mirtarbase-to-biopax

Originated from https://bitbucket.org/armish/gsoc14 and will continue here (ToDo).

MiRTarBase to BioPAX Level3 data converter.

This data resource is manually curated and it contains validated miRNA-target interactions. These interactions can easily be converted to BioPAX Level3 format.

Data source [now it looks outdated/discontinued; format is now different too]

• Home page: http://mirtarbase.mbc.nctu.edu.tw (also, - aliases.txt from http://www.mirbase.org)
• Type: microRNA-target interactions
• Format: XLS/TSV
• License: Free for academic use

Implementation details

The database provides downloadable miRNA-target relationships in Excel format. For each interaction, we have knowledge about the miRNA, the target gene, the organism and the coresponding publication that describes the interaction. Each miRNA has a unique MiRTarBase ID, but these IDs are registered in the Miriam database. This creates a problem for us when creating miRNA references with UnificationXrefs to them. To overcome this problem, we also import miRBase aliases which provides official unique IDs for given miRNA names.

We encode miRNA-target relationships with TemplateReactions through which the corresponding gene product is produced and the reaction is inhibitied by the corresponding miRNA. miRNAs are represented by Rna objects, where they have RelationshipXrefs to MiRTarBase and UnificationXrefs to miRBase. If a miRNA name is associated with multiple unique miRNAs, then we capture this information via adding different-named miRNAs as a MemberPhysicalEntity to the original miRBase reference.

We encapsulate each interaction in an organism-specific pathway so that users can only work with pathways that are of interest to them, for example human miRNA-targets.

The image below shows a partial Homo sapiens pathway:

Usage

Check out (git clone) and change to:

$ cd mirtarbase-to-biopax

build with Maven:

$ mvn clean package

This will create a single executable JAR file under the target/ directory, with the following file name: mirtarbase-to-biopax.jar. Once you have the "fat" JAR file, you can try to run it without any command line options to see the help text:

$ java -jar target/mirtarbase-to-biopax.jar
usage: MirtarbaseToBiopax
-o,--output <arg>               Output file (BioPAX) [required]
...

For a conversion, one input data file is required, and two more are optional (e.g., if you'd like to import organisms and aliases mapping from a specific miRBase release):

1. MiRTarBase Excel file - either full or partial (human);
2. miRBase aliases: ftp://mirbase.org/pub/mirbase/CURRENT/aliases.txt.gz (optional, - if you'd use the very latest data)
3. miRBase organisms: ftp://mirbase.org/pub/mirbase/CURRENT/organisms.txt.gz (optional)

Once downloaded and expanded, these can be converted to BioPAX using the following command:

$ java -Xmx4g -jar mirtarbase-to-biopax.jar -m aliases.txt -s organisms.txt -i hsa_MTI.xlsx -o out.biopax.owl