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25th BioModels Database Release

Hinxton, Tuesday 18th June 2013

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

BioModels Database now publicly provides 143013 models. This corresponds to 963 models published in the literature and 142050 models coming from the Path2Models project.

This release sees the publication of the first models making use of the latest version of SBML (L3 V1), in addition to some packages. That required the upgrade of our curation pipeline. Moreover, the behaviour of the generic search feature has been slightly modified to be more encompassing. Finally, efforts were made to clean and improve numerous older models' notes and annotations.


Support for SBML L3 and packages

The underlying curation pipeline has been updated in order to provide some initial support for models encoded in SBML L3 and making use of packages.

For models submitted in an older level and version, users can now access an automatic conversion to SBML L3 V1 Core. This is performed on demand by libSBML and is available for all models published in the literature from the "Download SBML" menu.

Search

The default search (available via the field displayed on the top right of all pages) now allows users to retrieve models from the Path2Models set. So far, this only takes into account the model identifier, name and organism, in order to not overload the number of results. A dedicated and detailed Path2Models search feature is available on the project page.

RDF

We are continuing our efforts to provide an RDF/XML version of the models published in the literature. All generated files are available in a dedicated archive on the FTP server.

Please refer to the previous release notes for more information about the data model used and the conversion tool developed. If you find this useful or have any comments or requests, please contact us.

Download

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

Content summary

Classification of the curated models based on their Gene Ontology annotation:

Classification of curated models based on GO (r25)

Statistics

Models published in the literature

ReleasesModelsSpeciesRelationsCross-references
18 June 2013963156665174986171432
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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