libSBOLj: SBOL Java library

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 files, and a validator to check the correctness of SBOL models.

Building libSBOLj

1. Create a GitHub account. link

2. Download and set up Git. link

3. Fork the libSBOLj repository and clone it to your machine. link

4. Download and set up Maven. link

5. Change to your libSBOLj directory via the command line and execute the following command:

   mvn package

This will create the libSBOLj JAR file and place it into a sub-directory named target. link

Using libSBOLj

libSBOLj command line

libSBOLj comes with a command-line interface (CLI) that can be used to validate SBOL files. After you build the libSBOLj-0.7.0-SNAPSHOT.jar as described above, you can use it to validate files as follows:

java -jar libSBOLj-0.7.0-SNAPSHOT.jar target/test-classes/test/data/BBa_I0462.xml

If validation is successful, the program will print the contents of the SBOL document. Use --quit option if you want to suppress this output.

If validation fails with an error, there will be a message printed about the validation error. To see an example, try the following command:

java -jar libSBOLj-0.7.0-SNAPSHOT.jar target/test-classes/test/data/invalid01_missing_displayId.xml

libSBOLj API (note the commands for this section are out of date)

The programs provided under examples/src directory show various examples of using libSBOLj library. You can compile these examples by running:

ant examples

This will create libSBOLj-examples.jar in the same directory and an example program can be run as follows:

java -cp libSBOLj-examples.jar org.sbolstandard.core.examples.Example01_Basics

More detailed information about libSBOLj API can be found in the javadocs. To generate the libSBOLj javadocs run:

ant javadoc

The javadoc output will be written to "javadocs" directory.

Serialization in libSBOLj

libSBOLj provides support for reading and writing libSBOLj documents in XML syntax. The structure of the documents is defined in two XML schema (XSD) files that can be found in the resources directory.

A very simple SBOL document looks like this in XML:

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<rdf:RDF xmlns="http://sbols.org/v1#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <DnaComponent rdf:about="http://example.com/MyDnaComponent">
        <displayId>MyDnaComponent</displayId>
        <name>myDNA</name>
        <description>This is a very simple example</description>
    </DnaComponent>
</rdf:RDF>

A more complete example can be found in examples/data directory.

Note that, the XML serialization of SBOL documents have been designed to be compatible with Resource Description Format (RDF). Any valid SBOL XML file can be parsed by a standard RDF tool that supports RDF/XML syntax. But different RDF serializations will not be valid if they do not match the constraints defined in the SBOL XML schema and cannot be read by libSBOLj.

libSBOLj provides also a more readable, human-friendly output format that aligns more closely with the SBOL object model defined in the specification. The above example would look as follows in this syntax:

SBOLDocument [
   DnaComponent [
      uri: http://example.com/MyDnaComponent
      displayId: MyDnaComponent
      description: This is a very simple example
   ]
]  

This format is only intended for presentation purposes and not to exchange libSBOLj structures and the library does not provide any means to read this syntax.