aigo towards a unified framework for the analysis and the inter-comparison of go functional annotations爱国者对一个统一的分析框架,进行功能注释.pdfVIP

Defoin-Platel et al. BMC Bioinformatics 2011, 12:431 /1471-2105/12/431 METHODOLOGY ARTICLE Open Access AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations 2* 1,3 3 3 2 Michael Defoin-Platel , Matthew M Hindle , Artem Lysenko , Stephen J Powers , Dimah Z Habash , Christopher J Rawlings2 and Mansoor Saqi2 Abstract Background: In response to the rapid growth of available genome sequences, efforts have been made to develop automatic inference methods to functionally characterize them. Pipelines that infer functional annotation are now routinely used to produce new annotations at a genome scale and for a broad variety of species. These pipelines differ widely in their inference algorithms, confidence thresholds and data sources for reasoning. This heterogeneity makes a comparison of the relative merits of each approach extremely complex. The evaluation of the quality of the resultant annotations is also challenging given there is often no existing gold-standard against which to evaluate precision and recall. Results: In this paper, we present a pragmatic approach to the study of functional annotations. An ensemble of 12 metrics, describing various aspects of functional annotations, is defined and implemented in a unified framework, which facilitates their systematic analysis and inter-comparison. The use of this framework is demonstrated on three illustrative examples: analysing the outputs of state-of-the-art inference pipelines, comparing electronic versus manual annotation methods, and monitoring the evolution of publicly available functional annotations. The framework is part of the AIGO library (/p/aigo) for the Analysis and the Inter-compari