Welcome to the Systems Biology platform semanticSBML2.0, a collection of new services within the semanticSBML project. SemanticSBML provides methods to process biochemical network models in SBML format and the semantic annotations therein.
For the basic tasks of model building, annotation, checking, and merging, please use our main site www.semanticsbml.org.

SemanticSBML 2.0 is organised as follows: you can upload your annotated SBML models and load models from the BioModels Database into your model list at the bottom of this page.
The links in each row allow you to display the XML code of your model, to add SBO terms for kinetic laws and parameters, to find similar models in BioModels Database, and to download the model again.

Further services are accessible in the sidebar. The CLUSTER link takes you to a page displaying the pairwise similarities of all models in your model list. REST API links to a documentation of our RESTful web services, NON-SBML leads to an annotation tool for non-SBML models and data sets.

Model Similarity

Search the model repository BioModels Database for models that resemble your query model. Query and target models are compared by their MIRIAM-compliant element annotations.

Usage: Add a model, use the 'find similar models' link in the My Models overview

Automatic Assignment of SBO Terms

SBO annotations are assigned automatically to kinetic rate laws and the local parameters representing kinetic constants.

Usage: Add a model, use the 'add SBO terms' link in the My Models overview

Clustering of Models

All models from the model list are clustered by their annotation similarities and arranged in a graph. Clustering is disabled if the model list contains less than two models.

Usage: Add more than one model, use the 'CLUSTER' link in the left navigation bar

HTML View of SBML Models

Export an SBML model and add a link to the SBML Browse stylesheet. This will enable browsers to display your model in a neat and practical way. Courtesy of Neil Swainston and Kieran Smallbone, MCISB.

Usage: Add a model, use the icon ("to HTML") link in the My Models overview

RESTful API

You can access all of semanticSBML 2.0s features through a RESTful interface. This allows you to easily integrate semanticSBML2.0 in your software application or web site.

Usage: use the 'REST API' link in the left navigation bar