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Java Library for Synthetic Biology Open Language (SBOL)
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README.md

libSBOLj provides the core Java interfaces and their implementation for the Synthetic Biology Open Language (SBOL). The library provides an API to work with SBOL objects, the functionality to read and write SBOL documents as XML/RDF files, and a validator to check the correctness of SBOL models.

Using the libSBOLj library

In a Maven project:

In a Maven project that utilizes the libSBOLj library, add a dependency in the Maven project's pom.xml file.

<dependency>
    <groupId>org.sbolstandard</groupId>
    <artifactId>libSBOLj</artifactId>
    <version>2.0.0</version>
</dependency>

In a non-Maven project:

Download libSBOLj-<version>-withDependencies.jar from the latest github release.

Running in the command line:

libSBOLj comes with a command-line interface (CLI) that can be used to validate SBOL files. You can execute libSBOLj-<version>-withDependencies.jar to validate and convert files as follows.

java -jar libSBOLj-<version>-withDependencies.jar <inputFile>

If validation is successful, the program will print the contents of the SBOL document. You can also output the result to a file.

java -jar libSBOLj-<version>-withDependencies.jar <inputFile> -o <outputFile>

If validation fails with an error, there will be a message printed about the validation error. In addition to checking all required validation rules, it will also check if the URIs are compliant and whether the SBOL document is complete (i.e., all referenced objects are contained within the file). These validation checks can be turned off with the -n and -i flags, respectively. It is also possible to turn-on best practices checking using the -b flag.

If the input file is an SBOL 1.1 file, then it will convert the file into an SBOL 2.0 file. This conversion should be provided a default URI prefix. It can also be provided a default version, if desired. Finally, the -t flag will insert the type of top level objects into the URI during conversion, if desired.

java -jar libSBOLj-<version>-withDependencies.jar <inFile> -o <outFile> -p <URIprefix> -v <version>

The command line interface can also convert GenBank files into SBOL 2.0 files using the command below:

java -jar libSBOLj-<version>-withDependencies.jar -g <inFile> -o <outFile> -p <URIprefix> -v <version>

Finally, it can convert a specifed top-level ComponentDefinition within an SBOL 2.0 file into a GenBank file using the following command:

java -jar libSBOLj-<version>-withDependencies.jar <inFile> -c <ComponentDefinitionURI> -o <outFile>

Using the latest libSBOLj SNAPSHOT

Getting the libSBOLj source

  1. Create a GitHub account.
  2. Setup Git on your machine.
  3. Clone the libSBOLj GitHub repository to your machine.

Compiling and Packaging libSBOLj

  1. Setup Apache Maven. A tutorial on using Apache Maven is provided here.

  2. In the command line, change to the libSBOLj directory (e.g. cd /path/to/libSBOLj) and execute the following command

mvn package

This will compile the libSBOLj source files, package the compiled source into a libSBOLj JAR file (libSBOLj-<version>-SNAPSHOT-withDependencies.jar), and place the JAR file into the core2/target sub-directory.

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