PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 9697222

DBGET/LinkDB: an integrated database retrieval system.

W Fujibuchi·S Goto·H Migimatsu·I Uchiyama·A Ogiwara·Y Akiyama·M Kanehisa
View original source ↗Export metadata ↓

Abstract

The integrated database retrieval system DBGET/LinkDB is the backbone of the Japanese GenomeNet service. DBGET is used to search and extract entries from a wide range of molecular biology databases, while LinkDB is used to search and compute links between entries in different databases. DBGET/LinkDB is designed to be a network distributed database system with an open architecture, which is suitable for incorporating local databases or establishing a specialized server environment. It also has an advantage of simple architecture allowing rapid daily updates of all the major databases. The WWW version of DBGET/LinkDB at GenomeNet is integrated with other search tools, such as BLAST, FASTA and MOTIF, and with local helper applications, such as RasMol. In addition to factual links between database entries, LinkDB is being extended to included similarity links and biological links toward computerization of logical reasoning processes.

Explore related subjects

Databases, FactualGenomeHumansInformation SystemsInternetJapanMolecular BiologySoftwareJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

W Fujibuchi, S Goto, H Migimatsu, I Uchiyama, A Ogiwara, Y Akiyama, M Kanehisa. 1998. DBGET/LinkDB: an integrated database retrieval system.. https://pubmed.ncbi.nlm.nih.gov/9697222/

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2000

Comparison of National Death Index and World Wide Web death searches.

The authors used the National Death Index and a World Wide Web Internet site that searches the Social Security Administration master files of deaths to determine the mortality status of 1,000 US subjects from the College Alumni Health Study. Subjects were classified as definitely dead, possibly dead, or presumed alive. Of 246 definite deaths pinpointed by the National Death Index, the World Wide Web identified 94.7% of them. Of 438 men presumed alive according to the National Death Index, the World Wide Web identified 97.5% of them. However, the World Wide Web was not useful for identifying deaths of women. This study demonstrated that the World Wide Web may provide an alternative, inexpensive method of determining the mortality status of subjects in relatively small epidemiologic studies.

Databases, Factual↗
PubMed2000

Automated extraction of information in molecular biology.

We review data mining techniques in molecular biology, specifically those that extract information from the scientific literature itself. As more of the biological literature is published electronically, there is an opportunity, and even a need, to automatically summarize the literature in a customized way, for example by associating keywords to a topic. These keywords can be extracted from relevant publications. The process of keyword extraction can be automated and optimized to keep literature pointers automatically up-to-date or to filter relevant information from the literature. To illustrate these points, OMIM (Online Mendelian Inheritance in Man), a database of human inherited diseases, was linked to the literature and keywords were derived that covered distinct aspects such as genetic information on the one hand and disease-specific protein and phenotypic information on the other. They were used to extract information that is helpful for keeping entries about disease up-to-date.

Databases, Factual↗
PubMed2000

The role of protein structure in genomics.

The genome projects produce an enormous amount of sequence data that needs to be annotated in terms of molecular structure and biological function. These tasks have triggered additional initiatives like structural genomics. The intention is to determine as many protein structures as possible, in the most efficient way, and to exploit the solved structures for the assignment of biological function to hypothetical proteins. We discuss the impact of these developments on protein classification, gene function prediction, and protein structure prediction.

Databases, Factual↗