PubChem BioAssay table

PubChem BioAssay is available as hundreds of different files.3 The files are named, for example, l.csv.gz, l.descr.xml, 2.csv.gz, 2.descr.xml. The xml files are descriptions of the data contained in the corresponding csv file, which results when the csv.gz file is unzipped. For example, the file l.descr.xml contains the information "Growth inhibition of the NCI H23 human Non-Small Cell Lung tumor cell line is measured as a screen for anti-cancer activity" as well as information about the various columns of data in the l.csv file. This information is used to define a table to hold the data in the l.csv file. Figure 6.2 shows a representation of the table, named nci h23. Using additional information in the l.descr.xml file and using the capabilities of the RDBMS to incorporate comments on tables and columns, the following SQL defines the nci h23 table. 

All of the other xml and csv data files from PubChem BioAssay can be used in a similar way to define other tables in the pubchem schema. Many of the assays use the same column names and descriptions as the above... 

Beyond a summary description, one would like to view, analyze, and display the actual bioassay data. PubChem provides an integrated suite of tools, each presented as an individual tab, for this purpose. One would use the bioactivity summary tool to, at a glance, be able to examine an overview of the bioassays tested for a list of substances or compounds. To be able to subset and analyze substances or compounds tested in a set of bioassays, one would use the structure-activity analysis tool. To view the actual bioassay outcomes, one would use the data table tool. 

FIGURE 12.8 Partial view of a concise Data Table for cytidine (CID 596) and it 2-D similarity neighbors for all bioassays tested within PubChem. 

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