Databases storing chemical information

In order to store chemical information, there is a need to store chemical structures in some type of database format. For most practical purposes chemical structures are stored in 2D formats as described below. 

It was reahzed quite some decades ago that the amount of information accumulated by chemists can, in the long run, be made accessible to the scientific community only in electronic form in other words, it has to be stored in databases. This new field, which deals with the storage, the manipulation, and the processing of chemical information, was emerging without a proper name. In most cases, the scientists active in the field said they were working in "Chemical Information . However, as this term did not make a distinction between librarianship and the development of computer methods, some scientists said they were working in "Computer Chemistry to stress the importance they attributed to the use of the computer for processing chemical information. However, the latter term could easily be confused with Computational Chemistry, which is perceived by others to be more limited to theoretical quantum mechanical calculations. 

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

As already mentioned (Section 5.3), the stored structure information in this type of database makes it possible to search for chemical structures in several ways. One method is to draw a structure (via a molecule editor) and to perform either a precise structure search (full structure search) or a search containing part of the input structure (substructure search) (see Sections 6.2-6.4). The databases also allow the searching of chemical names and molecular formulas (see Section 6.1). The search results are in most cases displayed in a graphical manner. 

Bibliographic/Technical. The principal databases in which bibhographic chemical information is stored are hsted in Table 1. Examples of the use of these databases include searching the CA file to find the pubhshed work of a certain author, or the World Textiles file to determine the extent of weft knitting machinery use in Europe. 

The CrossFire Beilstein database is the world s largest compilation of chemical facts. This database indexes three primary data domains substances, reactions and literature. The substance domain stores structural information with aU associated facts and literature references, including chemical, physical and bioactivity data. The reaction domain details the preparation of substances, enabling scientists to investigate specific reaction pathways with reaction search queries. The literature domain includes citations, titles and abstracts, which are hyperhnked to the substance and reaction domain entries. It contains over 320 million experimental data, over 10 million reactions and data indexed from over 175 journals. 

United Nations APELL (Awareness and Preparedness for Emergencies at the Local Level) [15] chemical accident database (storing information on about 300 major chemical accidents between 1970 and 1998) shows that ... 

The greatest benefit of RACHEL S component extraction method is that a massive property index of the entire corporate database is created. Along with the atomic coordinates of each component, a wealth of chemical information characterizing each building block is stored. Data such as the size of the component, atom composition, connectivity, ring structure, and electrostatic charges are included. As such, a means of rapidly cross-referencing chemical components on demand is available. 

Solvent extraction Database (SXD) software has been developed by A. Varnek et al.51 Each record of SXD corresponds to one extraction equilibrium and contains 90 fields to store bibliographic information, system descriptions, chemical structures of extractants, and thermodynamic and kinetic data in textual, numerical, and graphical forms. A search can be performed by any field including 2D structure. SXD tools allow the user to compare plots from different records and to select a subset of data according to user-defined constraints (identical metal, content of aqueous or organic phases, etc.). This database, containing about 3,500 records, is available on the INTERNET (http //infochim.u-strasbg.fr/sxd). 

Most corporate databases of chemical compounds (libraries) are of the 2D type. The databases are managed using software that allows fast registration of new structures, fast retrieval of previously stored compounds, and fast substructure searching. (For more information about chemical database management software, see www.mdl.com or www.daylight.com.)... 

Accord Enterprise Informatics (AEI) products integrate to offer an Oracle-based enterprise-wide solution for chemical information management. These products draw on the power of the Accord Chemistry Engine and Oracle databases to store, search, and analyze chemical structures, related biological and chemical data, experimental results, and registration information. 

Databases are used widely in commercial applications and have become the foundation of modern data processing. Various bibliographic, financial and chemical reference databases are perhaps the most familiar to scientists at this time. However, the proliferation of Laboratory Information Management Systems (LIMS) makes analytical laboratory databases accessible to most laboratory personnel. Such databases store analytical data and scientific information from which a variety of documents and reports are generated. 

Inventories (i.e., databases) storing information on chemicals, molecular structures, models, predictions, and experimental data. 

The goal of this book is to convince you that relational databases are the best way to store, search, and even operate on chemical information. Whether the database contains a hundred structures or ten million, a relational database provides ways to ensure data integrity, to formalize relationships among the data, and to extend the database when new data become available or when new ways of operating on data become of interest. 

Chapter 7 introduces ways in which RDBMS can be used to handle chemical structural information using SMILES and SMARTS representations. It shows how extensions to relational databases allow chemical structural information to be stored and searched efficiently. In this way, chemical structures themselves can be stored in data columns. Once chemical structures become proper data types, many search and computational options become available. Conversion between different chemical structure formats is also discussed, along with input and output of chemical structures. 

Through examples of good database design, this book shows you that relational databases are the best way to store, search, and operate on chemical information. 

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