Rlegaspi Week 6

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The FDA Drug Database

The United States Food and Drug Administration (FDA) provides, as a matter of public record, the full data set for its approved drugs at this website: http://www.fda.gov/Drugs/InformationOnDrugs/ucm079750.htm

The site includes both a link to the downloadable files (compressed in .zip format) and the schema (“entity relationship diagram”) for those files.

Using these files, what you have learned about sed and SQL thus far, and additional information found in this wiki and on the aforementioned FDA website, do the following:

  1. Download and uncompress the files.
  2. Define appropriate tables for the Application and Product entities.
  3. Process the data files for these entities then load them into those tables.
  4. Answer the questions below.

Electronic Lab Notebook

Downloading and Unzipping FDA Drug Information File

  • Like any other assignment using Putty, I logged through the Putty application on one of the SEA 120 computers.
  • I bypassed the website and downloaded the file directly to my.cs.lmu.edu using the following command provided on the Week 6 Assignment Page:
curl -O http://www.fda.gov/downloads/Drugs/InformationOnDrugs/UCM054599.zip
  • I unzipped the file, using this command (also provided on the Week 6 Assignment Page):
unzip UCM054599.zip
  • I was given the results that were expected from unzipping and now have the files application.txt and Product.txt in my home folder, which are the files needed for the rest of this assignment.

Defining appropriate tables for the Application and Product entities

Application

In order to analyze the data in application.txt, I ran the command more application.txt to discover what the columns of data stood for and recognized what kind of table values would be present in each column (int, varchar, boolean, etc.). The following SQL command created the table I needed for the data within the application.txt file: 

create table drugapplication (ApplNo int primary key, ApplType varchar, SponsorApplicant varchar, MostRecentLabelAvailableFlag boolean, CurrentPatentFlag boolean, ActionType varchar, Chemical_Type int, Ther_Potential varchar, Orphan_Code varchar);

Product

Similarly to the application.txt file, I ran the command more Product.txt in order to see the first line of data that provided the description of each column within the file. Therefore, I ran the following SQL command keeping in mind the names of the columns and the types of values present within the columns: 

create table Product (ApplNo int, ProductNo int, Form varchar, Dosage varchar, ProductMktStatus varchar, TECode varchar, ReferenceDrug int, drugname varchar, activeingred varchar);

Processing the data files for Application and Product entities to load into tables

Explanation here. 

Application.txt sed command pipeline to prepare for insertion into DrugApplication table:
cat application.txt | sed "s/\t/#/g" | sed -r "s/( ){2}//g" | sed "s/ \#/#/g" | sed "s/\# /#/g" | sed "s/##/#null#/g" | 
sed "s/##/#null#/g" | sed "s/#\r$/#null/g" | sed "s/#/,'/1" | sed "s/#/','/1" | sed "s/#/',/1" | sed "s/#/,/1" | sed "s/#/,'/1" | 
sed "s/#/',/1" | sed "s/#/,'/1" | sed "s/#/','/1" | sed "s/#/,'/1" | sed "s/\r$/'/g" | sed "s/'null'/null/g" | sed "s/'null/null/g" | 
sed "s/^/insert in drugapplication (ApplNo,ApplType,SponsorApplicant,MostRecentLabelAvailableFlag,CurrentPatentFlag,ActionType,Chemical_Type,Ther_Potential,Orphan_Code) values(/g" | 
sed "s/$/);/g" | sed 1D > ~/public_html/drugapplication.sql.txt

Product.txt sed command pipeline to prepare for insertion into DrugProduct table:
cat Product.txt | sed "s/\*\*Federal Register determination that product was not discontinued or withdrawn for safety or efficacy reasons\*\*//g" | 
sed "s/\*\*Federal Register determination that product was not discontinued or withdrawn for safety or efficacy\*\*//g" | 
sed "s/\*\*Federal Register notice determination that product was not discontinued or withdrawn for safety or efficacy reasons\*\*//g" | 
sed "s/\*\*Federal Registration determination that product was not discontinued or withdrawn for safety or efficacy reason\*\*//g" | 
sed "s/See current Annual Edition, 1.8 Description of Special Situations, Levothyroxine Sodium//g" | 
sed "s/'//g" | sed "s/\t/#/g" | sed -r "s/( ){2}//g" | sed "s/ \#/#/g" | sed "s/\# /#/g" | sed "s/\#\#/#null#/g" | sed "s/\#\#/#null#/g" | 
sed "s/\#/,/1" | sed "s/\#/,'/1" | sed "s/\#/','/1" | sed "s/\#/',/1" | sed "s/\#/,'/1" | sed "s/\#/',/1" | sed "s/\#/,'/1" | sed "s/\#/','/1" | 
sed "s/\r$/'/g" | sed "s/^/insert into drugproduct (ApplNo,ProductNo,Form,Dosage,ProductMktStatus,TECode,ReferenceDrug,drugname,activeingred) values(/g" | 
sed "s/$/);/g" | sed 1D > ~/public_html/drugproduct.sql.txt

