e-Mouse Atlas Project Anatomy Ontology
Abbreviation: EMAP
Homepage http://www.emouseatlas.org/emap/ema/home.php
Countries that developed this resource European Union , United Kingdom , United States
Created in 1991
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: EMAP; e-Mouse Atlas Project Anatomy Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8jns8; Last edited: Dec. 16, 2019, 10:27 a.m.; Last accessed: Jun 02 2020 10:20 a.m.
Record updated: Dec. 12, 2019, 5 p.m. by The FAIRsharing Team.
| FAQ | http://www.emouseatlas.org/emap/help/faq ... |
| forum | http://www.emouseatlas.org/emap/communit ... |
| online documentation | Stage definition |
| online documentation | Stage criteria |
| online documentation | Movies |
Additional Information
| Contact | General Contact |
External Links
| Bioportal | http://bioportal.bioontology.org/ontologies/EMAP |
| OBO | http://obofoundry.org/ontology/emap.html |
No XSD schemas defined
Conditions of Use
Applies to: Data useData Access
| Browse | http://www.emouseatlas.org/emap/ema/home.php |
| Download | http://www.emouseatlas.org/emap/ema/theiler_stages/downloads/downloads ... |
EMAGE mouse embryo spatial gene expression database: 2014 update.
Richardson L,Venkataraman S,Stevenson P,Yang Y,Moss J,Graham L,Burton N,Hill B,Rao J,Baldock RA,Armit C
Nucleic Acids Res 2013
Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data.
Hayamizu TF,Baldock RA,Ringwald M
Mamm Genome 2015
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update.
Hayamizu TF,Wicks MN,Davidson DR,Burger A,Ringwald M,Baldock RA
J Biomed Semantics 2013
Formalization of mouse embryo anatomy.
Burger A,Davidson D,Baldock R
Bioinformatics 2004
An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature.
Bard JL,Kaufman MH,Dubreuil C,Brune RM,Burger A,Baldock RA,Davidson DR
Mech Dev 1998
View in BioPortal.
View in OBO Foundry.
Reporting Guidelines
No guidelines defined
Terminology Artifacts
Models and Formats
No syntax standards defined
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.
MouseMine @ MGI
A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system development.
MGI Mouse Gene Expression Database
The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development.
e-Mouse Atlas
The e-Mouse Atlas (EMA) is a detailed model of the developing mouse. Its purpose is not only to provide information about the shape, gross anatomy and detailed histological structure of the mouse, but also to provide a framework into which information about gene function can be mapped. The spatial, temporal and anatomical integration achieved by mapping diverse data to the organism itself rather than simply to database tables, allows powerful computational analyses. The website presents 3D volumetric models of the embryo linked, in most cases, to comprehensive and detailed images of histological structure. The embryo models and anatomy in EMA are organized by standard developmental stage (TS. after Theiler, 1989) and age of the embryo in days post coitum (dpc.). Gene-expression and other image data is also available.
e-Mouse Atlas of Gene Expression
EMAGE is a database of in situ gene expression data in the mouse embryo. mRNA in situ hybridisation, protein immunohistochemistry, in situ transgenic reporter data, and in situ enhancer data is included. These are sourced from the community and curators take this data and describe it in a standardised way that allows data query and exchange. The description includes a text-based component but the unique aspect of EMAGE is its spatial annotation focus.
OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
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Funds
Medical Research Council (MRC), London, UK (Government body)
National Institute of Child Health and Human Development (NICHD), Rockville, MD, USA (Government body)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), Bethesda, MA, USA
Grant Number(s)
DK092983 (National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), Bethesda, MA, USA)
HD062499 (National Institute of Child Health and Human Development (NICHD), Rockville, MD, USA)
U.1275.2.4.4.1 (Medical Research Council (MRC), London, UK)
