Databases and Data Sources in Chemistry

Chemoinformatics A Textbook. Edited by Johann Gasieiger and Thomas Engel Copyright 2003 Wiley-VCH Verlag GmbH Co. KGaA. 

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Combinatorial chemistry and HT E are powerful tools in the hands of a scient ist, as they are a source for meaningful consistent records of data that would be hard to obtain via conventional methods within a decent timeframe. This blessing of fast data acquisition can turn into a curse if the experimentalist does not take precautions to carefully plan the experiments ahead and the means of handling the data and analyzing them afterwards. The two essential elements that ensure a successful execution of ambitious projects on a rational and efficient basis are, therefore, tools that enable the scientist to carefully plan experiments and get the most out of the minimum number of experiments in combination with the possibility of fast and reliable data retrieval from databases. Therefore, experimental planning and data management are complementary skillsets for the pre- and post experimental stages. 

TDSNUMERICA, This is another source for numeric databases (58). This company provides different on-line databases and software for chemistry, engineering, and environmental data. A summary of its databases is contained in Table 7. 

The terms bioinformatics and cheminformatics refer to the use of computational methods in the study of biology and chemistry. Information from DNA or protein sequences, protein structure, and chemical structure is used to build models of biochemical systems or models of the interaction of a biochemical system with a small molecule (e.g., a drug). There are mathematical and statistical methods for analysis, public databases, and literature associated with each of these disciplines. However, there is substantial value in considering the interaction between these areas and in building computational models that integrate data from both sources. In the most... 

Reliability of thermodynamic data in program databases are often a subject of controversy. Constants AS AH AZ ° from different sources for the same compound may turn out incompatible. This difference is especially prominent at comparison of the data from domestic and foreign sources. For instance, free enthalpy of KH PO formation after Kraynov et al. (2004) is -1,411.4 kJ-mole and after Lances Handbook of Chemistry (1999) -1,622.85 kj-mole" in case of H AsO " the same parameter has values -593,73 and -587,22 kj-mole in the same sources. Errors associated with this show up at the determination of pH, SI, etc. There is some level of consent between commonly available databases for most common minerals and water components. This does not mean, however, that the results are equally correct or precise. Sometimes it is caused by different notions of precision and correctness. The responsibihty for errors caused by database parameters is on the user, not on the program creator. For this reason critical evaluation of the utilized database by the user is a must. He has the right to edit his databases on his sole discretion regardless of the nature and intent of the program. In this connection he must be appraised of the current literature and current changes in necessary thermodynamic constants. 

Many chemical databases are available, usually on the Web. The CRC Handbook of Chemistry and Physics is the standard reference for many types of data and is available in Ubraries. The Merck Index is a standard reference for the properties of many organic compounds, especially ones of biological interest. WebElements (http //www.webelements. com/) is a good Web site for looking up the properties of the elements. Wolfram Alpha (http //www.wolframalpha.com/) can also be a source of useful information on substances, numerical values, and other data. 

The first place that one should generally look for thermochemical data is in the NIST Chemistry Web Book [24], available at http // webbook.nist.gov. This database contains thermochemical properties for more than 7000 small organic and inorganic compounds, and includes the entire contents of several other databases. Table 5 shows the enthalpies of formation and standard entropies of the species from the reaction mechanism in Table 4 that are available in the NIST WebBook. These properties were available for 10 of the 15 species. The source cited in the NIST WebBook for all these species was the NIST-JANAF Themochemical Tables [25], which have long been the first choice for finding thermochemical data for inorganic and very small organic... 

The empirical investigation is based on a random sample of 10,000 European chemical and pharmaceutical patents applied for at the EPO (European Patent Office, 1998) in 1986-1997. Each patent is allocated to a specific branch of the chemical industry biotechnology, materials, organic chemistry, pharmaceuticals and polymers. I use the zip code contained in the address of the inventors to assign each patent to the European region in which it was invented. Information on the characteristics of the innovations, of the regions in which these innovations are invented, and of the firms that developed them are collected from the EPO database and other data sources. 

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