Overview

The SBML Harvester creates a complex ontology-based representation of SBML models, utilizing both the structure of the SBML model and the models' MIRIAM annotations. This representation can then be used for the consistency verification of SBML models as well as complex queries across both models and biomedical ontologies.

User Guide

Have a look at the SBML Harvester's User Guide to learn how to use this software to integrate and verify SBML models and how to incorporate the results in your software systems.

Included resources

In its current version, SBML Harvester utilizes the Gene Ontology, ChEBI, the Celltype Ontology, the Foundational Model of Anatomy, KEGG, REACTOME, UniProt and Protein Ontology annotations.

Represented systems biology resources

We make an ontology-based representation of

the Biomodels repository, and
the Yeastnet consensus metabolic network

available for download.

Software and ontologies

Upper level ontology

We developed an upper-level ontology for integrating representations of in silico simulations and in vivo phenomena, and we make the OWL implementation of this ontology available. The taxonomic structure of the ontology is shown in this figure.

SBML Harvester

The SBML Harvester is available for download. The current version is 0.3.

Quickstart

Download archive
Unpack using tar xvzf sbmlharvester-0.3.tar.gz
Change to SBML Harvester directory: cd sbmlharvester-0.3
Run SBML Harvester: java -jar SBMLHarvester.jar and follow instructions
Example: java -jar SBMLHarvester.jar -m models/ -o /tmp/output.owl

Requirements

To use the SBML Harvester, you will need

libSBML installed
Java 6

Running the Harvester

The SBML Harvester takes three options:

 -h,--help                    this information
 -m,--model-directory <arg>   directory containing SBML model files
 -o,--output-file <arg>       Output file containing the SBML files
                              transformed into OWL
 -e,--el-compliant            make output EL compliant (to support
                              polynomial-time queries)

The model directory (-m) points to a directory with one or more SBML files. The software archive includes the models directory which includes all curated models from the Biomodels repository.

The output file (-o) is the filename to which the output ontology is written.

The option -e is new in version 0.3. It slightly changes the formalism used to express the resulting OWL ontology so that they are available in the OWL EL fragment, which supports polynomial-time queries.

Web interface

A prototypical web-interface to the SBML Harvester is available at http://bioonto.gen.cam.ac.uk/sbmlharvester/

The web interface allows the upload of annotated SBML models and will produce an OWL file that integrates these models in a common ontology and can subsequently be used for verification and querying.

Publication

The methods underlying the SBML Harvester software is published in BMC Systems Biology:

Robert Hoehndorf, Michel Dumontier, John H Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L Cook and Georgios V Gkoutos. Integrating systems biology models and biomedical ontologies. BMC Systems Biology 2011, 5:124.

Contact and support

For more information about the SBML Harvester and the converted SBML models or networks contact Robert.