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2006 MARCH–APRIL; 349
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March 27, 2006 [posted]

GEO Accession Numbers in MEDLINE®

a 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: // 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.

GEO accession numbers have a standard format which consists of one of four prefixes followed by one or more numbers. The four prefixes are:

GDS (for GEO Data Set)
GSE (for GEO SEries)
GPL (for GEO PLatform)
GSM (for GEO SaMple)

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:

Secondary Source ID:
  • GEO/GSE3847

GEO numbers may be searched in PubMed using the [si] search tag in the following ways:

  1. To retrieve a specific accession number:
    geo/gse3847 [si]
    or, more simply, as:
    gse3847 [si]
  2. To retrieve all GEO accession numbers:
    geo [si]
  3. Click on the search link in the Citation Display.

NLM® began to include GEO accession numbers in citations that have undergone data quality review afer February 8, 2006.

By Melissa Yorks
Index Section

Yorks M. GEO Accession Numbers in MEDLINE®. NLM Tech Bull. 2006 Mar-Apr;(349):e5.

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