Schema chemical structure

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

This creates a table of four columns in the schema achemcompany. The column named smiles is intended to store the SMILES representation of a chemical structure, the id column will store an integer identifier to be used for joining other tables, the column mw will store the molecular weight with a precision of 2 digits to the right of the decimal point, and the column named added will record when this structure was entered into the table. As defined above, any character string could be entered into the smiles column, any integer into the id column, and any valid... 

Today, I have turned my habit around. When I have a set of chemical structures or data files, my first task is to organize them in a relational database. After all, the tools I now use are designed to read and write tables in a database. Rather than creating folders to keep project files, I create a schema of tables with rows holding chemical structures and data imported from the files. For example, the PubChem project provides information on millions of compounds in the form of hundreds of chemical structure files and associated experimental data files. While PubChem provides excellent Web tools to search this data, for local use I developed a schema to hold the structures and data in related tables. One possible schema for this is shown in Chapter 6 of this book. 

Other structure-encoding schemas are developed by software vendors and academia such as Daylight Smiles, CambridgeSoft ChemDraw Exchange (CDX), and Chemical Markup Language (CML), and they all have advantages and disadvantages. The MDL CT File Format is the only one that is supported by almost all chemical informatics software vendors. 

The vast majority of chemical information consists of text or numerical data associated with a particular compound, or perhaps a mixture of compounds. Some chemical data cannot yet be associated with any particular structure, or has been measured for compounds whose structure is not yet known. It is important to consider these possibilities when designing a schema of tables to store chemical information. 

Just as the atom takes on a significance in learning about chemistry which is not justified in terms of the (lack of) role that discrete atoms play in chemical processes, once learners have been taught about molecules there is a tendency to apply the molecule schema to all structures. The role of valency in limiting, if not exactly determining, molecular formulae, may be extended to metals and to ionic materials. Metals may be seen by students to consist of discrete molecules of similar atoms, in a similar way to iodine or phosphoms. In the ionic case, valency is seen by many students to indicate the number of ionic bonds that can be formed, and not just the charge on the ions. 

Figure 1 shows a schema for an ideal distributed chemical information system. Several authors in this book refer to the need for standard interfaces. Ultimately, the personal computer will provide the graphics interface not only to personal computer databases but also to company databases running on the company mainframe, and possibly also through the same network to public hosts, so that the chemist using a personal workstation will be able to create queries which can be addressed to local files, company files and public files. Soon, chemical databases will be available on Compact Disk Read Only Memory (CD-ROM) searchable by both substructure and text. These too fit into the scheme of Figure 1. Databases such as infra-red spectra libraries will have structure-searchable components either on the personal computer or on the laboratory instrument and will also be used through the same graphical interface.

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