• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.14
• /
• pp.5545-5550
• /
• 2014

Background: Human biological materials from cancer patients are linked directly with public health issues in medical science research as foundational resources so securing "human biological material" is truly important in bio-industry. However, because South Korea's national R and D project lacks a proper managing system for establishing a national standard for the outputs of certain processes, high-value added human biological material produced by the national R and D project could be lost or neglected. As a result, it is necessary to develop a managing process, which can be started by establishing operating guidelines to handle the output of human biological materials. Materials and Methods: The current law and regulations related to submitting research outcome resources was reviewed, and the process of data 'acquisition' and data 'distribution' from the point of view of big data and health 2.0 was examined in order to arrive at a method for switching paradigms to better utilize human biological materials. Results: For the deposit of biological research resources, the original process was modified and a standard process with relative forms was developed. With deposit forms, research information, researchers, and deposit type are submitted. The checklist's 26 items are provided for publishing. This is a checklist of items that should be addressed in deposit reports. Lastly, XML-based deposit procedure forms were designed and developed to collect data in a structured form, to help researchers distribute their data in an electronic way. Conclusions: Through guidelines included with the plan for profit sharing between depositor and user it is possible to manage the material effectively and safely, so high-quality human biological material can be supplied and utilized by researchers from universities, industry and institutes. Furthermore, this will improve national competitiveness by leading to development in the national bio-science industry.

• Genomics & Informatics
• /
• v.6 no.4
• /
• pp.202-209
• /
• 2008

Biological pathways are known as collections of knowledge of certain biological processes. Although knowledge about a pathway is quite significant to further analysis, it covers only tiny portion of genes that exists. In this paper, we suggest a model to extend each individual pathway using a microarray expression data based on the known knowledge about the pathway. We take the Rosetta compendium dataset to extend pathways of Saccharomyces cerevisiae obtained from KEGG (Kyoto Encyclopedia of genes and genomes) database. Before applying our model, we verify the underlying assumption that microarray data reflect the interactive knowledge from pathway, and we evaluate our scoring system by introducing performance function. In the last step, we validate proposed candidates with the help of another type of biological information. We introduced a pathway extending model using its intrinsic structure and microarray expression data. The model provides the suitable candidate genes for each single biological pathway to extend it.

• The Transactions of the Korean Institute of Electrical Engineers D
• /
• v.52 no.5
• /
• pp.311-321
• /
• 2003

In an emergency telemedicine system such as the High-quality Multimedia based Real-time Emergency Telemedicine(HMRET) service, it is very important to examine the status of the patient continuously using the multimedia data including the biological signals(ECG, BP, Respiration, $SpO_2)$ of the patient. In order to transmit these data real time through the communication means which have the limited transmission capacity, it is also necessary to compress the biological data besides other multimedia data. For this purpose, we investigate and compare the ECG compression techniques in the time domain and in the wavelet transform domain, and present an effective lossless compression method of the biological signals using PEG Huffman table for an emergency telemedicine system. And, for the HMRET service, we developed the lossless compression and reconstruction program or the biological signals in MSVC++ 6.0 using DPCM method and JPEG Huffman table, and tested in an internet environment.

• Proceedings of the KOSOMBE Conference
• /
• v.1998 no.11
• /
• pp.197-198
• /
• 1998

We tested the capability of Pointwise Correlation Dimension(PD2), Approximate Entropy (ApEn) and LZ complexity, as alternative measures of a biological signal. For this purpose, we analyzed standard data and a healthy child's 24-hour heart rate variability. Our conclusion is as follows. First, PD2, ApEn and LZ complexity can be used for discerning chaotic attractor, white noise, and periodic signal. Second, these measures show different characteristics on day and night. Third, these measures can be used for detecting time-varying characteristics of biological signals.

• Genomics & Informatics
• /
• v.2 no.3
• /
• pp.142-146
• /
• 2004

Biological data and analysis tools are accumulated in distributed databases and web servers. For this reason, biologists who want to find information from the web should be aware of the various kinds of resources where it is located and how it is retrieved. Integrating the data from heterogeneous biological resources will enable biologists to discover new knowledge across the specific domain boundaries from sequences to expression, structure, and pathway. And inevitably biological databases contain noisy data. Therefore, consensus among databases will confirm the reliability of its contents. We have developed WeSAT that integrates distributed and heterogeneous biological databases and analysis tools, providing through Web Services protocols. In WeSAT, biologists are retrieved specific entries in SWISS-PROT/EMBL, PDB, and KEGG, which have annotated information about sequence, structure, and pathway. And further analysis is carried by integrated services for example homology search and multiple alignments. WeSAT makes it possible to retrieve real time updated data and analysis from the scattered databases in a single platform through Web Services.

