• International journal of advanced smart convergence
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• v.9 no.1
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• pp.90-97
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• 2020

Oncolytic viruses are characterized by their ability to selectively kill cancer cells, and thus they have potential for application as novel anticancer agents. Despite an increase in the number of studies on methodologies involving oncolytic viruses, bioinformatic studies generating useful data are lacking. We constructed a database for oncolytic virus research (the oncolytic virus database, OVDB) by integrating scattered genetic information on oncolytic viruses and proposed a systematic means of using the biological data in the database. Our database provides data on 14 oncolytic viral strains and other types of viruses for comparative analysis. We constructed the OVDB using the basic local alignment search tool, and therefore can provides genetic information on highly homologous oncolytic viruses. This study contributes to facilitate systematic bioinformatics research, providing valuable data for development of oncolytic virus-based anticancer therapies.

• Radiation Oncology Journal
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• v.30 no.1
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• pp.43-48
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• 2012

Purpose: To develop the dose volume histogram (DVH) management software which guides the evaluation of radiotherapy (RT) plan of a new case according to the biological consequences of the DVHs from the previously treated patients. Materials and Methods: We determined the radiation pneumonitis (RP) as an biological response parameter in order to develop DVH management software. We retrospectively reviewed the medical records of lung cancer patients treated with curative 3-dimensional conformal radiation therapy (3D-CRT). The biological event was defined as RP of the Radiation Therapy Oncology Group (RTOG) grade III or more. Results: The DVH management software consisted of three parts (pre-existing DVH database, graphical tool, and $Pinnacle^3$ script). The pre-existing DVH data were retrieved from 128 patients. RP events were tagged to the specific DVH data through retrospective review of patients' medical records. The graphical tool was developed to present the complication histogram derived from the preexisting database (DVH and RP) and was implemented into the radiation treatment planning (RTP) system, $Pinnacle^3$ v8.0 (Phillips Healthcare). The software was designed for the pre-existing database to be updated easily by tagging the specific DVH data with the new incidence of RP events at the time of patients' follow-up. Conclusion: We developed the DVH management software as an effective tool to incorporate the phenomenological consequences derived from the pre-existing database in the evaluation of a new RT plan. It can be used not only for lung cancer patients but also for the other disease site with different toxicity parameters.

• Proceedings of the KSRS Conference
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• 2005.10a
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• pp.770-773
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• 2005

In most biological laboratory, sequences from sequence machine are stored into file disks as simple files. It will be hard work to store and manage the sequence data with consistency and integrity such as storing redundant files. It is required needed to develop a system which integrated and managed genome data with consistency and integrity for accurate sequence analysis. There fore, in this paper, we not only store gene and protein sequence data through sequencing but also manage them. We also make a integrate schema for transforming the file formats and design database system using it. As integrated schema is designed as a BSML, it is possible to apply a style language of XSL. From this, we can transfer among heterogeneous sequence formats.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 1998.06a
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• pp.539-542
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• 1998

In this paper, we devised pulse rate diagnosis database system for provide basic index of Cold-Hot diagnosis. The system consist of database part and pulse rate detection part that for detection pulse wave, respiration and ECG. The database is constructed windows95 platform using DAO(Data Access Object). Search algorithm used ISAM algorithm. The database consist of patient information and medical report for a subject and detected biological signals.

• The Korean Journal of Malacology
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• v.30 no.4
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• pp.429-431
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• 2014

Since we reported a BLAST server for the mollusk in 2004, no work has reported the usability or modification of the server. To improve its usability, the BLAST server for the mollusk has been updated as version II (http://www.malacol.or.kr/blast) in the present study. The database was constructed by using the Intel server Platform ZSS130 dual Xeon 3.20 GHz CPU and Linux CentOS system and with NCBI WebBLAST package. We downloaded the mollusk nucleotide, amino acid, EST, GSS and mitochondrial genome sequences which can be opened through NCBI web BLAST and used them to build up the database. The updated database consists of 520,977 nucleotide sequences, 229,857 amino acid sequences, 586,498 EST sequences, 23,112 GSS and 565 mitochondrial genome sequences. Total database size is 1.2 GB. Furthermore, we have added repeat sequences, Escherichia coli sequences and vector sequences to facilitate data validation. The newly updated BLAST server for the mollusk will be useful for many malacological researchers as it will save time to identify and study various molluscan genes.

