The Drosophila phenotype ontology

Journal of Biomedical Semantics

Georgios V Gkoutos¹  Nicholas H Brown⁴  Kathleen Falls³  Raymund Stefancsik²  Laura Ponting²  Peter A McQuilton²  Gillian H Millburn²  Steven J Marygold²  David Osumi-Sutherland² 

[1] Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK;FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK;The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA, USA;Gurdon Institute & Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge, UK

关键词: FlyBase;    Gene ontology;    OBO;    OWL;    Ontology;    Phenotype;    Drosophila;   

Others  :  806620
DOI  :  10.1186/2041-1480-4-30

 received in 2013-07-01, accepted in 2013-10-11,  发布年份 2013

【 摘 要 】

Background

Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype ontology (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions.

Results

We have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable.

Conclusions

The DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila community, which may ultimately result in its extension to cover a broader range of phenotypes.

【 授权许可】

   
2013 Osumi-Sutherland et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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