• Journal of Biomedical Engineering Research
• /
• v.5 no.1
• /
• pp.93-102
• /
• 1984

In this paper, the real-time compressed code generation method for the biological signal data, especially for the Electrocardiogram, is studied. For this purpose, variable length code is introduced. And from this code, we get a exactly the same reconstructed signal data as the original. Experimental results show that this program reduces the data rate by a factor of about 8, and codes the result in a form convenient for analysis.

• Proceedings of the KIEE Conference
• /
• 2002.07d
• /
• pp.2727-2729
• /
• 2002

In an emergency telemedicine system such as High-quality Multimedia based Real-time Emergency Telemedicine(HMRET) service, it is very important to examine the status of the patient continuously using the multimedia data including the biological signals(ECG, BP, Respiration, $SpO_2$) of the patient. In order to transmit these data real time through the communication means which have the limited transmission capacity. It is also necessary to compress the biological data besides other multimedia data. For the HMRET service, we developed the lossless biological signal compression program in MSVC++ 6.0 using DPCM method and JPEG Huffman table, and tested in an internet environment.

• Molecules and Cells
• /
• v.26 no.4
• /
• pp.338-343
• /
• 2008

An embryonic stem cell is a powerful tool for investigation of early development in vitro. The study of embryonic stem cell mediated neuronal differentiation allows for improved understanding of the mechanisms involved in embryonic neuronal development. We investigated expression profile changes using time course cDNA microarray to identify clues for the signaling network of neuronal differentiation. For the short time course microarray data, pattern analysis based on the quadratic regression method is an effective approach for identification and classification of a variety of expressed genes that have biological relevance. We studied the expression patterns, at each of 5 stages, after neuronal induction at the mRNA level of embryonic stem cells using the quadratic regression method for pattern analysis. As a result, a total of 316 genes (3.1%) including 166 (1.7%) informative genes in 8 possible expression patterns were identified by pattern analysis. Among the selected genes associated with neurological system, all three genes showing linearly increasing pattern over time, and one gene showing decreasing pattern over time, were verified by RT-PCR. Therefore, an increase in gene expression over time, in a linear pattern, may be associated with embryonic development. The genes: Tcfap2c, Ttr, Wnt3a, Btg2 and Foxk1 detected by pattern analysis, and verified by RT-PCR simultaneously, may be candidate markers associated with the development of the nervous system. Our study shows that pattern analysis, using the quadratic regression method, is very useful for investigation of time course cDNA microarray data. The pattern analysis used in this study has biological significance for the study of embryonic stem cells.

• BMB Reports
• /
• v.50 no.1
• /
• pp.12-19
• /
• 2017

Traditionally, biologists have devoted their careers to studying individual biological entities of their own interest, partly due to lack of available data regarding that entity. Large, high-throughput data, too complex for conventional processing methods (i.e., "big data"), has accumulated in cancer biology, which is freely available in public data repositories. Such challenges urge biologists to inspect their biological entities of interest using novel approaches, firstly including repository data retrieval. Essentially, these revolutionary changes demand new interpretations of huge datasets at a systems-level, by so called "systems biology". One of the representative applications of systems biology is to generate a biological network from high-throughput big data, providing a global map of molecular events associated with specific phenotype changes. In this review, we introduce the repositories of cancer big data and cutting-edge systems biology tools for network generation, and improved identification of therapeutic targets.

• International Journal of Contents
• /
• v.3 no.2
• /
• pp.18-24
• /
• 2007

Biological sequences such as DNA and amino acid sequences typically contain a large number of items. They have contiguous sequences that ordinarily consist of more than hundreds of frequent items. In biological sequences analysis(BSA), a frequent contiguous sequence search is one of the most important operations. Many studies have been done for mining sequential patterns efficiently. Most of the existing methods for mining sequential patterns are based on the Apriori algorithm. In particular, the prefixSpan algorithm is one of the most efficient sequential pattern mining schemes based on the Apriori algorithm. However, since the algorithm expands the sequential patterns from frequent patterns with length-1, it is not suitable for biological datasets with long frequent contiguous sequences. In recent years, the MacosVSpan algorithm was proposed based on the idea of the prefixSpan algorithm to significantly reduce its recursive process. However, the algorithm is still inefficient for mining frequent contiguous sequences from long biological data sequences. In this paper, we propose an efficient method to mine maximal frequent contiguous sequences in large biological data sequences by constructing the spanning tree with a fixed length. To verify the superiority of the proposed method, we perform experiments in various environments. The experiments show that the proposed method is much more efficient than MacosVSpan in terms of retrieval performance.