Topics databases

In addition to the above mentioned databases that try to cover the entire world of enzymes, there are a number of more topical databases focusing on particular enzyme families. The MEROPS database, maintained at the Babraham Institute in Cambridge, provides a catalog and a structure-based classification scheme for all proteolytic enzymes 58. In addition to the classification, the database also provides a digest of published information on the peptidases as well as dadograms and multiple sequence alignments of the peptidase families. 

In view of the wealth of data now obtained for brucine in this example, it may be of interest to the reader to augment this set of results by pursuing the search into a topics database, such as the CAS file. To round off this example, the 3D information on brucine can be obtained from one of the medium-sized databases, such as the CSD file. A substructure search produced 13 examples of brucine complexes, such as the example hown in Table 10. In the CSD file, it is also easy to obtain a list of all of the text and numeric data for the entries (space group, cell parameters, etc.) and the corresponding coordinates for graphical display and computational purposes. 

A wider variety of reaction types involving reactions at bonds to oxygen atom bearing functional groups was investigated by the same kind of methodology [30]. Reaction classification is an essential step in knowledge extraction from reaction databases. This topic is discussed in Section 10.3.1 of this book. 

To get to know various databases covering the topics of bibliographic data, physicochemical properties, and spectroscopic, crystallographic, biological, structural, reaction, and patent data... 

The initial step is to identify which database, from a few thousands worldwide (about 10 000 in 2002), provides the requested information. The next step is to determine which subsection of the topic is of interest, and to identify typical search terms or keywords (synonyms, homonyms, different languages, or abbreviations) (Table 5-1). During the search in a database, this strategy is then executed (money is charged for spending time on some chemical databases). The resulting hits may be further refined by combining keywords or database fields, respectively, with Boolean operators (Table 5-2). The final results should be saved in electronic or printed form. 

More than 10 000 databases exist that provide a small or large amount of data on various topics (including chemistry). The contents in databases are supplied by approximately 3500 database developers (e.g., the Chemical Abstracts Service, MDL Information Systems, etc.). Since there is a variety of topics from economics to science, as well as a variety of structures of the database, only some of the vendors (-2000) offer one or more databases as either local or as online databases (Figure 5-4) [4]. Usually, databases are provided by hosts that permit direct access to more than one database. The search occurs primarily through different individual soft-... 

The Chemical Abstracts System (CAS) produces a set of various databases ranging from bibliographic to chemical structure and reaction databases. All the databases originate from the printed media of Chemical Abstracts, which was first published in 1907 and is divided into different topics. Author index, general index, chemical structure index, formula index, and index guide arc entries to the corresponding database (Table 5-3). 

The reinaining five search topics (Research Topic, Author Name, Document Identifier, Company Namc/Organii ation, and Browse Table of Contents arc conducted in a similar fashion, with the input being the only difference between the criteria. Thus, in Research Topic" the entry can be any, or even several, keywords or phrases. In "Author Name", literature written by a specific author will be Found, including alternative spelling, Document Identifier" can also be entered directly in the query. Document identifiers arc CA abstract numbers, patent numbers, patent application numbers, or priority application numbers. The last two search topics (Company Name/Organi2ation, and Browse Table ofContents) allow one to search for literature from specific companies or to view the list of journals which are available in the database. 

Many biochemical databases with sophisticated topics have been developed for solving various problems. Since 1996 the first issue of each journal volume of Nucleic Acid Research has been reserved for the presentation of molecular biology databases [28]. A comprehensive catalog on the Internet is DBCAT, currently listing 511 databases [29, 30). 

A most important task in the handling of molecular data is the evaluation of "hidden information in large chemical data sets. One of the differences between data mining techniques and conventional database queries is the generation of new data that are used subsequently to characterize molecular features in a more general way. Generally, it is not possible to hold all the potentially important information in a data set of chemical structures. Thus, the extraction of relevant information and the production of reliable secondary information are important topics. 

Daily Report for Executives Environment Reporter Environmental Compliance Update Environmental Health News (EHN) Environmental Law Reporter Guide to Eederal Environmental Laws Statens Naturvardsverk Toxic Law Reporter WESTI AW Environmental Administrative Law Database WESTI AW Environmental Law Library WESTLAW Topical Hivblivhts ... 

There is also a growing number of specialized databases available on specific topics such as CEC Replacement, effluents and pesticides, environmental chemical data, etc. These are usually on CD-ROM or floppy disk (3). 

Subject Categories. The deterrninant for user selection of a database is usually subject matter. That is, when chemical information is desired, a chemical database is selected. The form or media of the database is of secondary importance. The type of search may dictate the need for a full-text or statistical database. If none exists, however, a bibhographic database in the topic area may be used to locate full-text or numeric compilations in hard-copy form. 

Databases may be viewed as a research tool for those in highly competitive fields such as science, engineering, and technology. This tool makes information available so that its user can make decisions based on comprehensive and timely data (7). A guide to commercially available databases relating to topics associated with science and technology follows. 

NIOSHTIC on compact disc from the Canadian Center for Occupational Health and Safety (ean buy at CCOHS web site). "NIOSHTIC(R) is a bibliographie database which provides comprehensive international coverage of documents on occupational health and safety, as well as related fields. It eontains detailed summaries of over 200,000 articles, reports and publications, spanning over 100 years. NIOSHTIC(R) sources include over 160 scientific and technical journals, NIOSH reports (published and unpublished), NIOSH research bibliographies, abstracts from CIS Abstracts, and personal files from respected professionals on selected topics. 

The CESARS database contains comprehensive environmental and health information on chemicals. It provides detailed descriptions of chemical toxicity to humans, mammals, aquatic and plant life, as well as data on physical chemical properties, and environmental fate and persistence. Each record consists of chemical identification information and provides descriptive data on up to 23 topic areas, ranging from chemical properties to toxicity to environmental transport and fate. Records are in English. Available online through CCINFOline from the Canadian Centre For Occupational Health and Safety (CCOHS) and Chemical Information System (CIS) on CD-ROM through CCIN-FOdisc. 

This chapter provides the basic knowledge and skills required to implement a computer-based vibrationmonitoring program. It discusses the following topics (1) typical machine-train monitoring parameters, (2) database development, (3) data-acquisition equipment and methods, and (4) data analysis. 

We should not minimize the effects that electronic searching of patents has had on the business of research. In 1990, CAS introduced MARPAT, which is a database of Markush (generic) structures found in patent documents [1]. This database provided a valuable tool for patent searching in a more comprehensive way than had been available previously. In 1995, CAS launched SciFinder, which provided access to the patent literature for chemists on their desktops. Using the SciFinder interface, one may search for research topics, authors, companies, or structures/reactions. From a practical viewpoint, SciFinder did more to enhance the searching capabilities of the medicinal chemist than any other tool. Even today, SciFinder continues to provide a first pass through the patent literature when chemists want to include patents in their searching. Indeed, when a search is performed, patent references are included in the answer set. Only very recently have there been additional tools to search the patent literature that have found widespread use. 

The safety professional s online library, covering topics related to safety, safety management, ergonomics, fleet and environment. The Safety Library contains over 40 environmental databases and over 70 databases of chemical profiles. Subscription is required. 

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