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2006 MARCH–APRIL; 349
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<div class="actions">March 27, 2006 <span class="status">[posted]</span>
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<h1>GEO Accession Numbers in MEDLINE<span class="registered">®</span></h1>
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<img src="../new_tb_graphics/a.gif" class="initcap" alt=""
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width="35" height="43" />
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<p class="first">
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<span class="initcap">a</span>
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ccession numbers for a new database, the Gene Expression Omnibus (GEO), are now being added to MEDLINE records when a journal article reports that new data has been added to this database. GEO is a "gene expression/molecular abundance repository supporting Minimum Information About Microarray Experiment (MIAME) compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval." Additional information is available at: <a href="//www.ncbi.nlm.nih.gov/geo/">//www.ncbi.nlm.nih.gov/geo/</a>. GEO was developed and is maintained by the National Center for Biotechnology (NCBI). It consists of three different types of entries: Platform, Sample, and Series. The Platform record contains lists of elements on an array (such as a oligonucleotide microarray) or a list of elements that may be detected or quantified in the experiment. The Sample record is a description of the handling of a Sample. The Series record defines a set of related Samples.
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</p>
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<p>
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GEO accession numbers have a standard format which consists of one of four prefixes followed by one or more numbers. The four prefixes are:
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</p>
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<br />
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<table width="191" border="0" cellpadding="2" cellspacing="0" summary="The four prefixes of GEO accession numbers followed by one or more numbers. ">
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<tr>
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<td width="53">GDS</td>
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<td width="263">(for GEO Data Set)</td>
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</tr>
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<tr>
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<td>GSE</td>
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<td>(for GEO SEries)</td>
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</tr>
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<tr>
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<td>GPL</td>
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<td>(for GEO PLatform)</td>
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</tr>
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<tr>
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<td>GSM</td>
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<td>(for GEO SaMple)</td>
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</tr>
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</table>
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<br />
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<br />
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<p>
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GEO accession numbers will display in the Secondary Source Identifier (SI) field in PubMed's Citation and MEDLINE display formats (and in the <DataBankList> area of the XML format). Here's an example from the Citation display:
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</p>
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<dl>
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<dd>
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Secondary Source ID:
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<ul>
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<li>GEO/GSE3847</li>
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</ul>
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</dd>
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</dl>
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<p>
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GEO numbers may be searched in PubMed using the [si] search tag in the following ways:
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</p>
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<ol>
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<li>To retrieve a specific accession number:<br />
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geo/gse3847 [si]<br />
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or, more simply, as:<br />
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gse3847 [si] <br /> </li>
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<li>To retrieve all GEO accession numbers:<br />
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geo [si]
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</li>
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<li>
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Click on the search link in the Citation Display.
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</li>
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</ol>
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<br /><br />
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<p>
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NLM<span class="registered">®</span> began to include GEO accession numbers in citations that have undergone data quality review afer February 8, 2006.
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</p>
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<p class="authors">
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By
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Melissa Yorks<br />
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Index Section<br />
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<!--************************CHANGE CITATION INFORMATION BELOW*****************************-->
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<p class="citation">Yorks M. GEO Accession Numbers in MEDLINE<span class="registered">®</span>. NLM Tech Bull. 2006 Mar-Apr;(349):e5. </p>
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