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EMAGE mouse embryo spatial gene expression database: 2010 update
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 dev...
Autores principales: | , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808994/ https://www.ncbi.nlm.nih.gov/pubmed/19767607 http://dx.doi.org/10.1093/nar/gkp763 |
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author | Richardson, Lorna Venkataraman, Shanmugasundaram Stevenson, Peter Yang, Yiya Burton, Nicholas Rao, Jianguo Fisher, Malcolm Baldock, Richard A. Davidson, Duncan R. Christiansen, Jeffrey H. |
author_facet | Richardson, Lorna Venkataraman, Shanmugasundaram Stevenson, Peter Yang, Yiya Burton, Nicholas Rao, Jianguo Fisher, Malcolm Baldock, Richard A. Davidson, Duncan R. Christiansen, Jeffrey H. |
author_sort | Richardson, Lorna |
collection | PubMed |
description | 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 (∼19 000 gene) ‘EURExpress’ dataset into EMAGE. |
format | Text |
id | pubmed-2808994 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-28089942010-01-20 EMAGE mouse embryo spatial gene expression database: 2010 update Richardson, Lorna Venkataraman, Shanmugasundaram Stevenson, Peter Yang, Yiya Burton, Nicholas Rao, Jianguo Fisher, Malcolm Baldock, Richard A. Davidson, Duncan R. Christiansen, Jeffrey H. Nucleic Acids Res Articles 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 (∼19 000 gene) ‘EURExpress’ dataset into EMAGE. Oxford University Press 2010-01 2009-09-18 /pmc/articles/PMC2808994/ /pubmed/19767607 http://dx.doi.org/10.1093/nar/gkp763 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Richardson, Lorna Venkataraman, Shanmugasundaram Stevenson, Peter Yang, Yiya Burton, Nicholas Rao, Jianguo Fisher, Malcolm Baldock, Richard A. Davidson, Duncan R. Christiansen, Jeffrey H. EMAGE mouse embryo spatial gene expression database: 2010 update |
title | EMAGE mouse embryo spatial gene expression database: 2010 update |
title_full | EMAGE mouse embryo spatial gene expression database: 2010 update |
title_fullStr | EMAGE mouse embryo spatial gene expression database: 2010 update |
title_full_unstemmed | EMAGE mouse embryo spatial gene expression database: 2010 update |
title_short | EMAGE mouse embryo spatial gene expression database: 2010 update |
title_sort | emage mouse embryo spatial gene expression database: 2010 update |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808994/ https://www.ncbi.nlm.nih.gov/pubmed/19767607 http://dx.doi.org/10.1093/nar/gkp763 |
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