Experimental Chemical and Biological Data Integration

The first section of this chapter showed how a schema of tables could be used to create a compound registry. Using that schema, this section will show how experimental data can be integrated with compound data. A separate schema will be used to store the experimental data. In fact, several schemas will be created in order to segregate data tables for separate assays or projects. This is not essential, but is handy for browsing data tables in a large database. Schemas are analogous to folders in a file system. 

Each set of experimental data will likely have to be considered separately. Some measurements may require several columns, while other will require only one. Some measurements may have measured or estimated uncertainties, while others may be more indefinite, such as active or inactive. All measurements will have a date associated with them and this should be stored. Many experimental values will be noninteger numbers. These may be stored using the numeric data type or float or double, depending on the accuracy needed and whether computations on these values will be carried 

A table of experimental data could be defined as follows. 

Create Table hiv.protease (id Integer References registry.structure, ic50 Float, ec50 Float, updated Timestamp Default current timestamp)  

This table is intended to hold results of assays testing compounds in reg-istry.structure for activity as human immunodeficiency virus (HIV) protease inhibitors. As new assays are added, the test results can be added to newly created tables with similar definitions. For example, there might be tables for HIV reverse transcriptase inhibitors stored in a table named hiv.rt. Other assay results might be stored in new schemas, for example, fpr.htfc for high-throughput flow cytometry results for the formyl peptide receptor (FPR), or f pr.ca for FPR cell adhesion assay results. Each of these tables would have columns of data named and typed appropriately for each assay. Each table would have a column containing a compound id that references compounds in the registry, structure table. 

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