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).