• Interdisciplinary Bio Central
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• v.2 no.4
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• pp.13.1-13.8
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• 2010

The National BioResource Project of Japan is a governmental project to promote domestic/international research activities using biological resources. The project has 27 biological resources including three cereal resources. The core center and sub-center which historically collected the cereal resources were selected for each cereal program. These resources are categorized into several different types in the project; germplasm, genetic stocks, genome resources and database information. Contents of rice resources are wild species, local varieties in East and Southwest Asia & wild relatives, MNU-induced chemical mutant lines, marker tester lines, chromosome substitution lines and other experimental lines. Contents of wheat resources are wild strains, cultivated strains, experimental lines, rye wild and cultivated strains; EST clones and full-length cDNA clones. Contents of barley resources are cultivar and experimental lines, core collection, EST/cDNA clones, BAC clones, their filters and superpool DNA. Each resource is accessible from the online database to see the contents and information about the resources. Links to the genome information and genomic tools are also important function of each database. The major contents and some examples are presented here.

• Genomics & Informatics
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• v.3 no.3
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• pp.53-62
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• 2005

MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the 'tight' tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.

• Genomics & Informatics
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• v.19 no.1
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• pp.4.1-4.9
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• 2021

Lip and oral cavity cancer, which can occur in any part of the mouth, is the 11th most common type of cancer worldwide. The major obstacles to patients' survival are the poor prognosis, lack of specific biomarkers, and expensive therapeutic alternatives. This study aimed to identify the main genes and pathways associated with lip and oral cavity carcinoma using network analysis and to analyze its molecular mechanism and prognostic significance further. In this study, 472 genes causing lip and oral cavity carcinoma were retrieved from the DisGeNET database. A protein-protein interaction network was developed for network analysis using the STRING database. VEGFA, IL6, MAPK3, INS, TNF, MAPK8, MMP9, CXCL8, EGF, and PTGS2 were recognized as network hub genes using the maximum clique centrality algorithm available in cytoHubba, and nine potential drug candidates (ranibizumab, siltuximab, sulindac, pomalidomide, dexrazoxane, endostatin, pamidronic acid, cetuximab, and apricoxib) for lip and oral cavity cancer were identified from the DGIdb database. Gene enrichment analysis was also performed to identify the gene ontology categorization of cellular components, biological processes, molecular functions, and biological pathways. The genes identified in this study could furnish a new understanding of the underlying molecular mechanisms of carcinogenesis and provide more reliable biomarkers for early diagnosis, prognostication, and treatment of lip and oral cavity cancer.

• Journal of Environmental Science International
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• v.14 no.12
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• pp.1119-1127
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• 2005

The management of data on biological diversity is presently complex and confusing. This study was initiated to construct a database so that such data could be stored in a data management, and analysis instrument to correct the problems inherent in the current incoherent storage methods. MySQL was used in DBMS(DataBase Management System), and the program was basically produced using Java technology Also, the program was developed so people could adapt to the requirements that are changing every minute. We hope this was accomplished by modifying easily and quickly the advanced programming technology and patterns. To this end, an effective and flexible database schema was devised to store and analyze diversity databases. Even users with no knowledge of databases should be able to access this management instrument and easily manage the database through the World Wide Web. On a basis of databases stored in this manner, it could become routinely used for various databases using this analysis instrument supplied on the World Wide Web. Supplying the derived results by using a simple table and making results visible using simple charts, researchers could easily adapt these methods to various data analyses. As the diversity data was stored in a database, not in a general file, this study makes the precise, error-free and high -quality storage in a consistent manner. The methods proposed here should also minimize the errors that might appear in each data search, data movement, or data conversion by supplying management instrumentation on the Web. Also, this study was to deduce the various results to the level we required and execute the comparative analysis without the lengthy time necessary to supply the analytical instrument with similar results as provided by various other methods of analysis. The results of this research may be summerized as follows: 1)This study suggests methods of storage by giving consistency to diversity data. 2)This study prepared a suggested foundation for comparative analysis of various data. 3)It may suggest further research, which could lead to more and better standardization of diversity data and to better methods for predicting changes in species diversity.

• Molecules and Cells
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• v.43 no.10
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• pp.880-888
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• 2020

Inherited peripheral neuropathy is a heterogeneous group of peripheral neurodegenerative disorders including Charcot-Marie-Tooth disease. Many peripheral neuropathies often accompany impaired axonal construction and function. To study the molecular and cellular basis of axon-defective peripheral neuropathy, we explore the possibility of using Caenorhabditis elegans, a powerful nematode model equipped with a variety of genetics and imaging tools. In search of potential candidates of C. elegans peripheral neuropathy models, we monitored the movement and the body posture patterns of 26 C. elegans strains with disruption of genes associated with various peripheral neuropathies and compiled a database of their phenotypes. Our assay showed that movement features of the worms with mutations in HSPB1, MFN2, DYNC1H1, and KIF1B human homologues are significantly different from the control strain, suggesting they are viable candidates for C. elegans peripheral neuropathy models.