Schemas for PubChem Data

National Institutes of Health PubChem project contains information on millions of chemical compounds.1 The data are divided into three main sections. PubChem Substance contains structures supplied by depositors. PubChem Compound contains unique structures with computed properties. PubChem BioAssay contains bioactivity assay results supplied by depositors. The data in these three sections are recorded independently, yet there are chemical relationships among these sections. For example, information available as a PubChem BioAssay is associated with a particular substance for which the data were collected. A substance may be a single compound or a mixture of several compounds. 

In order to find structures and data in PubChem, there are search tools available online.2 This may suffice for your needs. The data are also available in the form of SDF files and csv (comma-separated values) files. 

This section will show how these files can be used to populate a schema of tables designed for PubChem data. While your chemical information may not correspond exactly to this schema, it should be instructive to see how the PubChem schema is designed and used. 

NCI H23 human Non-Small Cell Lung tumor cell line is measured as a screen for anti-cancer activity. Cells are grown in 96 well plates and exposed to the test compound for 48 hours. Compounds are tested at 5 different concentrations and three endpoints are estimated from this dose response curve GI50, concentration required for 50% inhibition of growth TGI, the concentration required for complete inhibition of growth and LC50, the concentration required for 50% reduction in cell number. These estimates are done by simple linear interpolation between the concentrations that surround the appropriate level. If a compound doesn t cause inhibition to the appropriate level, the endpoint is set to the highest concentration tested.  

Comment on column pubchem.nci h23. ext datasource regid is Space holder for PubChem external datasource RegID, empty by default  

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