Integrated database retrieval systems

Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M. (1998). DBGET/LinkDB an Integrated Database Retrieval System. Pacific Symp. Biocomputing 98. R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein, eds.), pp. 683-694, World Scientific, Singapore. 

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

Table 4 Integrated Database Retrieval and Analysis Systems ...

Entrez (http //www.ncbi.nih.gov/entrez), information retrieval system, integrating NCBI databases of protein and nucleotide sequences, genomes, macromolecular stmctures, and MEDLINE literature database. 

MAECIS contains five major sections that are integrated into a single system. At its center is a database management system that handles the storage and updating of data and chemical structures. Associated with this section is an information retrieval section that allows one to search the database for specific information composed of any combination of data and/or substructures. Once information is retrieved, it can be displayed on a computer terminal or sent to a printer for hardcopy output using the display section of MAECIS which includes the ability to display chemical structures in various formats. The final two sections of MAECIS allow for the manipulation of chemical structures and the calculation of various molecular properties that are related to chemical structures. 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

NCBI s Molecular Modeling Database (MMDB Hogue et al., 1996) is an integral part of NCBTs Entrez information retrieval system (cf. Chapter 7). It is a compilation of all the Brookhaven Protein Data Bank (Bernstein et al., 1977) three-dimensional... 

Two comprehensive integrated retrieval systems for nucleic acids and proteins, Entrez of NCBI, and SRS of EBI will be described briefly. The molecular biology database and retrieval system, Entrez (Schuler et al 1996) was developed at and maintained by NCBI of NIH to allow retrieval of biochemical data and bibliographic citation from its integrated databases. Entrez typically provides access to ... 

While end user chemists had never been involved in our in-house chemical database development, when it became practical to look at graphics alternatives, they were an integral part of the decisionmaking. A task force of information specialists, systems analysts, and chemists evaluated the course of action whether to build a graphics system in-house, or to buy existing software. Economic factors continued to prevail, and it was seen that in-house development, however much preferred from a customization standpoint, would take too long to complete. The result of several months of discussion, demonstrations and site visits, was the decision to license Molecular Design Ltd. s MACCS system, the now well-known molecular connectivity-based retrieval system. 

A geographic information system (GIS) is an integrated computer mapping and spatial database management system that provides a broad array of functions for the storage, retrieval, management, analysis, and display of geographically referenced data. 

Most in-house systems permit links to other database management software, in particular to relational database systems such as ORACLE, in order to integrate large amounts of textual or numeric data that already exist there with reaction databases. As many of the reaction retrieval systems mentioned here are able to import and export files in MolFile or RxnFile formats (originally proprietary file formats of MDL, later published), or in the SMD format, even exchange of reaction databases between different retrieval systems is often possible. ... 

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