sbol-data

APIs to manage SBOL-shaped data documents.

Introduction

SBOL is a data model and data exchange standard for synthetic biology. It captures various information about the design and function of DNA, and how DNA has been enginered. The native serialization is in RDF. However, to support tools that don't have access to a full RDF stack, the serialization is highly constrained. sbol-data provides a data model that exactly captures these constraints upon how the RDF is serialized.

Although designed for use with SBOL, the sbol-data data model is schema-agnostic. It can be used to encode a wide range of data structures.

Through the IO providers framework, sbol-data supports a range of human- and machine-readable input and output formats, including:

• RDF
• JSON
• Mock-Turtle (almost RDF-Turtle)
• Graphviz (export only)

Overview

The sbol-data structures form a forest of trees. DocumentRoot is the top-level element, and it contains a list of TopLevelDocument children. Each of these is a self-contained data record. These have a collection of named properties, which can have literal values (e.g. strings or ints), or can point to a NestedDocument child. These can also have named properties that may themselves point to nested documents, and so on.

Cyclic references are not allowed. If you use the Datatree factory object, they are not possible.

Each document (TopLevelDocument or NestedDocument) has an associated URI that is its identity. This uniquely identifies the document. If one document needs to refer to another one, then this is done by having a named property were the value is a URI referencing the other document.

Use

import org.sbolstandard.core.datatree.*;
import static org.sbolstandard.core.datatree.Datatree;
import org.sbolstandard.examples.Sbol2Terms;

...

TopLevelDocument<QName> modelLacIInverter = TopLevelDocument(
  NamespaceBindings(utah),
  Sbol2Terms.model.model,
  sbolExample.namespacedUri("model/LacI_inverter"),
  NamedProperties(
    NamedProperty(Sbol2Terms.documented.name, "LacI Inverter Model"),
    NamedProperty(Sbol2Terms.model.source,URI.create("http://www.async.ece.utah.edu/LacI_Inverter.xml")),
    NamedProperty(Sbol2Terms.model.language,"SBML"),
    NamedProperty(Sbol2Terms.model.framework,"ODE"),
    NamedProperty(Sbol2Terms.model.role,"simulation")
  )
);

DocumentRoot<QName> root = DocumentRoot(
  NamespaceBindings(RdfTerms.rdf, SbolTerms.sbol2),
  TopLevelDocuments(moduleLacIInverter,modelLacIInverter),
  Datatree.LiteralProperties()
);

XMLStreamWriter xmlWriter = new IndentingXMLStreamWriter(
  XMLOutputFactory.newInstance().createXMLStreamWriter(
    System.out));
RdfIo rdfIo = new RdfIo();
rdfIo.createIoWriter(xmlWriter).write(root);
xmlWriter.close();

##Change Log v0.1.0, 29/08/2014 Initial release

v0.1.1, 20/01/2015 Fixed the RDF prefix mapping to read SBOL1 files

v0.1.2, 29/05/2015 Exposed Boolean and Double property values

v0.1.3, 17/05/2016 Added equals and toString methods