EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update

Journal of Biomedical Semantics

Richard A Baldock¹  Martin Ringwald²  Albert Burger³  Duncan R Davidson¹  Michael N Wicks¹  Terry F Hayamizu² 

[1] MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, UK;The Jackson Laboratory, Bar Harbor, USA;Department of Computer Science, Heriot-Watt University, Edinburgh, UK

关键词: OBO format;    Developmental anatomy;    Anatomy ontology;    Mouse development;   

Others  :  824717
DOI  :  10.1186/2041-1480-4-15

 received in 2013-06-21, accepted in 2013-08-19,  发布年份 2013

【 摘 要 】

Background

The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy provides a standard nomenclature for describing normal and mutant mouse embryo anatomy. The ontology forms the core of the EMAP atlas and is used for annotating gene expression data by the mouse Gene Expression Database (GXD), Edinburgh Mouse Atlas of Gene Expression (EMAGE) and other database resources.

Findings

The original EMAP ontology listed anatomical entities for each developmental stage separately, presented as uniparental graphs organized as a strict partonomy. An "abstract" (i.e. non-stage-specific) representation of mouse developmental anatomy has since been developed. In this version (EMAPA) all instances for a given anatomical entity are presented as a single term, together with the first and last stage at which it is considered to be present. Timed-component anatomies are now derived using staging information in the "primary" non-timed version. Anatomical entities are presented as a directed acyclic graph enabling multiple parental relationships. Subsumption classification as well as partonomic and other types of relationships can now be represented. Most concept names are unique, with compound names constructed using standardized nomenclature conventions, and alternative names associated as synonyms.

Conclusions

The ontology has been extended and refined in a collaborative effort between EMAP and GXD, with additional input from others. Efforts are also underway to improve the revision process with regards to updating and editorial control. The revised EMAPA ontology is freely available from the OBO Foundry resource, with descriptive information and other documentation presented in associated Wiki pages (http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page webcite).

【 授权许可】

   
2013 Hayamizu et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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