Data Storage, Searching, and Manipulation - Design and Use of Relational Databases in Chemistry - page 55

"assaydata_comment" Text,
"assaydata_revoke" Text,
"log_gi50_M" Numeric,
"log_gi50_ugml" Numeric,
"log_gi50_v" Numeric,
"indngi50" Integer,
"stddevgi50" Numeric,
"logtgi_m" Numeric,
"logtgi_ugml" Numeric,
"logtgi_v" Numeric,
"indntgi" Integer,
"stddevtgi" Numeric
);
Comment on table pubchem.nci_h23 is 'Growth inhibition of the
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."sid" is
'PubChem Substance ID SID';
Comment on column pubchem.nci_h23."ext_datasource_regid" is 'Space
holder for PubChem external datasource RegID, empty by default';
Comment on column pubchem.nci_h23."cid" is 'Pubchem Compound ID';
It is important to include comments when defining tables in a schema.
Comments on only the first few columns are shown in the given exam-
ple. Whenever information is available from the data source, it should be
incorporated as comments. When defining tables using your own data, it
is advisable to use comments to include a thorough description of each
table and each column of data.
Once this pubchem.nci _ h23 table is defined, the data in the csv file
can be copied into the table, typically using the SQL copy command. For
example:
Copy pubchem.nci_h23 From Stdin Delimiter ',';
After unzipping 1.csv.gz and removing the first line containing col-
umn names rather than data, the file can be used with the copy command
above to copy data into the pubchem.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