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Identifiers - GO Wiki

<!DOCTYPE html> <html class="client-nojs" lang="en" dir="ltr"> <head> <meta charset="UTF-8"/> <title>Identifiers - 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":"Z0OEBbZYCFUBeuY1tjGrBAAAC9U","wgCSPNonce":false,"wgCanonicalNamespace":"","wgCanonicalSpecialPageName":false,"wgNamespaceNumber":0,"wgPageName":"Identifiers","wgTitle":"Identifiers","wgCurRevisionId":82577,"wgRevisionId":82577,"wgArticleId":4447,"wgIsArticle":true,"wgIsRedirect":false,"wgAction":"view","wgUserName":null,"wgUserGroups":["*"],"wgCategories":["Annotation"],"wgPageContentLanguage":"en","wgPageContentModel":"wikitext","wgRelevantPageName":"Identifiers","wgRelevantArticleId":4447,"wgIsProbablyEditable":false,"wgRelevantPageIsProbablyEditable":false,"wgRestrictionEdit":[],"wgRestrictionMove":[],"wgVector2022PreviewPages":[]};RLSTATE={"site.styles":"ready", "user.styles":"ready","user":"ready","user.options":"loading","skins.vector.styles.legacy":"ready"};RLPAGEMODULES=["site","mediawiki.page.ready","mediawiki.toc","skins.vector.legacy.js"];</script> <script>(RLQ=window.RLQ||[]).push(function(){mw.loader.implement("user.options@12s5i",function($,jQuery,require,module){mw.user.tokens.set({"patrolToken":"+\\","watchToken":"+\\","csrfToken":"+\\"});});});</script> <link rel="stylesheet" href="/load.php?lang=en&amp;modules=skins.vector.styles.legacy&amp;only=styles&amp;skin=vector"/> <script async="" src="/load.php?lang=en&amp;modules=startup&amp;only=scripts&amp;raw=1&amp;skin=vector"></script> <meta name="ResourceLoaderDynamicStyles" content=""/> <link rel="stylesheet" href="/load.php?lang=en&amp;modules=site.styles&amp;only=styles&amp;skin=vector"/> <meta name="generator" content="MediaWiki 1.40.0"/> <meta name="robots" content="max-image-preview:standard"/> <meta name="format-detection" content="telephone=no"/> <meta name="viewport" content="width=1000"/> <link rel="icon" href="/favicon.ico"/> <link rel="search" type="application/opensearchdescription+xml" href="/opensearch_desc.php" title="GO Wiki (en)"/> <link rel="EditURI" type="application/rsd+xml" href="https://wiki.geneontology.org/api.php?action=rsd"/> <link rel="alternate" type="application/atom+xml" title="GO Wiki Atom feed" href="/index.php?title=Special:RecentChanges&amp;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> <h1 id="firstHeading" class="firstHeading mw-first-heading"><span class="mw-page-title-main">Identifiers</span></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"><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> <ul><li>Prefixes (aka Database): Each prefix must be registered in the GO xrefs registry metadata yaml file (see below). 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/authority. The characters must all be printable ascii characters, excluding spaces.</li></ul> <p>We use the term 'identifier' as synonymous with GlobalID, although confusingly some use 'identifier' to refer to what we call LocalID. Our concept of GlobalID corresponds with the W3C standard for CURIEs, see below </p><p><br /> </p> <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="#Identifiers,_CURIES_and_URIs"><span class="tocnumber">4</span> <span class="toctext">Identifiers, CURIES and URIs</span></a></li> <li class="toclevel-1 tocsection-5"><a href="#Problems_with_existing_usage"><span class="tocnumber">5</span> <span class="toctext">Problems with existing usage</span></a> <ul> <li class="toclevel-2 tocsection-6"><a href="#MGI_and_prefix_doubling"><span class="tocnumber">5.1</span> <span class="toctext">MGI and prefix doubling</span></a></li> <li class="toclevel-2 tocsection-7"><a href="#FlyBase_vs_FB"><span class="tocnumber">5.2</span> <span class="toctext">FlyBase vs FB</span></a></li> </ul> </li> <li class="toclevel-1 tocsection-8"><a href="#See_Also"><span class="tocnumber">6</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> <li>FlyBase:FBgn0011293 <ul><li>Database=FlyBase LocalID=FBgn0011293</li></ul></li></ul> <h2><span class="mw-headline" id="Identifiers_in_GAFs">Identifiers in GAFs</span></h2> <p><i>IMPORTANT NOTE ON THE GAF FORMAT</i> </p><p>In