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… (More)
MOTIVATION The Edinburgh Mouse Atlas and Gene Expression Database project has developed a digital atlas of mouse development to provide a spatio-temporal framework for spatially mapped data such as in situ gene expression and cell lineage. As part of this database, a mouse embryo anatomy ontology has been created. A formalization of this anatomy is required… (More)
The structured description of mutant phenotypes presents a major conceptual and practical problem. A general model for generating mouse phenotype ontologies that involves combing a variety of different ontologies to better link and describe phenotypes is presented. This model is based on the Phenotype and Trait Ontology schema proposal and incorporates… (More)
This paper provides a simple introduction to the reconstructions and data-handling tools stored on the Edinburgh Mouse Atlas CD, together with some of the ways in which the viewers and software can be used to understand mouse development and analyse data. The key aspect of the Mouse Atlas is that the underlying models are a complete representation of the… (More)
The Edinburgh Mouse Atlas Project (EMAP) has developed a digital atlas of mouse development which provides a bioinformatics framework to spatially reference biological data. The EMAP core database contains 3D grey-level reconstructions of the mouse embryo at various stages of development , a systematic nomenclature of the embryo anatomy, and defined 3D… (More)
We describe our use of an existing resource , the Mouse Anatomical Nomenclature , to improve a symbolic interface to anatomically-indexed gene expression data. The goal is to reduce user effort in specifying anatomical structures of interest and increase precision and recall.
Ontologies have increasingly been used in the representation of a variety of biological data. The major alternative ontologies available for mouse phenotype description are the MPO (Mammalian Phenotype Ontology) and PaTO (Phenotype and Trait Ontology). Ontologies have the potential of contributing to the analysis of mutant phenotypes by providing a… (More)
The molecular biology literature is believed to contain a wealth of information that has not yet made it into any structured database. Of particular current interest is information about genetic pathways, and there are many ongoing studies into automatically extracting such pathways from the molecular biology literature. In the area of development ,… (More)