Advances in high-throughput experimental techniques in the past decade have enabled the explosive increase of omics data, while effective organization, interpretation, and exchange of these data require standard and controlled vocabularies in the domain of biological and biomedical studies. Ontologies, as abstract description systems for domain-specific knowledge composition, hence receive more and more attention in computational biology and bioinformatics. Particularly, many applications relying on domain ontologies require quantitative measures of relationships between terms in the ontologies, making it indispensable to develop computational methods for the derivation of ontology-based semantic similarity between terms. Nevertheless, with a variety of methods available, how to choose a suitable method for a specific application becomes a problem. With this understanding, we review a majority of existing methods that rely on ontologies to calculate semantic similarity between terms. We classify existing methods into five categories: methods based on semantic distance, methods based on information content, methods based on properties of terms, methods based on ontology hierarchy, and hybrid methods. We summarize characteristics of each category, with emphasis on basic notions, advantages and disadvantages of these methods. Further, we extend our review to software tools implementing these methods and applications using these methods.

MotivationThe inference of genes that are truly associated with inherited human diseases from a set of candidates resulting from genetic linkage studies has been one of the most challenging tasks in human genetics. Although several computational approaches have been proposed to prioritize candidate genes relying on protein-protein interaction (PPI) networks, these methods can usually cover less than half of known human genes.ResultsWe propose to rely on the biological process domain of the gene ontology to construct a gene semantic similarity network and then use the network to infer disease genes. We show that the constructed network covers about 50% more genes than a typical PPI network. By analyzing the gene semantic similarity network with the PPI network, we show that gene pairs tend to have higher semantic similarity scores if the corresponding proteins are closer to each other in the PPI network. By analyzing the gene semantic similarity network with a phenotype similarity network, we show that semantic similarity scores of genes associated with similar diseases are significantly different from those of genes selected at random, and that genes with higher semantic similarity scores tend to be associated with diseases with higher phenotype similarity scores. We further use the gene semantic similarity network with a random walk with restart model to infer disease genes. Through a series of large-scale leave-one-out cross-validation experiments, we show that the gene semantic similarity network can achieve not only higher coverage but also higher accuracy than the PPI network in the inference of disease genes.Contactruijiang@tsinghua.edu.cn

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Personalized recommender systems have been receiving more and more attention in addressing the serious problem of information overload accompanying the rapid evolution of the world-wide-web. Although traditional collaborative filtering approaches based on similarities between users have achieved remarkable success, it has been shown that the existence of popular objects may adversely influence the correct scoring of candidate objects, which lead to unreasonable recommendation results. Meanwhile, recent advances have demonstrated that approaches based on diffusion and random walk processes exhibit superior performance over collaborative filtering methods in both the recommendation accuracy and diversity. Building on these results, we adopt three strategies (power-law adjustment, nearest neighbor, and threshold filtration) to adjust a user similarity network from user similarity scores calculated on historical data, and then propose a random walk with restart model on the constructed network to achieve personalized recommendations. We perform cross-validation experiments on two real data sets (MovieLens and Netflix) and compare the performance of our method against the existing state-of-the-art methods. Results show that our method outperforms existing methods in not only recommendation accuracy and diversity, but also retrieval performance.