Integration—chemical structures with text

Software for drawing and displa)dng chemical structures on microcomputers has been a growth area in the last year or two. Graphics for chemical structures, and integration of the structures with text or data, is the subject of a recent book. ... 

Patent databases are therefore integrated databases because facts, text, tables, graphics, and structures are combined. In patents that include chemical aspects (mostly synthesis or processing), the chemical compounds are often represented by Markush structures (see Chapter 2, Section 2.7.1). These generic structures cover many compound families in a very compact maimer. A Markush structure has a core structure diagram with specific atoms and with variable parts (R-groups), which are defined in a text caption. The retrieval of chemical compounds from Markush structures is a complicated task that is not yet solved completely satisfactorily. 

Bradshaw et al. have disclosed a rapid and facile method for the dereplication of a purified natural product library [58]. The method integrates the molecular weight from low resolution MS data with the exact count of the number of methyl, methylene and methine groups obtained from ]H-13C NMR correlation data. Those structure properties were converted into a searchable text file that could be downloaded into a customized software program with chemical structure information in a specific format - SMILES. In the program, more than 120,000 unique structures were derived from commercial databases, such as Dictionary of Natural Products and Beilstein. 

Of course, it will be important to store the chemical structure itself. Clearly, a complete chemical structure cannot be represented using basic SQL data types, such as numeric or text. While a compound name (text) might be considered a good representation of molecular structure, there are better ways to represent molecular structure. In this chapter, a compound will simply be identified with a unique compound id serving as a foreign key to a more complete representation of structure in another table. The following chapters will show ways that chemical structures can be fully integrated into the tables of a database. This chapter concentrates on the proper use of chemical data and ways in which multiple relational tables can be used. 

Hanson, R.M., The Threefold Challenge of Integrating Text with Chemical Graphics. Chapter 11 in Graphics for Chemical Structures Warr, W. Ed. ACS Symposium Series 341 American Chemical Society Washington, 1987. 

The first attempt to integrate the chemical system with the external literature took the form of an Information Imaging Technology Patent Information System, ITPAIS. This is a collaborative venture of Kodak with Agfa, Fuji and the Rochester Institute of Technology. ITPAIS uses a photoscience thesaurus and contains 95,000 chemical accession numbers. Microfilm indexes to text and chemical structures are disseminated to the collaborating companies and DIALOG provides text access to the participants. 

Some consumers now have requirements for integration of documents, text, and graphics, or images with the rest of their chemical information. The community is still struggling with individual standards for chemical structures, for data, and for documents. Standards for integration are not even being considered. Unless we are careful, this will lead to another round of software systems to solve today s problems, and another round of incompatible systems in the future. 

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