https://github.com/synbiodex/sbol-data

APIs to manage SBOL-shaped data documents.
https://github.com/synbiodex/sbol-data

Last synced: 4 days ago
JSON representation

APIs to manage SBOL-shaped data documents.

• Host: GitHub
• URL: https://github.com/synbiodex/sbol-data
• Owner: SynBioDex
• License: apache-2.0
• Created: 2014-06-20T13:53:31.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2018-05-02T13:38:08.000Z (over 6 years ago)
• Last Synced: 2024-12-22T09:52:03.415Z (24 days ago)
• Language: Java
• Size: 538 KB
• Stars: 0
• Watchers: 4
• Forks: 1
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
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

```java

import org.sbolstandard.core.datatree.*;

import static org.sbolstandard.core.datatree.Datatree;

import org.sbolstandard.examples.Sbol2Terms;

...

TopLevelDocument 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 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