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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 Identifiers.org 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 Identifiers.org 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 Identifiers.org 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 BioModels.net Team will abandon its copyright on the encoded form of the models and release them in the public domain.

Archives

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 Identifiers.org 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.

Miscellaneous

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.


Acknowledgements

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.

Statistics


ReleaseModelsSpeciesRelationsCross-references
08 February 2012829130800151274106210
01 September 201176411974513588924666
15 April 20116999211211392522969
30 September 2010630792249874520426
27 April 2010473378525152518950
26 January 2010453337024760817228
02 September 2009429320144538616492
16 June 2009412289014227414611
25 March 2009335287263846513818
03 December 2008293272383545113206
21 August 2008259217832803210811
28 March 2008244209452655510498
25 September 200719210482130689810
05 June 2007145602773477692
05 January 2007128569767335651
03 October 200696412550203074
05 June 20065483714043542
31 January 20065076112193126
28 July 2005445969952373
01 June 2005304257821609
11 April 2005203226581084
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