Databases reaction

A complicating factor is that there are many non-stoichiometric reactions in REACCS databases. Reactions are represented in REACCS in a manner similar to the way they appear in the literature grossly unbalanced, some structures left out, large fragments have disappeared, and so forth. Many reactions represent summaries of several steps, where reacting centres are poorly localised. These reactions are characterised by the following attributes ... 

By definition, any target structure that is a substructure (or superstructure) of the database molecule will have a subsimilarity (or supersimilarity) of 1.0, and hence a subsimilarity (supersimilarity) search can be viewed as a form of fuzzy substructure (superstructure) search. A further difference from the systems described thus far is in the nature of the output. The description of similarity searching that has been given previously assumes that a user browses down a ranked output until sufficient database structures have been identified. Here, conversely, the user specifies a threshold similarity value, and the output consists of an unordered list of all database structures (or database reactions) that have a similarity to the target that exceeds the chosen threshold value. 

In 1967, work was presented from a Sheffield group on indexing chemical reactions for database budding. In 1969, a Harvard group presented its first steps in the development of a system for computer-assisted synthesis design. Soon afterwards, groups at Brandeis University and TU Munich, Germany, presented their work in this area. 

Other related coding languages are derived from enhancements of SMILES (XSMILES, SMARTS, SMIRKS, STRAPS, CHUCKLES, CHORTLES, CHARTS [22]). Each of them was designed to represent special molecular structures or to allow particular applications (polymers, mixtures, reactions, or database-handling). 

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

When is a compound to be considered as a starting material, and when as a reagent There is certainly some arbitrariness involved in such a distinction, because both a starting material and a reagent might contribute atoms to the reaction products. Some reaction databases consider a compound to be a starting material when... 

Unfortunately, in most cases not all the available information on a reaction is given in the reaction equation in a publication, and even less so in reaction databases. To obtain a fuller picture of the reaction that was performed, the text describing the experimental procedure in the publication or a lab journal) would have to be consulted. Reaction products that are considered as trivial, such as water, alcohol, ammonia, nitrogen, etc., are generally not included in the reaction equation or mentioned in the text describing the experimental work. This poses serious problems for the automatic identification of the reaction center. It is highly desirable to have the full stoichiometry of a reaction specified in the equation. 

The reaction center has either to be spedfied when inputting a reaction into a database, or it has to be determined automatically. Specification on input is time-consuming but it can benefit from the insight of the human expert, particularly so if the reaction input is done by the primary investigator as is the case in an electronic notebook. Automatic determination of reaction centers is difficult, particularly so when incomplete readion equations are given where the stoichiometry of a reaction is not balanced see Section 3.1). One approach is to try first to complete the stoichiometry of a reaction equation by filling in the missing molecules such as water, N2, etc. and then to start with reaction center determination. A few systems for automatic reaction center specification are available. However, little has been published on this matter and therefore it is not discussed in any detail here. 

The next question is how to represent the reacting bonds of the reaction center. We wanted to develop a method for reaction classification that can be used for knowledge extraction from reaction databases for the prediction of the products of a reaction. Thus, we could only use physicochemical values of the reactants, because these should tell us what products we obtain. 

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. 

Specification of the reaction center is important for many queries to reaction databases. 

Reaction classification is an essential step in knowledge acquisition from reaction databases. 

Sf The Chemlnjbrm RX reaction database is produced by FIZ Chemie, Berlin, Germany, and marketed by MDL Information Systems, Inc., San Leandro, CA, USA. 

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

Reaction databases additionally contain information on chemical reactions, giving the reaction participants and reaction conditions of both single- and multi-step reactions. 

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). 

CASREACT The CASREACT Eile (The Chemical Absiracts Reaction Search Service) is a chemical reaction database with reaction inlormatioii derived from journal documients from 1974 to the present and from patent documeiiis from 1982 to date. Thie document-based file conlains both 3 million single-step and 3.0 million multi-step reactions (Pcbiniaiy, 2003). 

Thus, if the user wants to look for literature including requested chemicals or reactions, it is possible to query the database by the first option Chemical Substance or Reaction , The compound can be entered as a query in three different ways drawing the chemical structure in a molecule editor (Chemical Structure) searching by names or identification number, such as the CAS Number (Structure Identifier) and searching by molecular formula (Figure 5-12). 

This tutorial, which is based on the Beilstein update BS0202PR (May, 2002) and on the retrieval program Cro.ssFire Commander V6,. shows. some typical advanced search examples in the Beilstein database. It is assumed that the user already knows some of the basic features of the retrieval program. Moreover, in this tutorial the CrossFire Structure Editor is used instead of the (SIS/Draw Structure Editor. The first example is a combined application of structure aiM fact retrieval, whereas the second example demonstrates reaction retrieval. 

After return to the Commander window, the reaction retrieval may be executed separately 629 Dicls-Aldcr reactions between aliphatic dienes and cyclic dicno-pliiles are found. This partial result can be narrowed down by restricting tlie reaction conditions by means of the fact editor, The search field codes for the yield and the temperature can be found to be RX.NYD and RX.T, respectively, either by browsing the database structure or by applying the Find option, as described in the first example. To ensure that the retrieved reaction conditions belong to the same experiment, both search terms must be connected by means of the PROXIMITY operator. Before the retrieval is started, the option "Refine results in... 

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. 

A review on reaction databases can be found in Ref [40] and an introductory section on searching in the Cheminform Reaction Database is contained in the tutorial in Section 5.13. 

CASREACT (Chemical Abstracts Reaction Search Service) is a reaction database started in 1985 with more than 6.7 million reactions (3 million single-step and 3.7 million multi-step reactions) (March, 2003) derived from 400 000 documents (journals, patents, etc.). The records contain the following information ... 

This tutorial describes briefly some of the search capabilities possible with Cheminform RX and MDL" ISIS used as the retrieval system. In this tutorial, the CIRX database. of the years 1992-1996 arc used, containing altogether 334 855 reactions. 

In this section, the basic concepts of reaction retrieval are explained. The first example is concerned with finding an efficient way to reduce a 3-methy]cydohex-2-cnonc derivative to the corresponding 3-mcthylcyclohcx-2-cnol compound (see Figure 5-24). As this is a conventional organic reaction, the CIRX database should contain valuable information on how to syntbesi2e this product easily. 

First, a quei y must be drawn using the MOL" ISIS/Draw program. By using this reaction query, a eurrent reaction search " can be performed. This type of reaction retrieval compares the starting material and the product of the reaction query with all the reactions in the CIRX database. Both query structures must match exactly, including the implicit hydrogen atoms not shown in the reaction query. In this case, one hit is found in the CIRX databases. 

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