Integrated retrieval systems

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 ... 

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. 

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. 

In the bioinformatics realm, SRS (Sequence Retrieval System) [2] is a popular system, which uses a centralized collection of data resources primarily in flat text file form and, more recently, handles XML (Extensible Markup Language) files as well. Data resources are treated in a federated manner since each is maintained in its original form. However, SRS contains a large number of cross-references between corresponding fields in various data sources, so that keyword searches can be done across them. SRS thus performs more structured searches across the information than what a simple text search provides (such as web indexes perform, for example). Even though the data model implicit in the cross-reference tables is not very deep, SRS provides a useful way for users to browse and do simple queries across a large number of data sources as well as to integrate results from some computational methods. 

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

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. 

FIGURE 14.9 Integration of inventory system with other components of operational informatics environment (right) and with compound storage and retrieval system (CSRS) and plate and sample manipulation instrumentation (left). 

U.S. EPA. 1996. Carcinogenicity Assessment for Benzo[a]pyrene. Integrated Risk Information Retrieval System, U.S. Environmental Protection Agency, Washington, DC. Online file... 

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... 

Figure 7.1. Overview of the relationships in the Entrez integrated information retrieval system. Each square represents one of the elements that can be accessed through Entrez, and the lines represent how each element connects to the other elements. Entrez is under continuous evolution, with both new components being added and the interrelationships between the elements changing dynamically.

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. 

Wang, J. Y., and Yih, Y. (1997), Using Neural Networks to Select a Control Strategy for Automated Storage and Retrieval Systems (AS/RS), International Journal of Computer Integrated Manufacturing, Vol. 10, No. 6, pp. 487 95. 

Integration of a synthesis planning system and a reaction retrieval system to explore individual steps for literature precedents would result in an extremely powerful design tool. 

There is no sense in collecting data if you are not going to use it, and if you do collect it how are you going to store it so you can find it when you want it Whatever system is used must match identified needs and integrate with existing data storage and retrieval systems. 

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