Experimental data PubChem

When the desired data is in two different tables, a join is required. It is often helpful to begin to develop complex SQL statements by considering one table at a time. For example, data from the nci h23 table of pubchem schema was considered earlier in this chapter. The experimental data to be selected from that table was the substance id (called sid in the table), activity outcome, log gi50 M and n.log gi50 ugml. This is accomplished by the simple SQL... 

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. 

Pubchem [32] Pubchem is a database maintained by the National Center for Biotechnology Information (NCBI), which is part of the US National Institutes of Health (NIH). PubChem can be freely accessed through a web user interface or is downloadable by File Transfer Protocol (FTP) at http //pubchem.ncbi.nlm.nih.gov. Pubchem is organized into three main parts substances ( 126 million entries of compound mixtures, extracts, etc.), pure compounds (48 million unique structures), and bioassays (-740,000 records). Users can search the database by name, Pub-Chem identifiers, structures of molecules to retrieve small molecules, calculated physicochemical data, and experimental biological data. Structure-activity relationship tools are available for further analysis of the extracted results. 

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