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: //www.ncbi.nlm.nih.gov/geo/. 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:

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.