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BioModels Database

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24th BioModels Database Release

Hinxton, Wednesday 12th December 2012

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

BioModels Database now publicly provides 142973 models. This corresponds to 923 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 versions of the metabolic and non-metabolic models were generated by the Path2Models project, as well as graphical representations in SBGN for the metabolic ones. Finally we are introducing, for testing and feedback purposes, a RDF/XML version of the models published in the literature. Please read below for more information about this release.


Path2Models

BioModels Database now provides access to updated versions of the metabolic and non-metabolic models, which were recently generated by Path2Models. One of the changes to those models is the fact that experimentally-determined rate laws and parameter values were retrieve from SABIO-RK and incorporated into the models.

Graphical representations of the metabolic models are now available. Those follow the SBGN standard and are available in two formats (PNG and SBGN-ML) and can be downloaded from the "additional files" menu.

Finally, now only one version of the SBML files is provided for each model: SBML L3 Core for metabolic models and SBML L3 Core + Qual for non-metabolic models.

RDF

Building on the work of the RICORDO project, an early RDF/XML conversion of SBML models has been developed. One of the long term aim is to make all models available in a triple store, readily accessible for Semantic Web applications.

At this stage, only RDF/XML versions of the models published in the literature were created. All generated files are available in a dedicated archive on the FTP server.

The SBML to RDF/XML converter developed is hosted on GitHub, as well as some documentation.

We are calling for feedbacks regarding the RDF/XML files produced. Please refer to the contact page for means to provide us with your comments.

This is an on-going work, so the RDF might evolve in subsequent releases.

SBML files with Identifiers.org URLs

As announced previously, all SBML files provided for download now contain, by default, annotations making use of Identifiers.org URLs. The possibility to download the models with annotations using the old MIRIAM URNs is still available via the download menu as well as in the archives.

Caltech mirror

The content of the Caltech mirror will be updated in the forthcoming days.

Download

All the models of this release are provided in the followning archives from our FTP server:

Content summary

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

Classification of curated models based on GO (r24)

Statistics

Models published in the literature

ReleasesModelsSpeciesRelationsCross-references
12 December 2012923145746165473134852
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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