Factual database

Factual databases mainly contain alphanumeric data on chemical compounds. In contrast to bibliographic databases, factual databases directly describe the objects primary data on chemical compounds) and provide the required information on them. Factual databases can be divided into numeric databases, metadatabases, research project databases, and catalogs of chemical compounds. 

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Chemical Abstracts Service Information System Chemical Engineering Databases Environmental Information Databases Factual Information Databases Online Databases in Chemistry. 

Benchmark Studies on Small Molecules Cambridge Structural Database Chemical Engineering Databases Factual Information Databases Force Fields A General Discussion Inorganic Chemistry Databases Quality Control, Data Analysis Rates of Chemical Reactions Spectroscopic Databases. 

Chemical Abstracts Service Information System Chromatography Processing of Information Electronic Laboratory Notebooks Electronic Publishing of Scientific Manuscripts Environmental Information Databases Factual Information Databases Internet Internet-based Computational Chemistry Tools Laboratory Information Management Systems (LIMS) Online Databases in Chemistry Spectroscopic Databases Structure and Substructure Searching Structure Databases. 

Numerical databases -> factual databases with a large variety of single fields with numeric data, e.g. physico-chemical properties, which can be searched by numeric operators. Sometimes calculations are possible as well. 

The user is often more interested in the contents than in the technical organization of databases. The wide variety of data allows the classification of databases in chemistry into literature, factual (alphanumeric), and structural types (Figure 5-10) [12, 13). 

A strict separation of these three types of databases is difficult hence most databases contain a mixture of data types. Therefore the classification given here is based on the predominating data type. For example, the major emphasis of a patent database is on hterature, whereas it also comprises numeric and structural data. Another type is the integrated database, which provides a supplement of additional information, especially bibhographic data. Thus, different database types are merged, a textual database and one or more factual databases. 

In addition to the numeric data (color, solubility, refraction index, spectra, etc.), these factual databases also include a bibliographic section with references or sources and a section with information for the identification of a compound (e.g., name, CAS Registry Number, molecular weight). 

Factual databases may provide the electronic version of printed catalogs on chemical compoimds. The catalogs of different suppliers of chemicals serve to identify chemical compounds with their appropriate synonyms, molecular formulas, molecular weight, structure diagrams, and - of course - the price. Sometimes the data are linked to other databases that contain additional information. Structure and substructure search possibihties have now been included in most of the databases of chemical suppliers. 

Research project databases include information on abstracts and reports categorized by research projects. Such factual databases allow one to search for projects in various fields of science and technology wdth numeric and textual queries. 

Beilstein and Gmelin are the world s largest factual databases in chemistiy. Beil-stein contains facts and structures relating to organic chemistry, whereas Gmelin provides information on inorganic, coordination, and organomctallic compounds. 

Specinfo, from Chemical Concepts, is a factual database information system for spectroscopic data with more than 660000 digital spectra of 150000 associated structures [24], The database covers nuclear magnetic resonance spectra ( H-, C-, N-, O-, F-, P-NMR), infrared spectra (IR), and mass spectra (MS). In addition, experimental conditions (instrument, solvent, temperature), coupling constants, relaxation time, and bibliographic data are included. The data is cross-linked to CAS Registry, Beilstein, and NUMERIGUIDE. 

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. 

They are classified as bibliographic, factual, and structure databases. 

Beilstein and Cmelin are the world s largest factual databases in chemistry. 

This chapter has only scratched the surface of the multitude of databases and data reviews that are now available. For instance, more than 100 materials databases of many kinds are listed by Wawrousek et al. (1989), in an article published by one of the major repositories of such databases. More and more of them are accessible via the internet. The most comprehensive recent overview of Electronic access to factual materials information the state of the art is by Westbrook et al. (1995), This highly informative essay includes a taxonomy of materials information , focusing on the many different property considerations and property types which an investigator can be concerned with. Special attention is paid to mechanical properties. The authors focus also on the quality and relutbility of data, quality of source, reproducibility, evaluation status, etc., all come into this, and alarmingly. 

The need for an overall and combined chemical structure and data search system became clear to us some time ago, and resulted in the decision to build CHIRBASE, a molecular-oriented factual database. The concept utilized in this database approach is related to the importance of molecular interactions in chiral recognition mechanisms. Solely a chemical information system permits the recognition of the molecular key fingerprints given by the new compound among thousands of fingerprints of known compounds available in a database. 

Beilstein. Beilstein [63], a structure and factual database covering organic chemistry, contains more than 7,688,485 substance records (3/2000). The organic substance records contain reviewed and evaluated documents from the Beilstein Handbook of Organic Chemistry as well as data from 120 journals in organic chemistry covering the period 1779 to the present. Beilstein Database is commercially available in several electronic formats. 

These databases are a rich source of information, yet they do not capture an element of interest, namely the biological endpoint there is no searchable field to identify, in a quantitative manner, what is the target-related activity of a particular compound. Such information is important if one considers that (a) not all chemotypes indexed in patent databases are indeed active - some are just patent claims with no factual basis and that (b) not aU chemotypes disclosed as active are equally active, or selective for that matter, on the target of choice. Furthermore, should one decide to pursue a certain interaction hotspot in a given ligand-receptor structure (assuming good structure-activity models are available), it would be very convenient to mine structure-activity databases for similar chemotypes to use as potential bioisosteric replacements. 

GCMs are particularly useful in property estimation when used in combination with a factual database and molecular-similarity-based devices. This approach is discussed in the next section. 

JICST/JOIS. The Japan Information Center for Science and Technology (JICST) Mass Spectral Database is accessible to users in Japan through the JICST Factual Database System (fOIS-F). The database uses the NIST/EPA/ MSCD data collection supplemented by spectra from the Mass Spectrometry Society of Japan (84). 

The TOXNET databases contain various types of information. One group of these databases, sometimes referred to as the factual databanks , contain... 

Multi-Database—searches all factual chemical databases for toxicological information. 

Lawson AJ, Jochum CJ. Factual information databases. In Schleyer PvR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer HF, Schreiner PR, editors. The encyclopedia of computational chemistry, Vol. 2. New York Wiley, 1998. p. 983-1002. 

TOXNET http //toxnet.nlm.nih.gov User-friendly Web site that allows searching of a cluster of bibliographic and factual databases with information on toxicology and environmental health. Includes the Hazardous Substances Databank (HSDB), with detailed information about 4500 chemicals, and TOXLINE, containing >3 million citations to journal articles and technical reports. 

There are a number of toxicology databases available on the internet, and recently there has been an amalgamation of the best in the form of TOXNET (http //toxnet.nlm. nih.gov/), a cluster of databases on toxicology, hazardous chemicals, and related areas. The web site provides access to an impressive array of files containing factual information related to the toxicity and other hazards of chemicals. Users can readily extract toxicology data and literature references, as well as toxic release information, on particular chemicals. Alternately, one can perform a search with subject terms to identify chemicals that cause certain effects. A variety of display and sorting options are available. 

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