Büchel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek, Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and van Iersel, Martijn and Keating, Sarah M. and Rall, Matthias and Wybrow, Michael and Hermjakob, Henning and Hucka, Michael and B Kell, Douglas and Müller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya, Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe, Camille and Dräger, Andreas and Le Novère, Nicolas

Path2Models: large-scale generation of computational models from biochemical pathway maps

BMC Systems Biology vol. 7 (2013), no. 1, pp. 116


Abstract

Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.

Results: To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps.

Conclusions: To date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.


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BibTeX

@article{Buechel2013b,
  author = {B\"uchel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek,
	Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian
	and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and
	{van Iersel}, Martijn and Keating, Sarah M. and Rall, Matthias and Wybrow,
	Michael and Hermjakob, Henning and Hucka, Michael and {B Kell}, Douglas
	and M\"uller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya,
	Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe,
	Camille and Dr\"ager, Andreas and {Le Nov\`{e}re}, Nicolas},
  title = {{Path2Models: large-scale generation of computational models from
	biochemical pathway maps}},
  journal = {BMC Systems Biology},
  year = {2013},
  volume = {7},
  pages = {116},
  number = {1},
  month = nov,
  abstract = {Background: Systems biology projects and omics technologies have
    led to a growing number of biochemical pathway models and reconstructions.
	However, the majority of these models are still created de novo,
	based on literature mining and the manual processing of pathway data.

	Results: To increase the efficiency of model creation, the Path2Models
	representations using a suite of freely available software. Data
	sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on
	the source data, three types of models are provided: kinetic, logical
	and constraint-based. Models from over 2~600 organisms are encoded
	consistently in SBML, and are made freely available through BioModels
	Database at \url{http://www.ebi.ac.uk/biomodels-main/path2models}.
	Each model contains the list of participants, their interactions,
	the relevant mathematical constructs, and initial parameter values.
	Most models are also available as easy-to-understand graphical SBGN
	maps.

	Conclusions: To date, the project has resulted in more than
	140~000 freely available models. Such a resource can tremendously
	accelerate the development of mathematical models by providing initial
	starting models for simulation and analysis, which can be subsequently
	curated and further parameterized.},
  doi = {10.1186/1752-0509-7-116},
  keywords = {Modular rate law, Constraint based models, Logical models, SBGN, SBML},
  pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-116.pdf},
  url = {http://www.biomedcentral.com/1752-0509/7/116}
}