Gultekin Ozsoyoglu

Learn More
In this paper, we discuss the properties of biological data and challenges it poses for data management, and argue that, in order to meet the data management requirements for 'digital biology', careful integration of the existing technologies and the development of new data management techniques for biological data are needed. Based on this premise, we(More)
BACKGROUND Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment(More)
VISUAL is a graphical query language designed for scientific databases. VISUAL is icon-based and is suitable for domains where visualization of the relationships are important for the domain scientist to express queries. Graphical objects are not tied to the underlying formalism; instead, they represent the relationships of the application domain. VISUAL(More)
BACKGROUND Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the(More)
Integration of metabolic pathways resources and metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation of metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic(More)
Metabolomics is a relatively new "omics" platform, which analyzes a discrete set of metabolites detected in bio-fluids or tissue samples of organisms. It has been used in a diverse array of studies to detect biomarkers and to determine activity rates for pathways based on changes due to disease or drugs. Recent improvements in analytical methodology and(More)
BACKGROUND Kyoto Encyclopedia of Genes and Genomes (KEGG) is an online and integrated molecular database for several organisms. KEGG has been a highly useful site, helping domain scientists understand, research, study, and teach metabolisms by linking sequenced genomes to higher level systematic functions. KEGG databases are accessible through the web pages(More)
Electronic book is an application with a multimedia database of instructional resources, which include hyperlinked text, instructor's audio/video clips, slides, animation, still images, etc. as well as content-based information about these data, and metadata such as annotations, tags, and cross-referencing information. Electronic books in the Internet or on(More)
VISUAL is a graphical icon-based query language designed for scientific databases where visualization of the relationships are important for the domain scientist to express queries. Graphical objects are not tied to the underlying formalism; instead, they represent the relationships of the application domain. VISUAL supports relational, nested, and(More)
A metabolic network describes how different cellular processes (i.e., pathways) are connected and work together as part of a metabolism. The complexity of metabolisms and their working principles increase dramatically in higher order organisms (e.g., mammalians) in comparison to relatively lower level organisms (e.g., prokaryotes). As the complexity(More)