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.
First, clone the repository:
git clone git://github.com/SynBioDex/libSBOLj.git
To build libSBOLj use the following command:
ant clean jar test
This command will clean any previous binaries, create a libSBOLj.jar in the same directory and also run the unit tests to make sure that there are on errors in the library.
libSBOLj comes with a command-line interface (CLI) that can be used to validate SBOL files. After you build the libSBOLj.jar as described above, you can use it to validate files as follows:
java -jar libSBOLj.jar examples/data/BBa_I0462.xml
If validation is successful, the program will print the contents of the SBOL document. Use --quite 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.jar test/data/invalid01_missing_displayId.xml
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.
libSBOLj provides support for reading and writing libSBOLj documents in XML syntax. The structure of the documents is defined in an XML schema file that can be found in the schema 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.