Questions to Answer

  1. Provide the DDL (create table) statements that you used for your application and product tables.
    • DrugApplication Table: create table drugapplication (ApplNo int primary key, ApplType varchar, SponsorApplicant varchar, MostRecentLabelAvailableFlag boolean, CurrentPatentFlag boolean, ActionType varchar, Chemical_Type int, Ther_Potential varchar, Orphan_Code varchar);
    • DrugProduct Table: create table Product (ApplNo int, ProductNo int, Form varchar, Dosage varchar, ProductMktStatus varchar, TECode varchar, ReferenceDrug int, drugname varchar, activeingred varchar);
  2. Provide the sed command sequences that you used to convert the raw text files into sequences of SQL insert statements.
    • DrugApplication: cat application.txt | sed "s/\t/#/g" | sed -r "s/( ){2}//g" | sed "s/ \#/#/g" | sed "s/\# /#/g" | sed "s/##/#null#/g" | sed "s/##/#null#/g" | sed "s/#\r$/#null/g" | sed "s/#/,'/1" | sed "s/#/','/1" | sed "s/#/',/1" | sed "s/#/,/1" | sed "s/#/,'/1" | sed "s/#/',/1" | sed "s/#/,'/1" | sed "s/#/','/1" | sed "s/#/,'/1" | sed "s/\r$/'/g" | sed "s/'null'/null/g" | sed "s/'null/null/g" | sed "s/^/insert in drugapplication (ApplNo,ApplType,SponsorApplicant,MostRecentLabelAvailableFlag,CurrentPatentFlag,ActionType,Chemical_Type,Ther_Potential,Orphan_Code) values(/g" | sed "s/$/);/g" | sed 1D > ~/public_html/drugapplication.sql.txt
    • DrugProduct: cat Product.txt | sed "s/\*\*Federal Register determination that product was not discontinued or withdrawn for safety or efficacy reasons\*\*//g" | sed "s/\*\*Federal Register determination that product was not discontinued or withdrawn for safety or efficacy\*\*//g" | sed "s/\*\*Federal Register notice determination that product was not discontinued or withdrawn for safety or efficacy reasons\*\*//g" | sed "s/\*\*Federal Registration determination that product was not discontinued or withdrawn for safety or efficacy reason\*\*//g" | sed "s/See current Annual Edition, 1.8 Description of Special Situations, Levothyroxine Sodium//g" | sed "s/'//g" | sed "s/\t/#/g" | sed -r "s/( ){2}//g" | sed "s/ \#/#/g" | sed "s/\# /#/g" | sed "s/\#\#/#null#/g" | sed "s/\#\#/#null#/g" | sed "s/\#/,/1" | sed "s/\#/,'/1" | sed "s/\#/','/1" | sed "s/\#/',/1" | sed "s/\#/,'/1" | sed "s/\#/',/1" | sed "s/\#/,'/1" | sed "s/\#/','/1" | sed "s/\r$/'/g" | sed "s/^/insert into drugproduct (ApplNo,ProductNo,Form,Dosage,ProductMktStatus,TECode,ReferenceDrug,drugname,activeingred) values(/g" | sed "s/$/);/g" | sed 1D > ~/public_html/drugproduct.sql.txt
  3. Using the command line, how can you determine the number of records in each file? Provide the command.
    • application.txt - wc application.txt: 19747 lines of data; however, 1st line is column headings, so 19747 - 1 = 19746 records in application.txt file.
    • Product.txt - wc Product.txt: 32771 lines of data; however, 1st line is column headings, so 32771 - 1 = 32770 records in Product.txt file.
  4. Using SQL, how can you determine the number of records in the table corresponding to the file? Provide the SQL select statement.
    • application.txt - select count(*) from drugapplication: 19746 records
    • Product.txt - select count(*) from drugproduct: 32770 records
    • Note: Similar results compared to using command line, just as expected.
  5. In your database, are these numbers the same or different? Explain why you think so.
    • The numbers are the same because all of the lines of data from the text files was transferred into the SQL tables (except for the first line of each text file, which contained the column headings). The record numbers should equal each other.
