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eMouseAtlas informatics: embryo atlas and gene expression database
A significant proportion of developmental biology data is presented in the form of images at morphologically diverse stages of development. The curation of these datasets presents different challenges to that of sequence/text-based data. Towards this end, the eMouseAtlas project created a digital at...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer US
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602050/ https://www.ncbi.nlm.nih.gov/pubmed/26296321 http://dx.doi.org/10.1007/s00335-015-9596-5 |
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author | Armit, Chris Richardson, Lorna Hill, Bill Yang, Yiya Baldock, Richard A. |
author_facet | Armit, Chris Richardson, Lorna Hill, Bill Yang, Yiya Baldock, Richard A. |
author_sort | Armit, Chris |
collection | PubMed |
description | A significant proportion of developmental biology data is presented in the form of images at morphologically diverse stages of development. The curation of these datasets presents different challenges to that of sequence/text-based data. Towards this end, the eMouseAtlas project created a digital atlas of mouse embryo development as a means of understanding developmental anatomy and exploring the relationship between genes and development in a spatial context. Using the morphological staging system pioneered by Karl Theiler, the project has generated 3D models of post-implantation mouse development and used them as a spatial framework for the delineation of anatomical components and for archiving in situ gene expression data in the EMAGE database. This has allowed us to develop a unique online resource for mouse developmental biology. We describe here the underlying structure of the resource, as well as some of the tools that have been developed to allow users to mine the curated image data. These tools include our IIP3D/X3DOM viewer that allows 3D visualisation of anatomy and/or gene expression in the context of a web browser, and the eHistology resource that extends this functionality to allow visualisation of high-resolution cellular level images of histology sections. Furthermore, we review some of the informatics aspects of eMouseAtlas to provide a deeper insight into the use of the atlas and gene expression database. |
format | Online Article Text |
id | pubmed-4602050 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Springer US |
record_format | MEDLINE/PubMed |
spelling | pubmed-46020502015-10-16 eMouseAtlas informatics: embryo atlas and gene expression database Armit, Chris Richardson, Lorna Hill, Bill Yang, Yiya Baldock, Richard A. Mamm Genome Article A significant proportion of developmental biology data is presented in the form of images at morphologically diverse stages of development. The curation of these datasets presents different challenges to that of sequence/text-based data. Towards this end, the eMouseAtlas project created a digital atlas of mouse embryo development as a means of understanding developmental anatomy and exploring the relationship between genes and development in a spatial context. Using the morphological staging system pioneered by Karl Theiler, the project has generated 3D models of post-implantation mouse development and used them as a spatial framework for the delineation of anatomical components and for archiving in situ gene expression data in the EMAGE database. This has allowed us to develop a unique online resource for mouse developmental biology. We describe here the underlying structure of the resource, as well as some of the tools that have been developed to allow users to mine the curated image data. These tools include our IIP3D/X3DOM viewer that allows 3D visualisation of anatomy and/or gene expression in the context of a web browser, and the eHistology resource that extends this functionality to allow visualisation of high-resolution cellular level images of histology sections. Furthermore, we review some of the informatics aspects of eMouseAtlas to provide a deeper insight into the use of the atlas and gene expression database. Springer US 2015-08-22 2015 /pmc/articles/PMC4602050/ /pubmed/26296321 http://dx.doi.org/10.1007/s00335-015-9596-5 Text en © The Author(s) 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Article Armit, Chris Richardson, Lorna Hill, Bill Yang, Yiya Baldock, Richard A. eMouseAtlas informatics: embryo atlas and gene expression database |
title | eMouseAtlas informatics: embryo atlas and gene expression database |
title_full | eMouseAtlas informatics: embryo atlas and gene expression database |
title_fullStr | eMouseAtlas informatics: embryo atlas and gene expression database |
title_full_unstemmed | eMouseAtlas informatics: embryo atlas and gene expression database |
title_short | eMouseAtlas informatics: embryo atlas and gene expression database |
title_sort | emouseatlas informatics: embryo atlas and gene expression database |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602050/ https://www.ncbi.nlm.nih.gov/pubmed/26296321 http://dx.doi.org/10.1007/s00335-015-9596-5 |
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