Drugbank

We propose to use the Drugbank resource to track medications. According to the Drugbank website (2018-02-26), The latest release of DrugBank (version 5.0.11, released 2017-12-20) contains 10,999 drug entries including 2,504 approved small molecule drugs, 942 approved biotech (protein/peptide) drugs, 109 nutraceuticals and over 5,108 experimental drugs. A recent Nucleic Acid Research database article provides further details. Drugbank is licensed under a a Creative Common’s Attribution-NonCommercial 4.0 International License, and therefore can be used freely for non-commercial applications.

Our usage of drugbank

We used the Java JAXB tool xjc to create Java classes that mirror the XSD XML schema definition for Drugbase (the schema is available here: https://www.drugbank.ca/releases/latest). To use PDXIntegrator, you will need to download the Drugbase XML file (which requires free registration). Then follow these steps to unpack the XML file and to remove the space character from the file name.

$ unzip drugbank_all_full_database.xml.zip
    Archive:  drugbank_all_full_database.xml.zip
    inflating: full database.xml
$ mv full\ database.xml fulldatabase.xml

Now we can extract the contents of the XML file for use by PDXIntegrator. The following command does that and creates a new file in the data directory that is also used by PDXIntegrator to store downloaded files.

$ java -jar target/PdxIntegrator.jar drugbank --drugbank fulldatabase.xml

Adjust the path to fulldatabase.xml as necessary.

This will generate a new file in the data directory called drugbank.tab. The contents of this file look like this.

Denileukin diftitox     173146-27-5     DB00004 ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS
Etanercept      185243-69-0     DB00005 ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS
Bivalirudin     128270-60-0     DB00006 BLOOD AND BLOOD FORMING ORGANS
Leuprolide      53714-56-0      DB00007 ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS
Peginterferon alfa-2a   198153-51-4     DB00008 ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS
Alteplase       105857-23-6     DB00009 BLOOD AND BLOOD FORMING ORGANS
Sermorelin      86168-78-7      DB00010 SYSTEMIC HORMONAL PREPARATIONS, EXCL. SEX HORMONES AND INSULINS
Interferon alfa-n1      74899-72-2      DB00011 ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS

For the purposes of this demonstration program, we will use the antineoplastic agents. ToDO–if we choose to stick with DrugBank, we can exploit the hierarchy and will need to emit some RDF to represent the hierarchy that is recorded in the XML file (for now, we will treat these medications as literals for demo purposes).