A method for increasing expressivity of Gene Ontology annotations using a compositional approach

BMC Bioinformatics

Rachael P Huntley³  Midori A Harris⁶  Yasmin Alam-Faruque³  Judith A Blake⁴  Seth Carbon²  Heiko Dietze²  Emily C Dimmer³  Rebecca E Foulger³  David P Hill⁴  Varsha K Khodiyar¹  Antonia Lock⁶  Jane Lomax³  Ruth C Lovering¹  Prudence Mutowo-Meullenet³  Tony Sawford³  Kimberly Van Auken⁵  Valerie Wood⁶  Christopher J Mungall² 

[1] Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK

[2] Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 94720, USA

[3] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

[4] The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA

[5] California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125, USA

[6] Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK

关键词: Manual curation;    Annotation extension;    Functional annotation;    Gene Ontology;   

Others  :  818542
DOI  :  10.1186/1471-2105-15-155

 received in 2014-03-04, accepted in 2014-05-15,  发布年份 2014

【 摘 要 】

Background

The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational analyses for interpretation of high-throughput experimental and clinical data. The core data structure is the annotation, an association between a gene product and a term from one of the three ontologies comprising the GO. Historically, it has not been possible to provide additional information about the context of a GO term, such as the target gene or the location of a molecular function. This has limited the specificity of knowledge that can be expressed by GO annotations.

Results

The GO Consortium has introduced annotation extensions that enable manually curated GO annotations to capture additional contextual details. Extensions represent effector–target relationships such as localization dependencies, substrates of protein modifiers and regulation targets of signaling pathways and transcription factors as well as spatial and temporal aspects of processes such as cell or tissue type or developmental stage. We describe the content and structure of annotation extensions, provide examples, and summarize the current usage of annotation extensions.

Conclusions

The additional contextual information captured by annotation extensions improves the utility of functional annotation by representing dependencies between annotations to terms in the different ontologies of GO, external ontologies, or an organism’s gene products. These enhanced annotations can also support sophisticated queries and reasoning, and will provide curated, directional links between many gene products to support pathway and network reconstruction.

【 授权许可】

   
2014 Huntley et al.; licensee BioMed Central Ltd.

【 图 表 】

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