| In this work we describe the development and evaluation of the BioMiner system for protein functional annotation. BioMiner is the implementation of a novel uncertainty model for annotation and is based on the Uncertainty in Information Integration (UII) system, a general-purpose data integration system with extended functionality to handle uncertainty in data. The informatics contributions of our work are as follows: (1) we develop and implement a first-in-class uncertainty model for annotation and illustrate the validity of the model, (2) we show that the uncertainty model is reliable by evaluating its robustness through a principled methodology, and (3) we demonstrate that the uncertainty model performs better that existing, commonly utilized, approaches through a rigorous performance evaluation. The application of BioMiner also contributes to the expansion of domain knowledge by accurately identifying functions for proteins of unknown function, a problem of utmost importance to biology. |
