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BioModels Database


21st BioModels Database Release

Hinxton, Wednesday 8th February 2012

We are pleased to announce the twenty-first release of BioModels Database.

In this release, 68 new models have been published and numerous existing models have been updated.

BioModels Database now publicly provides 409 models in the curated and 420 in the non-curated branch. Together, these 829 models comprise 130800 species, 151274 relationships (which include reactions, rate rules, events and assignment rules), and 106210 cross-references.

Along with the data release, we would like to announce several important changes.

SBML files with URLs

In addition to the SBML versions of the models with annotations encoded with MIRIAM URNs, BioModels Database now provides an SBML file with annotations encoded using URLs.

Those files can be accessed from the Download SBML menu displayed on the top left of any model page.

One can also access them through the following URLs (where you should replace BIOMD0000000001 with any model identifier of your choice, which can be of the form BIOMD\d{10} or MODEL\d{10}):

The archives of the database also contain both forms of annotation.

BioModels Database will serve the URN form as the default until the next release of the database. Then the URL form will be provided as the default. The files with the URN annotations will still be available for a while. We encourage software developers to consider the version of MIRIAM URIs for any new development.

The MIRIAM Registry already provides services which can convert from one form to the other. Moreover, the SBFC converter framework also provides ways to convert whole SBML files with one type of annotations to the other.

Availability of the models

After consultation with BioModels Database's Scientific Advisory Board and to be more in agreement with the EBI terms of use, it was decided that from the next release (22nd), the Team will abandon its copyright on the encoded form of the models and release them in the public domain.


Model archives (from the releases and the automatic weekly generation) are now available from the EBI FTP Server.

Starting from this release, two archives are generated: one containing only the SBML files (with annotations encoded with MIRIAM URNs, as previously) and one containing the SBML files (two versions: one with MIRIAM URNs and one with URLs) as well as all the exports that we provide on the website.

Annotations in non-curated models

Various improvements were made to the underlying software infrastructure. The main publicly visible change is the fact that a major bug, dealing with the handling of annotations in the non-curated branch, has been fixed. This results in an major increase in the number of annotations from models in the non-curated branch.

However, we would like to emphasise that those annotations were provided during submission and are not checked by our curators.


Users now have the possibility to download models directly from a search result. This can be achieved by clicking on the small "floppy disk" icon on the right of the model identifier in the table of results. If the model comes from the curated branch, the curated version of the model will be downloaded.

Download of models in SBML L2V2 has been discontinued. This was previously available via an on-demand automatic generation, performed by libSBML. This is due to the non-usage of this feature.


We would like to thank all our collaborators, founders and submitters. We also want to thank the SBML community for their support and the tools they develop and provide.

BioModels Database is the result of numerous current and past collaborations and has received funding from multiple sources. Please refer to our acknowledgements page for up-to-date details.


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