Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database

Mounia Belmamoune, Fons J Verbeek
<span title="2008-08-25">2008</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
The Gene Expression Management System (GEMS) is a database system for patterns of gene expression. These patterns result from systematic whole-mount fluorescent in situ hybridization studies on zebrafish embryos. GEMS is an integrative platform that addresses one of the important challenges of developmental biology: how to integrate genetic data that underpin morphological changes during embryogenesis. Our motivation to build this system was by the need to be able to organize and compare
more &raquo; ... e patterns of gene expression at tissue level. Integration with other developmental and biomolecular databases will further support our understanding of development. The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS. The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term. These terms are extracted from a formal anatomical ontology, i.e. the Developmental Anatomy Ontology of Zebrafish (DAOZ). In the GEMS, anatomical terms from this ontology together with terms from the Gene Ontology (GO) are also used to annotate patterns of gene expression and in this manner providing mechanisms for integration and retrieval. The annotations are the glue for integration of patterns of gene expression in GEMS as well as in other biomolecular databases. At the one hand, zebrafish anatomy terminology allows gene expression data within GEMS to be integrated with phenotypical data in the 3D atlas of zebrafish development. At the other hand, GO terms extend GEMS expression patterns integration to a wide range of bioinformatics resources.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.2390/biecoll-jib-2008-92</a> <a target="_blank" rel="external noopener" href="">pmid:20134060</a> <a target="_blank" rel="external noopener" href="">fatcat:aeyoeaovafattonwa6hhestwb4</a> </span>
<a target="_blank" rel="noopener" href="" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href=""> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / </button> </a>