Searching and getting data from BioModels

Searching BioModels

Browse by GO classification

Allows categorised hierarchical retrieval of models. You can do this by following the GO term classification or tree that is provided on the BioModels homepage. All models are annotated with at least one GO term at the model level to represent the biological process it describes.

Quick search

Provides you with a list of models that contain any of your search terms in the model components, annotation, or additional information. This option is comprehensive but can return false-positive results. Searches done within quotes (“[Search Term”) give more precise results.

Advanced search

Allows you to streamline your search. You can combine several elementary searches on the model components, using accession numbers of the data resources used for annotation. For some data resources you can also search using text, for example names, synonyms or definitions.

Downloading models from BioModels

Models can be retrieved in various formats, in addition to SBML (Systems Biology Markup Language). The other formats include, BioPAX and VCML, but also configuration files for various simulators such as XPPAUT, Octave and SciLab. The reaction graphs can be downloaded in SVG and PNG formats (following the SBGN standard, Figure 5). The models can also be viewed as a downloadable PDF format.

SBGN Process Description map

Figure 5  SBGN Process Description map, representing the regulation of mitotic cell division by cyclin and cyclin dependent kinase. From: Tyson (1991).
View the original model in BioModels.