In the past years the increasing usage of electronic publication has led to an enormous growth of databases and repositories containing articles relevant to scientifically different domains. Of these databases, the electronically available database PubMed [Putnam, 1998] has emerged as the most relevant one for the biomedical community. As of today, PubMed consists of more than 20 million abstra...

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be s...

Today, the need to deal with ambiguous information in semantic web languages is increasing. Ontology is an important part of the W3C standards for the semantic web, used to define a conceptual standard vocabulary for the exchange of data between systems, the provision of reusable databases, and the facilitation of collaboration across multiple systems. However, classical ontology is not enough ...

The concept of a gene was established in the era of classical genetics and is now essential for life science for elucidating the molecular basis of the coding of genetic information necessary to realize the body of an organism and its biological functions. However, an ontology fully representing multiple aspects of a gene is still not available. In this study, we dissected the biological and on...

SUMMARY Despite the importance of using the semantic distance to improve the performance of conventional expression-based clustering, there are few freely available software that provides a clustering algorithm using the ontology-based semantic distances as prior knowledge. Here, we present the SICAGO (SemI-supervised Cluster Analysis using semantic distance between gene pairs in Gene Ontology)...

The Gene Ontology Categorizer, developed jointly by the Los Alamos National Laboratory and Procter & Gamble Corp., provides a capability for the categorization task in the Gene Ontology (GO): given a list of genes of interest, what are the best nodes of the GO to summarize or categorize that list? The motivating question is from a drug discovery process, where after some gene expression analysi...

Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that describe gene function and that can be used to summarize the results of the genome-scale experiments. However, making sense of such GO enrichment analyses may be ch...