Personal chemical databases

A number of software and database vendors provide programs and database systems to implement representation, registration, and searching of chemical information in a corporate environment. Some of these vendors have smaller personal chemical database systems that support registration and searching on a personal computer. A handful of academic and public domain systems are also available. Finally, an increasing number of chemical information systems are being made available on... 

It is important to note that theoretic argument and empiric study have shown that the LOO cross-validation approach is preferred to the use of an external test set for small to moderate sized chemical databases [39]. The problems with holding out an external test set include (1) structural features of the held out chemicals are not included in the modeling process, resulting in a loss of information, (2) predictions are made only on a subset of the available compounds, whereas LOO predicts the activity value for all compounds, and (3) personal bias can easily be introduced in selection of the external test set. The reader is referred to Hawkins et al. [39] and Kraker et al. [40] in addition to Section 31.6 for further discussion of proper model validation techniques. 

Earger chemical and pharmaceutical firms have, over the years, developed in-house systems with capabilities that are specific to the chemist s needs. Today, the costs of developing from scratch and maintaining an in-house system are prohibitive, especially because commercial chemical information systems are highly efficient and customizable. Personal chemical information software is still being developed and reported in the literature. Examples include a relational database patterned after the Upjohn Cousin system (108), and CheD, which is a SQL-based system with a Web client (109). 

Commercial personal database systems are available from several vendors, as described above. These products extend the productivity of an individual chemist or a small workgroup, but are not designed for corporate or enterprise applications. Other personal chemical... 

Information from a publication in the Journal of Medicinal Chemistry has been used to illustrate some potential applications of the Chemist s Personal Software Series, ranging from chemical database management to mini/mainframe database access to report generation. ChemBase, ChemTalk, ChemHost and ChemText work together to provide a complete workstation information management system. 

An important factor in the progress of bioinformatics has been the constant increase in computer speed and memory capacity of desktop computers and the increasing sophistication of data processing techniques. The computation power of common personal computers has increased within 12 years approximately 100-fold in processor speed, 250-fold in RAM memory space and 500-fold or more in hard disk space, while the price has nearly halved. This enables acquisition, transformation, visuahsation and interpretation of large amounts of data at a fraction of the cost compared to 12 years ago. Presently, bioanalytical databases are also growing quickly in size and many databases are directly accessible via the Internet One of the first chemical databases to be placed on the Internet was the Brookha-ven protein data bank, which contains very valuable three-dimensional structural data of proteins. The primary resource for proteomics is the ExPASy (Expert Protein Analysis System) database, which is dedicated to the analysis of protein sequences and structures and contains a rapidly growing index of 2D-gel electrophoresis maps. Some primary biomolecular database resources compiled from spectroscopic data are given in Tab. 14.1. 

Personal Computers. IBM PC s (personal computers) and clones with the MS-DOS operating system have become a popular microcomputing environment for the chemical/pharmaceutical industry. Many software products are available for this system including MDL s ChemText chemical word processor, ChemBase chemical database, and ChemTalk terminal program, ORACLE S RDBMS, and BBN s RS/1 statistics program. 

Figure 1 shows a schema for an ideal distributed chemical information system. Several authors in this book refer to the need for standard interfaces. Ultimately, the personal computer will provide the graphics interface not only to personal computer databases but also to company databases running on the company mainframe, and possibly also through the same network to public hosts, so that the chemist using a personal workstation will be able to create queries which can be addressed to local files, company files and public files. Soon, chemical databases will be available on Compact Disk Read Only Memory (CD-ROM) searchable by both substructure and text. These too fit into the scheme of Figure 1. Databases such as infra-red spectra libraries will have structure-searchable components either on the personal computer or on the laboratory instrument and will also be used through the same graphical interface.

The earliest chemical databases which became available on PC s were not structure-based. In the UK one of the first chemical databases distributed on personal computers was the hazards database CHEMDATA which was developed at the Chemical Emergency Centre at Harwell. This was a database created primarily for the emergency services to help deal with chemical emergencies. Initially, the database was offered as an online service, but obviously the need to keep this service operational 24 hours a day, 7 days a week, put tremendous strains on the operators of the service and as soon as the first microcomputers were introduced, the Chemical Emergency Centre recognised their potential for distributing the data in another form. 

The construction of literature databases has been carried out after the format of the personal database system TOOL-IR-PDB/Orion, which was initially designed as the sub-system of the database management system TOOL-IR in the Computation Center of the University of Tokyo. This personalliterature database system has been applied to construct several chemical databases including those for solvent extraction, nuclear magnetic resonance spectroscopy, abstracts and preprints of some important domestic symposia held in Japan, etc. [3]. 

All chemical shift data presented in this book come either from the primary literature or from spectra obtained in the author s laboratory. All spectra actually depicted in the book derive from spectra obtained by the author at the University of Florida. All data from the literature were obtained via searches using MDL Crossfire Commander or SciFinder Scholar. Persons interested in accessing such primary literature can do so readily via these databases by simply searching for the specific compound mentioned in the text. 

Cumulative distributions of the logarithms of NOELs were plotted separately for each of the stmcmral classes. The 5th percentile NOEL was estimated for each stmctural class and this was in mrn converted to a human exposure threshold by applying the conventional default safety factor of 100 (Section 5.2.1). The stmcmre-based, tiered TTC values established were 1800 p,g/person/ day (Class I), 540 pg/person/day (Class II), and 90 pg/person/day (Class III). Endpoints covered include systemic toxicity except mutagenicity and carcinogenicity. Later work increased the number of chemicals in the database from 613 to 900 without altering the cumulative distributions of NOELs (Barlow 2005). 

Research articles of interest to biochemists may appear in many types of research journals. Research libraries do not have the funds necessary to subscribe to every journal, nor do scientists have the time to survey every current journal copy for articles of interest. Two publications that help scientists to keep up with published articles are Chemical Titles (published every 2 weeks by the American Chemical Society) and the weekly Current Contents available in hard copy and computer disks (published by the Institute of Science Information). The Life Science edition of Current Contents is the most useful for biochemists. The computer revolution has reached into the chemical and biochemical literature, and most college and university libraries now subscribe to computer bibliographic search services. One such service is STN International, the scientific and technical information network. This on-line system allows direct access to some of the world s largest scientific databases. The STN databases of most value to life scientists include BIOSIS Pre-views/RN (produced by Bio Sciences Information Service covers original research reports, reviews, and U.S. patents in biology and biomedicine), CA (produced by Chemical Abstracts service covers research reports in all areas of chemistry), MEDLINE, and MEDLARS (produced by the U.S. National Library of Medicine and Index Medicus, respectively cover all areas of biomedicine). These networks provide on-line service and their databases can be accessed from personal computers in the office, laboratory, or library. Some... 

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