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22nd BioModels Database Release

Hinxton, Sunday 20th May 2012

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

BioModels Database now publicly provides 142904 models. This corresponds to 421 models in the curated branch, 433 models in the non-curated branch and 142050 models coming from the Path2Models project.

In addition to the typical work on the curated and non-curated branches, where several new models have been made available and numerous others updated, this release sees the availability of the models generated by the Path2Models project, a change in the terms of use and several improvements and new features. Please read below for more information.


Path2Models

The Path2Models project consists in the large scale generation of quantitative models form pathways. The initial pathways come from databases, such as KEGG, are completed with information coming from other resources (such as BioCarta and MetaCyc), converted into SBML and enriched with cross-references. Mathematical models are thereafter generated, using common modular rate law for the metabolic networks and logical models for the signalling pathways (encoded in the SBML Level 3 Qual package). In addition, whole genome metabolism models are reconstructed using flux balance constraint methods.

The first version of the models generated by the project are now made available from this dedicated page. Those 142050 models comprise 444026858 cross-references.

This is only the first step of the provision of automatically generated models. The current search engine does not yet encompass those models, but this is currently under development and will be released shortly. Moreover, downloadable archives will be provided very soon.

It is expected that improved versions of those models, with graphical representations, will be available in forthcoming releases.

Terms of use

As announced previously, all models distributed by BioModels Database are now in the public domain and available under the Creative Commons CC0 Public Domain Dedication license. Please refer to our new terms of use for more information.

Support of SBML Level 3

We are now officially supporting the submission of models encoded in SBML Level 3. Submitting models to the database can be performed via the online submission page.

Taxonomy cloud

Work has started to provide more flexible and powerful ways to find models of interest, using the annotations as a mean to classify them. A preliminary outcome is the release of the first version of the Taxonomy cloud, which allows users to find models related to a given organism.

SBML files with Identifiers.org URLs

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

For more information about those files and how to access them, please refer to the release notes of the previous release.

BioModels Database continues to serve the URN form as the default but this will change from the next release, when 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.

Web Services

The web services have been updated and new methods are now provided: getAuthorsByModelId, getDateLastModifByModelId, getEncodersByModelId, getPublicationByModelId, getSimpleModelsByIds. Moreover all the methods returning a SimpleModel (when using the Java library) have been updated and now provide more information (such as the list of encoders, the list of authors, the date of last modification, ...). Please refer to the list of web services for up-to-date documentation.

The version 1.21 of the Java library to access the web services has been released. This gives access to all the new services that are now provided.

Content summary

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

Classification of curated models based on GO (r22)

Statistics


ReleasesModelsSpeciesRelationsCross-references
20 May 20121429043992878210701734444133932
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

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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