    For the remaining questions, supply (a) the answer to the question and (b) the SQL statement that you used to answer the question.
  6. What are the names of the drug products that are administered in the form INJECTABLE;INTRAVENOUS, SUBCUTANEOUS?
    • a) ACTEMRA, AZACITIDINE, ENOXAPARIN SODIUM, LOVENOX, VELCADE, VIDAZA
    • b) select drugname from drugproduct where form = 'INJECTABLE;INTRAVENOUS, SUBCUTANEOUS';
  7. What are the names of the drug products whose active ingredient (activeingred) is ATROPINE?
    • a) ATROPEN, ATROPINE
    • b) select drugname from drugproduct where activeingred = 'ATROPINE';
  8. In what forms and dosages can the drug product named BENADRYL be administered?
    • a)"CAPSULE;ORAL";"50MG", "ELIXIR;ORAL";"12.5MG/5ML", "CAPSULE;ORAL";"25MG", "INJECTABLE;INJECTION";"10MG/ML", "INJECTABLE;INJECTION";"50MG/ML"
    • b)select form, dosage from drugproduct where drugname = 'BENADRYL';
  9. Which drug products have a name ending in ESTROL?
    • a)"DIETHYLSTILBESTROL", "STILBESTROL", "DIENESTROL"
    • b)select drugname from drugproduct where drugname like '%ESTROL';
  10. Produce a table listing all of the known values for the therapeutic_potential column in the application table and how many application records there are of each. (Side note: The therapeutic_potential codes are explained in the ReviewClass_Lookup.txt file, in case you’re interested.)
    • a) Therapeutic Potential.png
    • b)select ther_potential, count(*) from drugapplication group by ther_potential order by count desc
  11. Produce a table listing all of the known values for the chemical_type column in the application table and how many application records there are of each. (Side note: The chemical_type codes are explained in the ChemTypeLookup.txt file, in case you’re interested.)
    • a) Chemical Type.png
    • b)select chemical_type, count(*) from drugapplication group by chemical_type order by count desc
  12. What are the names of the drug products that are sponsored (sponsor applicant column) by MERCK?
    • a) DECADRON, HUMORSOL, NEO-HYDELTRASOL, PRINIVIL, MAXALT-MLT, HYDROCORTONE, PERIACTIN, PROPECIA, PROSCAR, CLINORIL, PRINZIDE, ELSPAR, ALDOMET, ALDORIL D30, EMEND, DIUPRES-500, NEODECADRON, ALDOCLOR-250, MEFOXIN IN DEXTROSE 5% IN PLASTIC CONTAINER, ARAMINE, TIAMATE, BLOCADREN, CANCIDAS, CHIBROXIN, CORTONE, PEPCID, TRUSOPT, REDISOL, VIOXX, FLOROPRYL, ALPHAREDISOL, DECADRON-LA, MEFOXIN IN SODIUM CHLORIDE 0.9% IN PLASTIC CONTAINER, PEPCID RPD, NOROXIN, ZOCOR, LERITINE, DECADERM, DOLOBID, MANNITOL 25%, DECADRON W/ XYLOCAINE, ALDORIL D50, TIMOLIDE 10-25, CYCLAINE, HYDROPRES 25, AMINOHIPPURATE SODIUM, MEVACOR, MODURETIC 5-50, ALDORIL 25, SINGULAIR, COLBENEMID, DIUPRES-250, HYDELTRA-TBA, PRIMAXIN, BENEMID, MAXALT, FOSAMAX PLUS D, HYDRODIURIL, HYDELTRASOL, HYDROPRES 50, ZOLINZA, ALDORIL 15, FOSAMAX, DECASPRAY, COGENTIN, ALDOCLOR-150, PEPCID PRESERVATIVE FREE
    • b) select drugname from product inner join application on (product.applno = application.applno) where sponsorapplicant = 'MERCK' group by drugname
  13. Which sponsor applicant companies have the text LABS in their names and have products whose active ingredients (activeingred) include both ASPIRIN and CAFFEINE?
    • a) ACTAVIS LABS UT INC and WATSON LABS
    • b) select sponsorapplicant from application inner join product on (application.applno = product.applno) where sponsorapplicant like '%LABS%' and activeingred like '%ASPIRIN%' and activeingred like '%CAFFEINE%' group by sponsorapplicant;

Links to User Page and Journal Pages

Ron Legaspi
BIOL 367, Fall 2015

Assignment Links
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Homework Partner: Jake Woodlee

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