the gene association (GAF) files, the global ID is split across two column: 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><p>Note that in GPAD and GPI formats, a single column with GlobalID is used </p> <h2><span class="mw-headline" id="Prefix_Registry">Prefix Registry</span></h2> <p>The Database <b>should</b> be registered in db-xrefs.yaml, available here: </p> <ul><li><a rel="nofollow" class="external free" href="https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml">https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml</a></li> <li><a rel="nofollow" class="external free" href="http://amigo.geneontology.org/xrefs">http://amigo.geneontology.org/xrefs</a></li></ul> <p>Our prefix registry is coordinated with identifiers.org and the prefixcommons project: <a rel="nofollow" class="external free" href="https://github.com/prefixcommons/biocontext">https://github.com/prefixcommons/biocontext</a> </p> <h2><span id="Identifiers.2C_CURIES_and_URIs"></span><span class="mw-headline" id="Identifiers,_CURIES_and_URIs">Identifiers, CURIES and URIs</span></h2> <p>The GO uses semantic web standards such as OWL and RDF. In these standards, URIs are used to uniquely identify ontology terms, genes and associated provenance entities such as publications. </p><p>In order to reconcile URIs with the identifier scheme used in formats such as obo, GAF, and how we display identifiers in publications and portals such as AmiGO, we conceive of GlobalIDs as *Compact URIs* (CURIES). </p> <ul><li><a rel="nofollow" class="external free" href="https://en.wikipedia.org/wiki/CURIE">https://en.wikipedia.org/wiki/CURIE</a></li> <li><a rel="nofollow" class="external free" href="http://www.w3.org/TR/curie/">http://www.w3.org/TR/curie/</a></li></ul> <p>We assume a constant set of prefixes. For all ontologies used in GO, we assume that these have an OBO library PURL URI, so we have an implicit set of prefix declarations: </p> <pre> @prefix GO: <a rel="nofollow" class="external free" href="http://purl.obolibrary.org/obo/GO_">http://purl.obolibrary.org/obo/GO_</a> @prefix CL: <a rel="nofollow" class="external free" href="http://purl.obolibrary.org/obo/CL_">http://purl.obolibrary.org/obo/CL_</a> @prefix CHEBI: <a rel="nofollow" class="external free" href="http://purl.obolibrary.org/obo/CHEBI_">http://purl.obolibrary.org/obo/CHEBI_</a> </pre> <h2><span class="mw-headline" id="Problems_with_existing_usage">Problems with existing usage</span></h2> <p>The term "identifier" is used in different ways which causes confusion. Our concept of GlobalID corresponds with W3C CURIEs and should be unambiguous. </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 composes 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 (but this seems to have changed) </p><p>recommendation: </p><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> <p><br /> </p> <h3><span class="mw-headline" id="FlyBase_vs_FB">FlyBase vs FB</span></h3> <p>In GO in our registry, FB is the canonical prefix, and FlyBase is included as a synonym. As of May 23, 2022: </p> <ul><li>identifers.org uses "FB"</li> <li>Bioregistry uses "FlyBase"</li> <li>NCBI uses "FLYBASE"</li></ul> <h2><span class="mw-headline" id="See_Also">See Also</span></h2> <p><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490878/pdf/pbio.2001414.pdf">McMurry et al 2017, Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data</a> </p> <!-- NewPP limit report Cached time: 20241124154749 Cache expiry: 86400 Reduced expiry: false Complications: [show鈥恡oc, no鈥恡oc鈥恈onversion] CPU time usage: 0.007 seconds Real time usage: 0.007 seconds Preprocessor visited node count: 25/1000000 Post鈥恊xpand include size: 0/2097152 bytes Template argument size: 0/2097152 bytes Highest expansion depth: 2/100 Expensive parser function count: 0/100 Unstrip recursion depth: 0/20 Unstrip post鈥恊xpand size: 0/5000000 bytes --> <!-- Transclusion expansion time report (%,ms,calls,template) 100.00% 0.000 1 -total --> <!-- Saved in parser cache with key geneontology_mediawiki:pcache:idhash:4447-0!canonical and timestamp 20241124154749 and revision id 82577. 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