-label="Change language variant" class="vector-menu-heading " > <span class="vector-menu-heading-label">English</span> </label> <div class="vector-menu-content"> <ul class="vector-menu-content-list"></ul> </div> </nav> </div> <div id="right-navigation"> <nav id="p-views" class="vector-menu mw-portlet mw-portlet-views vector-menu-tabs vector-menu-tabs-legacy" aria-labelledby="p-views-label" role="navigation" > <h3 id="p-views-label" class="vector-menu-heading " > <span class="vector-menu-heading-label">Views</span> </h3> <div class="vector-menu-content"> <ul class="vector-menu-content-list"><li id="ca-view" class="selected mw-list-item"><a href="/Identifiers"><span>Read</span></a></li><li id="ca-viewsource" class="mw-list-item"><a href="/index.php?title=Identifiers&action=edit&oldid=55485" title="This page is protected.
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