Retrieval using Structure Searching

As already stated above, the database has been developed using ISIS software. The program operation is very simple, and about 30 min to learn the particular commands of this structure-searching program. ISIS provides both storage and retrieval of chemical structures. It is also possible to store text and numeric data into database entries. Because molecular structures are searchable in many ways, ISIS software is an excellent tool for exploiting data, and not simply archiving it. 

Although an exact search can be useful, in most cases it does not give any more information than can be obtained from the printed CA. Substructure searches (SSS) are far more important, because there is no other way to get this information. If we do a substructure search on 4 in Figure A.l, we not only get all the answers we would get in an exact search, but all substances that contain, anywhere within their structure, the arrangement of atoms and bonds shown in 4. For example, 5,6,7, and 8 would all be retrieved in this search, but 9 would not be. The SSS searches typically retrieve from tens to hundreds of times as many answers as exact searches of the same stracture. Furthermore, the scope can be widened by the use of variable nodes. For example, the symbol X means any halogen, the symbol M any metal, and the symbol G allows the user to specify his or her own variable at that point (e.g., G =C1 or NO2 or Ph). As with an exact search, each answer can be displayed as described above. 

Current chemical information systems offer three principal types of search facility. Structure search involves the search of a file of compounds for the presence or absence of a specified query compound, for example, to retrieve physicochemical data associated with a particular substance. Substructure search involves the search of a file of compounds for all molecules containing some specified query substructure of interest. Finally, similarity search involves the search of a file of compounds for those molecules that are most similar to an input query molecule, using some quantitative definition of structural similarity. 

In the bioinformatics realm, SRS (Sequence Retrieval System) [2] is a popular system, which uses a centralized collection of data resources primarily in flat text file form and, more recently, handles XML (Extensible Markup Language) files as well. Data resources are treated in a federated manner since each is maintained in its original form. However, SRS contains a large number of cross-references between corresponding fields in various data sources, so that keyword searches can be done across them. SRS thus performs more structured searches across the information than what a simple text search provides (such as web indexes perform, for example). Even though the data model implicit in the cross-reference tables is not very deep, SRS provides a useful way for users to browse and do simple queries across a large number of data sources as well as to integrate results from some computational methods. 

The information retrieval in MAECIS is accomplished using one of three available commands SHOW, FIND, or SEARCH. The SHOW command is the simplest one to use and requires only a code number or registry number. It allows the user to retrieve all chemical structures and associated information stored under a particular code number. In most cases this fulfills the user s needs. The FIND command is used for complex searches involving various combinations of multiple data fields, handles substructure searching. Queries such structures with a molecular weight between 200 and 250 containing an ester substructure" are handled by the FIND command. Finally, the SEARCH command is used for chemical structure searches. This search takes only seconds and allows the chemist to determine if a particular molecule is already in the database. 

The Novosibirsk Institute of Oiganic Chemistry has developed a method for computer-aided retrieval of structural information from Tl-nmr using its database of 50,000 spectra (72). Fraser Williams Ltd. (Scientific Systems) has special software to search its 19F-nmr database (73). Protein nmr data have been compiled into a relational database at the University of Wisconsin (74). 

Flexmatch Search. Term used in MDL structure searching to allow "relaxed" exact match searching of structures. One can specify, for instance, that everything must match except bond orders, or stereochemistry, or valence at atom centers, etc. By turning on or off various flags, one can for a given structure query, retrieve isomers of various types, salts of a the structure, or instances of the structure that may contain different values of certain types of attached data. 

Exact 2D structure search All entries in the database that match exactly and completely to a unique query stracture have to be retrieved. The structures can be retrieved rapidly by using hashed lexicographic codes. ... 

We thus have the situation in which essentially three different kinds of computerised retrieval system have evolved. There are specialised S5retems dealing with structural and numeric data, with the emphasis on retrospective searching. There are also standard retrieval systems, using text searching, which are used for both current-awareness and retrospective searching, and which also cover structural and numeric data as far as document retrieval is concerned. We can now consider in more detail how each type of information fits into this pattern. 

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