title: EMAGE mouse embryo spatial gene expression database: 2010 update.
abstract: EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Here, we describe recent enhancements to EMAGE including: the release of a completely re-designed website, which offers integration of many different search functions in HTML web pages, improved user feedback and the ability to find similar expression patterns at the click of a button; back-end refactoring from an object oriented to relational architecture, allowing associated SQL access; and the provision of further access by standard formatted URLs and a Java API. We have also increased data coverage by sourcing from a greater selection of journals and developed automated methods for spatial data annotation that are being applied to spatially incorporate the genome-wide (approximately 19,000 gene) 'EURExpress' dataset into EMAGE.
authors.affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh EH4 2XU, UK.
authors.forename: Lorna
authors.initials: L
authors.lastname: Richardson
authors.forename: Shanmugasundaram
authors.initials: S
authors.lastname: Venkataraman
authors.forename: Peter
authors.initials: P
authors.lastname: Stevenson
authors.forename: Yiya
authors.initials: Y
authors.lastname: Yang
authors.forename: Nicholas
authors.initials: N
authors.lastname: Burton
authors.forename: Jianguo
authors.initials: J
authors.lastname: Rao
authors.forename: Malcolm
authors.initials: M
authors.lastname: Fisher
authors.forename: Richard A
authors.initials: RA
authors.lastname: Baldock
authors.forename: Duncan R
authors.initials: DR
authors.lastname: Davidson
authors.forename: Jeffrey H
authors.initials: JH
authors.lastname: Christiansen
mesh_terms: D022126:Access to Information; D000818:Animals; D001331:Automation; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D047108:Embryonic Development / Q000235:genetics; D015870:Gene Expression; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D051379:Mice; D011381:Programming Languages; D012984:Software