Medical Linked Open Data (MLOD)

MLOD includes integrated semantic knowledge for the detection of drug-drug and drug-illness interactions.

While relevant sources are freely available, such as DrugBank and DrugCentral, these exist in custom formats (XML, CSV) and are not interlinked. This limits the development of real-world solutions for detecting adverse interactions.

To fill this gap, we provide a semantic integrated MLOD, together with means for querying it and keeping it up-to-date.

The MLOD currently includes DrugBank and DrugCentral. The Bio2RDF drug vocabulary is used as a common vocabulary for the two drug-related sources. We utilized the Ontop Platform as a semantic layer on top of the DrugCentral SQL dump, as well as JAXB, Apache Jena TDB and JenaBean for converting the DrugBank XML dump into semantic format.

Setup

To retrieve and load the latest MLOD data, see the instructions below. These steps could take a while (10-20 minutes) depending on your machine, but they only need to be executed initially (and whenever you want to load updates).

• Drugbank: download the latest Drugbank XML dump, set its path in config.properties, and initialize the TDB using the Drugbank.initializeFromXml() method.

As shown in the config file, several custom folders also need to be created for storing internal XML, RDF and TDB files. The XML and RDF folders can be removed after the loading process is completed.

The initializeFromXml() method will segment the XML file, separately convert each XML segment into RDF, and load the RDF into a persistent Triple DataBase (TDB). If a particular step fails for some reason (e.g., loading into TDB), the prior steps do not have to be repeated. (Or, you can simply start from the segment where the process left off).

• Drugcentral: download the latest Drugcentral SQL dump, load it into a PostgreSQL database and set the database credentials in config.properties.

E.g., you can create a drugcentral database using pgAdmin and use psql -U postgres drugcentral < drugcentral.dump.010_05_2021.sql to populate the database (this assumes your root user is called postgres)

Test

See the wvw.mlod.test.Test class for tests.

Code

See mlod/docs for JavaDoc. When running the code, classes of interest include DrugRepository and its subclasses.

Troubleshooting

• If PostgreSQL throws the following error:

org.postgresql.util.PSQLException: The authentication type 10 is not supported. Check that you have configured the pg_hba.conf file to include the client's IP address or subnet, and that it is using an authentication scheme supported by the driver.

You should upgrade to the latest version of postgresql.

• If Ontop throws java.lang.ClassFormatError as below:

Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @24912924

You are likely using an older version of Ontop (e.g., v. 3); try reverting to an earlier version of the JDK (1.8 and 11 are tested, but newer ones may work as well).