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BioModels Database

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26th "Movember" BioModels Database Release

Hinxton, Monday 4th November 2013

We are proud to announce this Movember release of BioModels Database, in which we reached a new landmark of over 1000 models published in the literature!


One thousand model mark

Since its first release in April 2005, BioModels database has grown substantially from the original 20 models it contained. With this release, it now publicly distributes 143,135 models.

BioModels Database has evolved over this time to also accommodate models created through the automated processing of publicly available data sets: the Path2Models project has contributed 142,845 such models. Furthermore, BioModels Database also includes over one thousand (1085) models published in the scientific literature, either directly submitted by their authors or encoded by knowledgeable curators.

In achieving this milestone, we gratefully acknowledge the trust placed in us by scientific publishers who recommend deposition of models in BioModels Database, the faith shown in the resource from publication authors, the tremendous work done by curators, as well as the enormous number of contributions from the scientific community. Thank you all!

Path2Models

This release provides a completely updated set of the genome-scale metabolic reconstruction models. This uses the latest version of the workflow based on the SuBliMinaL Toolbox.

Additionally, the work behind the Path2Models project has now been published in Path2Models: large-scale generation of computational models from biochemical pathway maps.

RDF and SPARQL endpoint

Following our effort to provide access to the models in RDF/XML, we have now made available a SPARQL endpoint, to allow you to query BioModels Database's dataset and others using Semantic Web technologies. Please refer to the documentation and example queries, in order to get started.

This is part of a wider EBI effort, which so far encompasses 6 resources: the EBI RDF Platform.

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 (r26)

Statistics

Models published in the literature

ReleasesModelsSpeciesRelationsCross-references
04 November 201310854013523410111117506
18 June 2013963156665174986171432
12 December 2012923145746165473134852
11 August 2012867133559154456108345
20 May 2012854133263154145107074
08 February 2012829130800151274106210
Expand/collapse statistics for all releases.

Path2Models

 MetabolicNon-metabolicWhole genome metabolismTotal
Models 112,898 27,306 2,641 142,845
Species 16,306,840 843,144 8,937,630 26,087,614
Relations 2,795,659 193,081 6,495,608 9,484,348
Annotations 168,908,203 6,517,047 21,444,254 196,869,504

Movember

Movember is an independent global charity dedicated to raise vital funds and awareness for prostate and testicular cancer and mental health. Movember challenges men to grow a moustache for the 30-days of November, thereby changing their appearance and the face of men’s health. Don't hesitate to support the Mo Bros!

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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