Automated Literature Mining for Validation of High-Throughput Function Prediction

描述（由申请人提供）：数以百万计的蛋白质的功能仍然未知，自动化蛋白质功能预测系统的性能记录很差。我们将通过一种新的自动化系统来验证基于计算生物学技术的高通量预测，从而测试关于蛋白质功能位点的假设，该系统将挖掘与这些预测相关的目标信息的文献。我们的工作的影响将是使大规模、有效的蛋白质功能注释成为可能，从而促进治疗疾病的药物发现的进展。

DESCRIPTION (provided by applicant): The function of millions of proteins remains unknown, and automated protein function prediction systems have a poor record of performance. We will test hypotheses about protein functional sites by validating high-throughput predictions derived from computational biology techniques through a novel automated system that will mine the literature for targeted information relevant to those predictions. The impact of our work will be to enable large-scale, validated, annotation of protein function and in turn to facilitate progress in tackling drug discovery for treatment of diseases. High-throughput experiments and bioinformatics techniques are creating an exploding volume of data with which we hope to transcribe the genetic blueprints of life. Targeted experiments are required to validate biomedical discoveries from these sources. Fortunately, the information to confirm or refute a prediction is often already available in an existing publication and the biologist can take advantage of this supporting evidence for validation. However, the sheer volume of predictions from high throughput methods exceeds the capacity of researchers to perform even the necessary literature searches. This gap in capacity must be addressed using automated literature mining methods that perform comparably to a human expert; indeed, development of such methods is a grand challenge of modern Biology. We will mine the full text literature to validate computational predictions of functional sites in proteins. The innovations in our approach include: (1) using computational predictions as the context for a literature search; (2) information extraction of protein functional sites from full text journal publications; (3) high-throughput text mining; and (4) using primary information in protein databases to evaluate the methods. Understanding of protein function is a critical bottleneck in the progress of biomedical research. It is time to truly integrate the biological literature into the protein function prediction problem. By doing so, we will enable a critical advance in high-throughput protein function prediction