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23rd BioModels Database Release

Hinxton, Saturday 11th August 2012

We are pleased to announce the twenty-third release of BioModels Database!

BioModels Database now publicly provides 142916 models. This corresponds to 867 models published in the literature and 142050 models coming from the Path2Models project.

With this release, several new models have been published and numerous have been updated. Moreover new services are now available (for example related to the access to models from the Path2Models project) while others have been improved (such as the model browsing feature based on a tree of Gene Ontology terms or the BioPAX export). Please read below for more information.


Path2Models

A search engine is now provided for retrieving models coming from the Path2Models project. More information about how to use it is available from the Path2Models page.

For those wishing to obtain the complete set of those models, three archives are now available from our FTP server.

Finally performance improvements were made related to the speed of browsing those models.

Gene Ontology tree

The way to browse the curated models via Gene Ontology terms has been updated. The tree now fully works on all main web browsers. Moreover, when clicking on one GO term, the list of relevant models is displayed in the right panel.

BioPAX export

The BioPAX L3 converter used to generate our exports has been updated. As well as fixing several issues, this introduces the usage of Identifiers.org URLs. This should enable users to build on this RDF-based representation of the models for preforming cross repository queries.

Web services

The Java library provided to access the web services is now available via the EBI Maven repository (in addition to the download from SourceForge). For more information about this library and how to configure your Maven configuration file, please refer to the web services documentation page.

SBML files with Identifiers.org URLs

Since the 21st release, in addition to the SBML versions of the models with annotations encoded with MIRIAM URNs, BioModels Database provides SBML files with annotations encoded using Identifiers.org URLs.

From this release, the provided archives containing only SBML models make use of Identifiers.org URLs instead of the URNs. For the models published in the literature, archives with all the exports are available which still contain a copy of the models with URNs.

Content summary

Here is a classification of the curated models based on their Gene Ontology annotation:

Classification of curated models based on GO (r23)

Statistics

Models published in the literature

ReleasesModelsSpeciesRelationsCross-references
11 August 2012867133559154456108345
20 May 2012854133263154145107074
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

Path2Models

 MetabolicNon-metabolicWhole genome metabolismTotal
Models 112,898 27,306 1,846 142,050
Species 32,594,642 844,098 6,356,779 39,795,519
Relations 5,591,318 1,926 4,954,345 10,547,589
Annotations 404,248,120 16,914,269 22,861,664 444,024,053

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.


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