Example 1 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 

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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. 

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. 

Figure 11 An example of a modem reaction retrieval interface MDL s RXL Browser (reprinted with permission of MDL information Systems, Inc.)...

Figure 5-28. Reaction query for Example 2 "R indicates that the bond must be part of a ring system, and "53 represents an atom with three non-hydrogen attachments. The Chiral" flag is necessary to retrieve only molecules with the identical absolute stereoconfiguration.

A number of methods have been developed to introduce context to on-line databases, enabling searches to be refined to minimized false retrieval. One of the earliest techniques is proximity searching, in which two words are required to be adjacent, or within a limited distance from each other in text. The assignment of roles to chemical substances is a method of precoordinating concepts. A substance can be identified as a reactant, as a product, and in some systems in a number of additional roles. For example, by searching for documents in which formaldehyde is a product, documents in which it is a reactant, or in which it undergoes no reaction, are thus eliminated. 

Obviously a compound registration system is already a fundamental part of the informatics infrastructure for any pharmaceutical company. However, there is a powerful efficiency gain in not having scientists input information twice into different systems the reaction information into the ELN and then the product molecules into the registration system. One would rather have a mechanism of pushing the product molecule information from the ELN to the registration system. The obvious corollary to this is to have the ability to retrieve compound information from the registration system and have it automatically entered into the ELN—an example would be for the scientist to... 

A reasonable objection to any in vitro model is whether it accurately mirrors the actual process. A strength of this model is that the peptides in the array, mounted on the microscope glass slide, are the very same as the antibody epitopes in the native proteins. Therefore, the types of formaldehyde-induced chemical reactions at or near the epitope are the same as would likely occur in a tissue sample. An additional strength of the model is that the experimental data using the peptide array completely account for the loss of immunoreactivity after formalin fixation and the recovery of immunoreactivity after antigen retrieval (Fig. 16.5). Nonetheless, our data do not prove that the model accurately represents formaldehyde reactions in tissue specimens. For example, our data do not exclude other causes of steric interference. 

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