• Interdisciplinary Bio Central
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• v.1 no.3
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• pp.9.1-9.6
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• 2009

Introduction: In the mass spectrometry-based proteomics, biological samples are analyzed to identify proteins by mass spectrometer and database search. Database search is the process to select the best matches to the experimental mass spectra among the amino acid sequence database and we identify the protein as the matched sequence. The match score is defined to find the matches from the database and declare the highest scored hit as the most probable protein. According to the score definition, search result varies. In this study, the difference among search results of different search engines or different databases was investigated, in order to suggest a better way to identify more proteins with higher reliability. Materials and Methods: The protein extract of human mesenchymal stem cell was separated by several bands by one-dimensional electrophorysis. One-dimensional gel was excised one by one, digested by trypsin and analyzed by a mass spectrometer, FT LTQ. The tandem mass (MS/MS) spectra of peptide ions were applied to the database search of X!Tandem, Mascot and Sequest search engines with IPI human database and SwissProt database. The search result was filtered by several threshold probability values of the Trans-Proteomic Pipeline (TPP) of the Institute for Systems Biology. The analysis of the output which was generated from TPP was performed. Results and Discussion: For each MS/MS spectrum, the peptide sequences which were identified from different conditions such as search engines, threshold probability, and sequence database were compared. The main difference of peptide identification at high threshold probability was caused by not the difference of sequence database but the difference of the score. As the threshold probability decreases, the missed peptides appeared. Conversely, in the extremely high threshold level, we missed many true assignments. Conclusion and Prospects: The different identification result of the search engines was mainly caused by the different scoring algorithms. Usually in proteomics high-scored peptides are selected and low-scored peptides are discarded. Many of them are true negatives. By integrating the search results from different parameter and different search engines, the protein identification process can be improved.

• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.46-51
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• 2007

In the proteomics research using mass spectrometry, the protein database search gives the protein information from the peptide sequences that show the best match with the tandem mass spectra. The protein sequence database has been a powerful knowledgebase for this protein identification. However, as we accumulate the protein sequence information in the database, the database size gets to be huge. Now it becomes hard to consider all the protein sequences in the database search because it consumes much computing time. For the high-throughput analysis of the proteome, usually we have used the non-redundant refined database such as IPI human database of European Bioinformatics Institute. While the non-redundant database can supply the search result in high speed, it misses the variation of the protein sequences. In this study, we have concerned the proteomics data in the point of protein similarities and used the network analysis tool to build a new analysis method. This method will be able to save the computing time for the database search and keep the sequence variation to catch the modified peptides.

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.4 no.3
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• pp.288-291
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• 2004

This paper proposes an intelligent search modeling using avatar agent. This system consists of some modules such as agent interface, agent management, preprocessor, interface machine. Core-Symbol Database and Spell Checker are related to the preprocessor module and Interface Machine is connected with Best Aggregate Designer. Our avatar agent system does the indexing work that converts user's natural language type sentence to the proper words that is suitable for the specific branch information retrieval. Indexing is one of the preprocessing steps that make it possible to guarantee the specialty of user's input and increases the reliability of the result. It references a database that consists of synonym and specific branch dictionary. The resulting symbol after indexing is used for draft search by the internet search engine. The retrieval page position and link information are stored in the database. We experimented our system with the stock market keyword SAMSUNG_SDI, IBM, and SONY and compared the result with that of Altavista and Google search engine. It showed quite excellent results.

• Journal of the Korean Society for information Management
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• v.26 no.3
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• pp.111-129
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• 2009

This study examined the usability of text-based search and visual search of a large multidisciplinary library database to provide an empirical analysis of the acceptability of visual systems in the information retrieval environment. It also examined if there are differences in the usability assessment based on experimental order. The results indicated that the text-based search supported users' search behaviors more efficiently than the visual search. Also the text-based search was rated higher than the visual search in terms of user perceptions of four usability factors.

• Journal of Korean Library and Information Science Society
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• v.39 no.4
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• pp.331-352
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• 2008

The person information is a database given free most lively. This study investigates the construction of the domestic person information database and the service present situation. And I compare a search item and a search method with problems for the biographical database construction process and analyze it. I analyze the problems of the person information database and show the person idea who can solve this. I use term relations and the attribute data of the person which used thesaurus by biographical database construction with this purpose.

