SBML2SBML

From System Biology Format Converter framework (SBFC)
Jump to: navigation, search

Conversion from SBML to SBML, including annotation support

Introduction

About SBML
SBML is a machine-readable format for representing models. It is oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. An example of this is a network of biochemical reactions. SBML framework is suitable for representing models commonly found in research on a number of topics, including cell signalling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. If you want to know more, you can read the Basic Introduction on SBML.
About urn:miriam
MIRIAM is an effort to establish the essential, minimal set of information that is sufficient to annotate a model in such a way as to enable its reuse. This standard also describes the syntax by which annotations should be encoded: MIRIAM URIs. If you want to know more, you can read the Miriam FAQs.
About identifiers.org url
Identifiers.org URIs are stable, perennial and globally unique URIs which can be used to annotate a wide range of entities or concepts from a plethora of fields, including proteins, diseases, publications and ontological terms. They can be used unchanged for a wide range of tasks, as they are both unique and directly usable online. The aim is to provide a community-agreed means to create stable, perennial and globally unique identifiers, which can be used to reference data with a primary focus on life sciences. Additionally, the system decouples the identification of records from the physical locations on the web where they can be retrieved. If you want to know more, you can read the Identifiers.org documentation

Documentation

Conversion between SBML levels and versions
The conversion between different levels-versions of SBML is based on libsbml. Normally, models can be converted upward without difficulty (e.g., from SBML Level 1 to Level 2, or from an earlier Version of Level 2 to the latest Version of Level 2). Sometimes models can be translated downward as well, if they do not use constructs specific to more advanced Levels of SBML. For details about potential information loss on downward conversion, please consult this web page from the SBML website.
Conversion between urn:miriam and identifiers.org url
The conversion between urn:miriam and identifiers.org url is fully supported without any loss of information.


Download

You can download SBML2SBML here: sbfc-1.3.7.zip. This converter translates an SBML model of a level and version to another, SBML model annotation from identifiers.org url to miriam:urn, and model annotation from miriam:urn to identifiers.org url.


End users

To run SBML2SBML, URL2URN or URN2URL you need java 1.6 or higher.

After unpacking the zipped file, move to the folder that have been created and run:

    # Convert SBML (any *.xml files if you put a folder) to another SBML level-version.
    # The output file(s) will be in the same folder as the SBML file(s) with an extension .xml
    # x and y are the SBML level and version of the output model, respectively.
    ./sbml2sbml.sh [file.xml | folder] LxVy

    # Convert SBML model annotation from urn:miriam to identifiers.org url .
    ./urn2url.sh [file.xml | folder]

    # Convert SBML model annotation from identifiers.org url to from urn:miriam .
    ./url2urn.sh [file.xml | folder]


Developers

To compile SBML2SBML, URL2URN or URN2URL from source, you also need Apache Ant 1.6.5 or higher.

After editing the source code you can build the jar file by just typing in the SBML2SBML folder:

    # Generate the jar file
    ant jar

    # Generate Java documentation
    ant javadoc

Getting Help and Support

In case you discover a bug within SBFC or request new features, please let us know. There are two dedicated trackers:

For general discussions about SBFC, please use the forum:

sbfc-forum [at] googlegroups.com.

If you need further support or you wish to develop new modules in SBFC you can contact the team using the following e-mail address:

sbfc-devel [at] googlegroups.com.