title: EMAP and EMAGE: a framework for understanding spatially organized data.
abstract: The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.
authors.affiliation: MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK. Richard.Baldock@hgu.mrc.ac.uk
authors.forename: Richard A
authors.initials: RA
authors.lastname: Baldock
authors.forename: Jonathan B L
authors.initials: JB
authors.lastname: Bard
authors.forename: Albert
authors.initials: A
authors.lastname: Burger
authors.forename: Nicolas
authors.initials: N
authors.lastname: Burton
authors.forename: Jeff
authors.initials: J
authors.lastname: Christiansen
authors.forename: Guanjie
authors.initials: G
authors.lastname: Feng
authors.forename: Bill
authors.initials: B
authors.lastname: Hill
authors.forename: Derek
authors.initials: D
authors.lastname: Houghton
authors.forename: Matthew
authors.initials: M
authors.lastname: Kaufman
authors.forename: Jianguo
authors.initials: J
authors.lastname: Rao
authors.forename: James
authors.initials: J
authors.lastname: Sharpe
authors.forename: Allyson
authors.initials: A
authors.lastname: Ross
authors.forename: Peter
authors.initials: P
authors.lastname: Stevenson
authors.forename: Shanmugasundaram
authors.initials: S
authors.lastname: Venkataraman
authors.forename: Andrew
authors.initials: A
authors.lastname: Waterhouse
authors.forename: Yiya
authors.initials: Y
authors.lastname: Yang
authors.forename: Duncan R
authors.initials: DR
authors.lastname: Davidson
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D019295:Computational Biology; D003196:Computer Graphics; D016208:Databases, Factual; D004622:Embryo, Mammalian; D015870:Gene Expression; D007091:Image Processing, Computer-Assisted; D016247:Information Storage and Retrieval; D051379:Mice; D008953:Models, Anatomic; D009862:Online Systems; D011381:Programming Languages