Databases information retrieval

Budgeting. These changes in the storage and retrieval of chemical information requite that Hbraries and information centers now consider not only what should be purchased but also what monies should be allocated for the purchase of information in nonprint formats such as CD-ROMs (compact disk read-only memory) and on-line databases. Coupled with this is budgeting for the cost of hardware and software to enable the rapid and cost-effective deHvery of needed information (15). The geometric increase in sources, both printed and on-line, has increased the role of information speciaHst as an expert in the deHvery of chemical information. Retrieval from increasingly diverse and complex sources becomes the paramount issue for searchers of chemical Hterature in the 1990s. 

In 1982, the European Space Agency s Information Retrieval Service (ESA/IRS) introduced the ZOOM command, providing users with a mechanism to analy2e retrieved sets. In 1984, service at a baud rate of 2400 was made available by Tymnet and Telenet for pubHc access to on-line databases. In 1985, the first commercial CD-ROM drives for personal computers became available, along with the first commercial CD-ROM databases. 

Citation Searching. In the scholarly Hterature, authors cite earHer pubHcations that relate to the work being reported, thus a subject relationship exists between the citing and cited Hterature. This relationship has formed the basis for the Science Citation Index and related products, developed by the Institute for Scientific Information. Known as Scisearch in its on-line version, the Science Citation Index has become an important information retrieval tool in the second half of the twentieth century. It has been used for straightforward subject searching, in which mode it complements traditional indexed databases and indexes. It has also become a popular tool for hihliometric studies of various sorts, such as attempts to measure the relative impact of research carried out by different individuals or organizations, or the relative impact of pubHcations in different journals. 

Provides access to textual and numeric data in its databases for information retrieval and reporting needs. Features word proximity and phrase searching thesaurus and index. 

AQUIRE - Aquatic Toxicity Information Retrieval Database... 

NPIRS. 1986. National Pesticide Information Retrieval System (database). Chemical fact sheet for Methyl parathion. U S. Environmental Protection Agency, Office of Pesticide Programs, Washington, DC December, 1986. 

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. 

Chemithon film sulfonating-sulfating systems, 23 544-547 Chemithon reactor, 23 544 Chemoinformatics, 6 1-25 chemical databases, 6 19-20 chemical information retrieval, 6 6—19 chemical information storage, 6 2-6 chemical library design, 6 17-18 clustering techniques, 6 16-17 conformational flexibility, 6 10-11 conformational searches, 6 10-11 data analysis and preparation, 6 20-21 data searching, 6 6-19 diversity searches, 6 14-18... 

The DR lines link SWISS-PROT to other biomolecular databases. SWISS-PROT is currently linked to 29 different databases. The preceding example shows links to 19 different entries in 6 different databases. The cross references allow users to navigate to linked databases to retrieve part or all of the related information. The format of a DR line, except for cross references to PROSITE (Hofmann et al., 1999), Pfam (Bateman et al., 1999), and the EMBL nucleotide sequence databases (Stoesser et al., 1999), is the following ... 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

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 information retrieval in MAECIS is accomplished using one of three available commands SHOW, FIND, or SEARCH. The SHOW command is the simplest one to use and requires only a code number or registry number. It allows the user to retrieve all chemical structures and associated information stored under a particular code number. In most cases this fulfills the user s needs. The FIND command is used for complex searches involving various combinations of multiple data fields, handles substructure searching. Queries such structures with a molecular weight between 200 and 250 containing an ester substructure" are handled by the FIND command. Finally, the SEARCH command is used for chemical structure searches. This search takes only seconds and allows the chemist to determine if a particular molecule is already in the database. 

INFORMATION RETRIEVAL. The literature of chemistry and associated fields has increased enormously since 1980. Establishment of sub-specialties and newly defined disciplines as well as increased research output have led to an explosion of journals, books, and on-line databases, all of which attempt to capture, record, and disseminate this plethora of knowledge Tertiary reference tools in chemistry and technology (e.g., Kirk-Othmer, 4th ed.) help track the primary literature. Excellent references that discuss basic chemical information tools are The Literature Mutrix of Chemistry, Chemical Information Sources. and Hots- lo Find Chemical Information. 

WPIM (World Patents Index Markush), produced by Derwent Publications, Ltd., contains the specific and generic structure records for compounds in the patents included in Derwent Sections B (Farmdoc), C (Agdoc), and E (Chemdoc) since 1987. Sources include patents from 29 industrialized countries as well as European and PCT patents and also items from Research Disclosure and International Technology Disclosures. The compound numbers of relevant references found in WPIM can be searched in Derwent s WPI database to retrieve the corresponding bibliographic information. 

Figure 7.5. Search enzyme information at Brenda. Brenda is the comprehensive enzyme database for retrieving chemical, kinetic, and structural properties of enzymes via EC number, enzyme name, and organism (biological source). The search page by EC number is shown.

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. 

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