pattern

Pattern search software for BioPAX models

BioPAX is a language standard for describing biological networks. This software helps to define graph patterns with BioPAX objects, and searches them on BioPAX models.

Source code of the Pattern search project was moved to Paxtools, pattern module.

Below is about previous versions of the library (before it merged into Paxtools).

For versions 2.0.0-SNAPSHOT and earlier only

This tool is developed on top of Paxtools, and effective usage requires knowledge of BioPAX structure and some familiarity with Paxtools.

A pattern sample

A pattern is composed of fixed number of BioPAX elements and a list of constraints between. For instance the below illustrated pattern captures pairs of proteins that control two consecutive reactions (an output of first reaction is input to the second).

The Java code equivalent of this pattern is below.

Pattern p = new Pattern(ProteinReference.class, "PR1");
p.add(ConBox.erToPE(), "PR1", "P1");
p.add(ConBox.peToControlledConv(), "P1", "Conv1");
p.add(new Participant(RelType.OUTPUT),  "Conv1", "linker");
p.add(ConBox.equal(false), "linker", "P1");
p.add(new ParticipatesInConv(RelType.INPUT), "linker", "Conv2");
p.add(ConBox.equal(false), "Conv1", "Conv2");
p.add(ConBox.convToController(), "Conv2", "P2");
p.add(ConBox.equal(false), "linker", "P2");
p.add(ConBox.peToER(), "P2", "PR2");
p.add(ConBox.equal(false), "PR2", "PR1");

To learn how to use, please start with the Quick Start Guide.

A Javadoc is also available.

Searching for binary interactions

As an example use of this pattern search framework, we defined a set of patterns that capture useful binary interactions between proteins and small molecules in a BioPAX model. Binary interaction types include upstream-to-downstream signal transmissions, controlling expression changes, sequential catalysis by metabolic enzymes, controlling transportation, enzymes consuming or producing chemicals, etc. Read more.

Using the software

You can find a "fat" (with dependencies) biopax-pattern jar file in BioPAX Downloads.

Maven users can add the following lines to their project pom files to use biopax-pattern framework.

<repositories>
	<repository>
		<id>biopax.release.repo</id>
		<name>BioPAX releases</name>
		<url>http://www.biopax.org/m2repo/releases</url>
		<snapshots>
			<enabled>false</enabled>
		</snapshots>
	</repository>
	<repository>
		<id>biopax.snapshot.repo</id>
		<name>BioPAX snapshots</name>
		<url>http://www.biopax.org/m2repo/snapshots</url>
		<releases>
			<enabled>false</enabled>
		</releases>
	</repository>
</repositories>

<dependencies>
	<dependency>
		<groupId>org.biopax.paxtools</groupId>
		<artifactId>pattern</artifactId>
		<version>LATEST</version>
	</dependency>
</dependencies>

Searching for pre-defined patterns

This software is developed as a library, however it also supports searching BioPAX models using some pre-defined patterns and output formats, without any programming. To do this, run the biopax-pattern jar (from the BioPAX Maven repository or downloads) with the following command.

java -Xmx5G -jar biopax-pattern-{version}.jar

A dialog will appear and let you to select a model, a pattern, and output file name.

How to cite

If biopax-pattern framework was useful for your research, please cite the below article in your publications.

Ö Babur, BA Aksoy, I Rodchenkov, SO Sümer, C Sander, E Demir Pattern search in BioPAX models Bioinformatics (2014) 30 (1): 139-140. doi: 10.1093/bioinformatics/btt539

Contact

patternsearch@cbio.mskcc.org