Abstract
In recent years, the broad utilization of high-throughput experimental techniques resulted in a vast amount of expression and interaction data, accompanied by information on metabolic, cell signaling and gene regulatory pathways accumulated in the literature and databases. Thus, one of the major goals of modern bioinformatics is to process and integrate heterogeneous biological data to provide an insight into the inner workings of a cell governed by complex interaction networks. The paper reviews the current development of semantic network (SN) technologies and their applications to the integration of genomic and proteomic data. We also elaborate on our own work that applies a semantic network approach to modeling complex cell signaling pathways and simulating the cause-effect of molecular interactions in human macrophages. The review is concluded with a discussion of the prospective use of semantic networks in bioinformatics practice as an efficient and general language for data integration, knowledge representation and inference.
Keywords: Semantic networks, biological data integration, protein interactions, knowledge representation, ontology, semantic web
Call for Papers in Thematic Issues
AI-Based Prediction of Functional Proteins
Functional proteins are vital molecules involved in a variety of physiological and pathological processes within the body. Understanding the relationship between protein structure and function is key to unraveling the mechanisms of life sciences, disease processes, and drug discovery. However, traditional experimental methods are often time-consuming, costly, and constrained by ...read more
Application of Large Language Models in Bioinformatics
Large language models (LLMs) are increasingly transforming the field of bioinformatics by enabling scalable, data-driven solutions to complex biological and biomedical challenges. Recent advances in domain-specific foundation models have shown strong performance across a wide range of applications, including protein structure and function prediction, gene annotation, drug discovery, multi-omics data ...read more
Hot Topics in Computational Genomics
Computational genomics has emerged since the beginning of the 21st century. Recently, along with the sequencing technology at single-cell level, computational genomics step forward to the level of singe-cell resolution. Several topics are well studied in this area. Several other topics are still challenging tasks for bioinformatics. This thematic issue ...read more
Related Books
Microbial Insights into Wastewater Treatment and Environmental Sustainability
Biological Control for Plant Protection: Recent Advances in Research and Sustainability
From Genes to Algorithms: Navigating the Biotechnology Data Revolution
Phytochemical Arsenal: Understanding Plant Defense Mechanisms Against Nematodes
Controlled Environment Horticulture: Where Plant Biotechnology Meets Sustainable Future
Genetic Diversity of Coronaviruses: From SARSCoV to SARS-CoV-2 – (Part 2)
Wild Vegetables: Morphology, Phytochemistry and Utility - (Part 2)
A Practical Approach to Molecular Cloning
Organoid Technology: Disease Modelling, Drug Discovery, and Personalized Medicine
Arid and Semi-Arid Zones of Mexico: A Comprehensive Exploration of Biodiversity, Ecology, and Conservation
2