• International journal of advanced smart convergence
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• v.9 no.3
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• pp.239-245
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• 2020

The Ewha Music Database (EMDB) is an online database comprised of primary source materials related to music education from East Asia during the modern era (1880 to 1945) when Korea, Japan, and China were geopolitically and culturally intertwined. We developed the incipit search in EMDB as an embedded tool. This is the first attempt in Korea to implement a unique search function of musical data using alphabets of musical notes. Unlike in traditional search system that uses general literature information search conditions, such as author, title, publisher, year, number of pages, etc., it offers a new way of searching a musical piece/work and sheet music. This study confirms that digital information technology is an important methodology for research of music culture as a field of humanities.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.407-411
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• 2005

KUGI (Korean UniGene Information) database contains the annotation information of the cDNA sequences obtained from the disease samples prevalent in Korean. A total of about 157,000 5'-EST high throughput sequences collected from cDNA libraries of stomach, liver, and some cancer tissues or established cell lines from Korean patients were clustered to about 35,000 contigs. From each cluster a representative clone having the longest high quality sequence or the start codon was selected. We stored the sequences of the representative clones and the clustered contigs in the KUGI database together with their information analyzed by running Blast against RefSeq, human mRNA, and UniGene databases from NCBI. We provide a web-based search engine fur the KUGI database using two types of user interfaces: attribute-based search and similarity search of the sequences. For attribute-based search, we use DBMS technology while we use BLAST that supports various similarity search options. The search system allows not only multiple queries, but also various query types. The results are as follows: 1) information of clones and libraries, 2) accession keys, location on genome, gene ontology, and pathways to public databases, 3) links to external programs, and 4) sequence information of contig and 5'-end of clones. We believe that the KUGI database and search system may provide very useful information that can be used in the study for elucidating the causes of the disease that are prevalent in Korean.

• Journal of Microbiology and Biotechnology
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• v.6 no.1
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• pp.54-59
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• 1996

In the research and development of bioactive compounds, determining whether a compound is novel is necessary at almost every stage. Fast and efficient determination can save money, time and effort, and thereby increase efficiency. Analysis and investigation of empirical results for previously determined compounds is also important in such research. The need to communicate research findings between workers is necessary. In effect, a systematic, centralized communication medium is required. Therefore, we have developed and constructed our own database and search systems. We have developed a search system on DOS and constructed a source file for our own database. To support multiple users, we have developed another specific and comprehensive search system, including powerful searching and output management features. The system has been developed to be simple and user-friendly, using the curses library of UNIX, while still allowing complicated queries to be performed easily with simple full-screen facilities. This UNIX version will be available for use by researchers on a computer network and is expected to make numerous contributions to basic research in universities. It will also have direct applications for institutes and industry.

• Proceedings of the Korean Information Science Society Conference
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• 2010.06c
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• pp.62-65
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• 2010

Image annotations allow users to access a large image database with textual queries. But since the surrounding text of Web images is generally noisy. an efficient image annotation and retrieval system is highly desired. which requires effective image search techniques. Data mining techniques can be adopted to de-noise and figure out salient terms or phrases from the search results. Clustering algorithms make it possible to represent visual features of images with finite symbols. Annotationbased image search engines can obtains thousands of images for a given query; but their results also consist of visually noise. In this paper. we present a new algorithm Double-Circles that allows a user to remove noise results and characterize more precise representative annotations. We demonstrate our approach on images collected from Flickr image search. Experiments conducted on real Web images show the effectiveness and efficiency of the proposed model.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.7 no.5
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• pp.1328-1342
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• 2013

Searchable encryption is a cryptographic protocol for searching a document in encrypted databases. A simple searchable encryption protocol, which is capable of using only one keyword at one time, is very limited and cannot satisfy demands of various applications. Thus, designing a searchable encryption with useful additional functions, for example, conjunctive keyword search, is one of the most important goals. There have been many attempts to construct a searchable encryption with conjunctive keyword search. However, most of the previously proposed protocols are based on public-key cryptosystems which require a large amount of computational cost. Moreover, the amount of computation in search procedure depends on the number of documents stored in the database. These previously proposed protocols are not suitable for extremely large data sets. In this paper, we propose a new searchable encryption protocol with a conjunctive keyword search based on a linked tree structure instead of public-key based techniques. The protocol requires a remarkably small computational cost, particularly when applied to extremely large databases. Actually, the amount of computation in search procedure depends on the number of documents matched to the query, instead of the size of the entire database.