• Genomics & Informatics
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• 제3권3호
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• pp.94-97
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• 2005

We have built a database server called Patome which contains the annotation information for patented bio-sequences from the Korean Intellectual Property Office (KIPO). The aims of the Patome are to annotate Korean patent bio-sequences and to provide information on patent relationship of public database entries. The patent sequences were annotated with Reference Sequence (RefSeq) or NCBI's nr database. The raw patent data and the annotated data were stored in the database. Annotation information can be used to determine whether a particular RefSeq ID or NCBI's nr ID is related to Korean patent. Patome infrastructure consists of three components­the database itself, a sequence data loader, and an online database query interface. The database can be queried using submission number, organism, title, applicant name, or accession number. Patome can be accessed at http://www.patome.net. The information will be updated every two months.

• Genomics & Informatics
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• 제7권3호
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• pp.175-177
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• 2009

We have developed WinBioDBs with Windows interfaces, which include importing modules and searching interfaces for 10 major public databases such as GenBank, PIR, SwissProt, Pathway, EPD, ENZYME, REBASE, Prosite, Blocks, and Pfam. User databases can be constructed with searching results of queries and their entries can be edited. The program is a stand-alone database searching program on Windows PC. Database update features are supported by importing raw database files and indexing after downloading them. Users can adjust their own searching environments and report format and construct their own projects consisting of a combination of a local databases. WinBioDBs are implemented with VC++ and its database is based on MySQL.

• 대한원격탐사학회:학술대회논문집
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• 대한원격탐사학회 2005년도 Proceedings of ISRS 2005
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• pp.280-282
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved algorithm provides better levels of performance than the originals.

• Genomics & Informatics
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• 제3권1호
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• pp.35-38
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• 2005

We present BioSubroutine, an open depository server that automatically categorizes various subroutines frequently used in bioinformatics research. We processed a large bioinformatics subroutine library called Bio.pl that was the first Bioperl subroutine library built in 1995. Over 1000 subroutines were processed automatically and an HTML interface has been created. BioSubroutine can accept new subroutines and algorithms from any such subroutine library, as well as provide interactive user forms. The subroutines are stored in an SQL database for quick searching and accessing. BioSubroutine is an open access project under the BioLicense license scheme.

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2009년도 춘계 종합학술대회 논문집
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• pp.1180-1185
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• 2009

정보 콘텐츠 기술의 발달로 인하여 모든 정보들이 데이터베이스화 되어가고 있다. 하지만 아직 가축의 생체정보의 데이터베이스 구축은 생체정보의 수집단계의 어려움으로 그 발전이 미약하다. 본 논문은 젖소의 생체정보를 수집 관리하기 위하여 지그비 RF(Radio frequency)통신을 이용한 가축의 생체정보의 수집을 통해 젖소들의 생체상태를 센싱 할 수 있는 시스템을 개발하였고 이를 데이터베이스 구축에 활용하기 위한 논문이다. 센싱 시스템은 8Bit 마이크로 컨트롤러와 기울기센서, 온도센서, RF 모듈로 구성되었다.

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2003년도 추계종합학술대회 논문집
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• pp.285-289
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• 2003

본 논문에서는 Bio-XML 문서를 효율적으로 객체 데이터베이스에 저장하고, XML 질의에서 주로 사용되는 경로식을 효과적으로 처리할 수 있는 DTD의존적인 객체 데이터베이스 스키마 설계기법을 제안한다. XML DTD와 객체데이터베이스의 스키마는 구조적으로 비슷하고, 객체 데이터베이스의 고유특성인 객체 참조와 집합값 속성은 XML 데이터를 저장하는데 유리하다. 본 논문에서는 객체 데이터베이스의 고유 특성을 충분히 반영하여 두 가지의 스키마 설계기법인 기본적 방법과 인라인 방법을 제안한다. 뿐만 아니라, 각각 설계 기법에 대하여 시스템성능 평가를 수행하였으며, 설계 기법에 따른 공간효율과 시간 효율을 비교 및 분석하였다.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2005년도 추계학술발표대회 및 정기총회
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• pp.15-18
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved prediction algorithm provides better levels of performance than the originals.

• Genomics & Informatics
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• 제6권2호
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• pp.95-97
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• 2008

Many bioinformatics sites have managed local bio-databases, including major databases such as GenBank and PIR with update load. We have developed several programs to monitor the update status of these databases and to FTP them automatically. These programs can be used for maintaining local bio-databases as recent versions and providing up-to-date databases through FTP sites. Currently, the program serves major bio-databases and will extend to accommodate many more bio-databases.

• 한국축산시설환경학회지
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• 제21권1호
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• pp.9-20
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• 2015

The livestock manure recycling have been performed worldwide because of its environmental and economic benefits. However, domestic standard protocol was nothing for high solid manure. Therefore, This paper was conducted to review database configuration of manure characteristics, analysis methods, bio-methane potential test for high solid manure recycling. In American society of agricultural engineers standard, manure characteristics indicated about sort of thirty types. This is important information to determine for manure recycling method. Furthermore, in order to determine exact manure characteristics recommended that synchronized chemical analysis method among studies. Bio-methane potential tests are widely performed in studies about estimation of organic substrates methane production. Although various methods and parameters were used, was no standard protocol and guideline in domestic. Bio-methane potential test methods and parameters were reviewed through various researches. Consequently, this paper is expected that assist to additional studies and manure characteristic database.

• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 2003년도 ISIS 2003
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• pp.11-15
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• 2003

Amount of biological data information has been increasing exponentially. In order to cope with this bio-information explosion, it is necessary to construct a biological data information integration system. The integration system could provide useful services for bio-application developers by answering general complex queries that require accessing information from heterogeneous bio data sources, and easily accommodate a new database into the integrated systems. In this paper, we analyze architectures and mechanisms of existing integration systems with their advantages and disadvantages. Based on this analysis and user requirement studies, we propose an integration system framework that embraces advantages of the existing systems. More specifically, we propose an integration system architecture composed of a mediator and wrappers, which can offer a service interface layer for various other applications as well as independent biologists, thus playing the role of database management system for biology applications. In other words, the system can help abstract the heterogeneous information structures and formats from the application layer. In the system, the wrappers send database-specific queries and report the result to the mediator using XML. The proposed system could facilitate in silico knowledge discovery by allowing combination of numerous discrete biological information databases.