Integrated database retrieval

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 ...

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

Patent databases are therefore integrated databases because facts, text, tables, graphics, and structures are combined. In patents that include chemical aspects (mostly synthesis or processing), the chemical compounds are often represented by Markush structures (see Chapter 2, Section 2.7.1). These generic structures cover many compound families in a very compact maimer. A Markush structure has a core structure diagram with specific atoms and with variable parts (R-groups), which are defined in a text caption. The retrieval of chemical compounds from Markush structures is a complicated task that is not yet solved completely satisfactorily. 

With the aim of integrating databases to offer sensible queries where only the pertinent information is retrieved, the structure of data is important. 

Entrez, to be clear, is not a database itself—it is the interface through which all of its component databases can be accessed and traversed. The Entrez information space includes PubMed records, nucleotide and protein sequence data, three-dimensional structure information, and mapping information. The strength of Entrez lies in the fact that all of this information can be accessed by issuing one and only one query. Entrez is able to offer integrated information retrieval through the use of two types of coimection between database entries neighboring and hard links. 

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 ... 

This type of integrated database is costly in production and needs special skill and/or special software to retrieve the information wanted. The need and importance for this kind of integrated data will drive forward the production of these databases and the development of retrieval software. 

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. 

---