Editorial
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World J Biol Chem. Feb 26, 2012; 3(2): 27-33
Published online Feb 26, 2012. doi: 10.4331/wjbc.v3.i2.27
Knowledge acquisition, semantic text mining, and security risks in health and biomedical informatics
Jingshan Huang, Dejing Dou, Jiangbo Dang, J Harold Pardue, Xiao Qin, Jun Huan, William T Gerthoffer, Ming Tan
Jingshan Huang, J Harold Pardue, School of Computer and Information Sciences, University of South Alabama, Mobile, AL 36688, United States
Dejing Dou, Computer and Information Science Department, University of Oregon, Eugene, OR 97403, United States
Jiangbo Dang, Knowledge and Decision Systems Group, Siemens Corporate Research, Princeton, NY 08540, United States
Xiao Qin, Department of Computer Science and Software Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, AL 36849, United States
Jun Huan, Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66047, United States
William T Gerthoffer, Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, United States
Ming Tan, Mitchell Cancer Institute; Department of Cell Biology and Neuroscience, University of South Alabama, Mobile, AL 36688, United States
Author contributions: Huang J, Tan M and Gerthoffer WT organize the whole paper; Huang J, Qin X and Huan J contributed to introduction and research motivation, current bio-ontologies, and concluding remarks; Huang J and Qin X contributed to background knowledge in ontologies; Dou D and Qin X contributed to ontological techniques in medical and biological research; Dang J contributed to semantic text mining on clinical and biomedical data section; Pardue JH contributed to security risks to medical data research.
Correspondence to: Jingshan Huang, PhD, Assistant Professor, School of Computer and Information Sciences, University of South Alabama, FCW 20, School of CIS, 307 University Blvd. N., Mobile, AL 36688, United States. huang@usouthal.edu
Telephone: +1-251-4607612 Fax: +1-251-4607274
Received: October 28, 2011
Revised: December 7, 2011
Accepted: December 14, 2011
Published online: February 26, 2012
Abstract

Computational techniques have been adopted in medical and biological systems for a long time. There is no doubt that the development and application of computational methods will render great help in better understanding biomedical and biological functions. Large amounts of datasets have been produced by biomedical and biological experiments and simulations. In order for researchers to gain knowledge from original data, nontrivial transformation is necessary, which is regarded as a critical link in the chain of knowledge acquisition, sharing, and reuse. Challenges that have been encountered include: how to efficiently and effectively represent human knowledge in formal computing models, how to take advantage of semantic text mining techniques rather than traditional syntactic text mining, and how to handle security issues during the knowledge sharing and reuse. This paper summarizes the state-of-the-art in these research directions. We aim to provide readers with an introduction of major computing themes to be applied to the medical and biological research.

Keywords: Biomedical informatics; Bioinformatics; Knowledge sharing; Ontology matching; Heterogeneous semantics; Semantic integration; Semantic data mining; Semantic text mining; Security risk