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| - Introduction of Bioinformatic Portal System. | ||
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Rapidly increasing data from genomics research require informatics systems for data management and mining. Such data need to be integrated to support subsequent analysis at various contexts; however, currently available systems cannot fully support such functionality mainly due to the lack of standardization in exchanging heterogeneous data and a platform supporting various biological inquires. We have established a multi-system platform, Bioinformatics Portal System (BPS), that consists of three systems and nine analysis pipelines with standardized communication protocol. The CFGP (Comparative Fungal Genomics Platfor; http://cfgp.snu.ac.kr; Park et al, 2007), a web-based bioinformatic portal system, houses more than 110 genome databases and an annotation database providing various features of proteins based on InterPro and GO. At least 30 independent system for managing experimental data and connecting them to an appropriate genome database have been developed based on the BPS. During its development, the development standard protocol, managed in the web site, http://www.bio-os.net/, was used. In this web site, functions and development histories have been managed in each system. Among systems based on the BPS, various objects, defined for heterogeneous data, can be managed by a OBJECT system that provides the web-based interface similar to windows explorer (FOLDER system). It also serves the standard for exchanging heterogeneous data via encapsulation of all objects under the BPS. With this system design, time and cost of development of pipelines are reduced while functionality of the user interface is enhanced. |
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| - Introduction of distributed BPS (dBPS). | ||
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At whole genome level various experimental methods, such as genome sequencing technology, microarray and CGH, scale have been developed and optimized. They have led to emerge a number of systems to manage, generating huge and high-condensed information. However, it is very difficult to put them together in one system because no standardized protocol for exchanging large-scale data exists. Here is the multi-system platform, Bioinformatic Portal System (BPS), showing 31 systems with the standardized communication protocol and database. Basically, it manages large number of genome database covering from prokaryotic to eukaryotic genomes. The genome databases connect to annotation database including InterPro, GO, EC, PSORT and SignalP. Based on this, experimental database systems are built with several bioinformatics tools, such as ClustalW and BLAST. To construct standard for interchanging heterogeneous between systems, object system encapsulate these data as object with common library. Each object, such as sequences, annotated results, microarray results and species, can be managed via folder system which offers user interface like windows explorer. At user interface, template engine guides to build the standardized user interface. For personalized database and authentication, membership system in BPS provides account management and communication system via messages and email. These components of BPS can be represented the new standardized protocol for huge and complicated analyses of phylogenetic and comparative genomics. |
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- Related posters - 2006, KSBI Posters Bioinformatics Portal System (BPS): A versatile platform supporting comparative genomics and phylogenetic analyses Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Sunghyung Kong, Jaejin Park, Seryun Kim, Soonok Kim and Yong-Hwan Lee Fungal Bioinformatics Lab, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea  - 2006, KSBI Poster A new standard for integrating heterogeneous biological dataor object-oriented bioinformatics system Bongsoo Park, Jongsun Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Soonok Kim and Yong-Hwan Lee Fungal Bioinformatics Lab, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea  - 2005, KSBI Poster CROSS-FPP, a Web-based Bioinformatic Portal System for Comparative Genomics Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Soonok Kim and Yong-Hwan Lee Fungal Bioinformatics Lab., Seoul National University, Seoul 151-742, Korea  - 2005, KOGO Poster CROSS-FPP, a New Integrated Environment or Comparative and Phylogenetic Analysis Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Soonok Kim and Yong-Hwan Lee Fungal Bioinformatics Lab., Seoul National University, Seoul 151-742, Korea  |
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