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
Current Bioinformatics
Title: Integration of Biological Data with Semantic Networks
Volume: 1 Issue: 3
Author(s): Michael Hsing and Artem Cherkasov
Affiliation:
Keywords: Semantic networks, biological data integration, protein interactions, knowledge representation, ontology, semantic web
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.
Export Options
About this article
Cite this article as:
Hsing Michael and Cherkasov Artem, Integration of Biological Data with Semantic Networks, Current Bioinformatics 2006; 1 (3) . https://dx.doi.org/10.2174/157489306777827946
DOI https://dx.doi.org/10.2174/157489306777827946 |
Print ISSN 1574-8936 |
Publisher Name Bentham Science Publisher |
Online ISSN 2212-392X |
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
Related Articles
-
Plasma Clusterin as a Potential Biomarker for Alzheimer’s Disease-A Systematic Review and Meta-analysis
Current Alzheimer Research Current Concepts of Mild Cognitive Impairment and their Applicability to Persons At-Risk for Familial Alzheimers Disease
Current Alzheimer Research Role of Psychiatrists in the Diagnosis and Management of Alzheimer's Disease “Revisited”: A Review and Clinical Opinion
Current Psychiatry Reviews A Survey of Recent Patents on CB2 Agonists in the Management of Pain
Recent Patents on CNS Drug Discovery (Discontinued) Potentials of ES Cell Therapy in Neurodegenerative Diseases
Current Pharmaceutical Design Multiple Sclerosis: Current and Future Treatment Options
Endocrine, Metabolic & Immune Disorders - Drug Targets PREPL, a Prolyl Endopeptidase-Like Enzyme by Name Only? – Lessons from Patients
CNS & Neurological Disorders - Drug Targets Clinical Pharmacotherapy for Obesity: Current Drugs and Those in Advanced Development
Current Drug Targets Depression and Self-Efficacy in Patients with Type 2 Diabetes in Northern Greece
Endocrine, Metabolic & Immune Disorders - Drug Targets Melanocortin Receptors, Melanotropic Peptides and Penile Erection
Current Topics in Medicinal Chemistry Analysis of TLC-Bioautography and TLC-Spot Visualization of <i>Atropa accuminata</i> and <i>Atropa belladonna</i> Extracts as Antioxidant and Antibacterial Agents Against Human Pathogenic Bacteria
Current Pharmaceutical Analysis EDITORIAL: Neuroprotection Mechanisms and their Potential Applications
Current Neuropharmacology The Influence of Host Factors on the Prognosis of Breast Cancer: Stroma and Immune Cell Components as Cancer Biomarkers
Current Cancer Drug Targets Denouement of Chemicals on Amyotrophic Lateral Sclerosis: Is Green Chemistry the Answer
Medicinal Chemistry GABA and Neuroactive Steroid Interactions in Glia: New Roles for Old Players?
Current Neuropharmacology First Phase Insulin Secretion and Type 2 Diabetes
Current Molecular Medicine Zinc in the Glutamatergic Theory of Depression
Current Neuropharmacology MicroRNA-130b Promotes Wear Particle-Induced Osteolysis via Downregulating Frizzled-Related Protein (FRZB)
Current Neurovascular Research Biomarkers as a Guide of Medical Treatment in Cardiovascular Diseases
Current Medicinal Chemistry Evaluation of Metabolic and Synaptic Dysfunction Hypotheses of Alzheimer's Disease (AD): A Meta-Analysis of CSF Markers
Current Alzheimer Research