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

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

doi:10.1186/1752-0509-7-116

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

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

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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. © 2013 Büchel et al.; licensee BioMed Central Ltd.

Original language	English
Article number	116
Journal	BMC Systems Biology
Volume	7
DOIs	https://doi.org/10.1186/1752-0509-7-116
Publication status	Published - 1 Nov 2013

Keywords

Constraint based models
Logical models
Modular rate law
SBGN
SBML

Research Beacons, Institutes and Platforms

Manchester Institute of Biotechnology

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Pedrosa Mendes, P., Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., Mittag, F., Schubert, M., Glont, M., Golebiewski, M., van Iersel, M., Keating, S., Rall, M., Wybrow, M., Hermjakob, H., Hucka, M., Kell, D. B., Müller, W., ... Le Novère, N. (2013). Path2Models: Large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology, 7, Article 116. https://doi.org/10.1186/1752-0509-7-116

@article{bd98dbafb5f2454f990bb012cbce8331,

title = "Path2Models: Large-scale generation of computational models from biochemical pathway maps",

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. {\textcopyright} 2013 B{\"u}chel et al.; licensee BioMed Central Ltd.",

keywords = "Constraint based models, Logical models, Modular rate law, SBGN, SBML",

author = "{Pedrosa Mendes}, Pedro and Finja B{\"u}chel and Nicolas Rodriguez and Neil Swainston and Clemens Wrzodek and Tobias Czauderna and Roland Keller and Florian Mittag and Michael Schubert and Mihai Glont and Martin Golebiewski and {van Iersel}, Martijn and Sarah Keating and Matthias Rall and Michael Wybrow and Henning Hermjakob and Michael Hucka and Kell, {Douglas B.} and Wolfgang M{\"u}ller and Pedro Mendes and Andreas Zell and Claudine Chaouiya and Julio Saez-Rodriguez and Falk Schreiber and Camille Laibe and Andreas Dr{\"a}ger and {Le Nov{\`e}re}, Nicolas",

note = "NS and PM acknowledge support from the European Union FP7 project UNICELLSYS (grant number: 201142). MvI and PM received financial aid from the EU project BioPreDyn (ECFP7-KBBE-2011-5 Grant number 289434). PM acknowledges support from the BBSRC (grant number BB/J019259/1).All models generated by the project are availaible from BioModels Database.",

year = "2013",

month = nov,

day = "1",

doi = "10.1186/1752-0509-7-116",

language = "English",

volume = "7",

journal = "BMC Systems Biology",

issn = "1752-0509",

publisher = "Springer Nature",

}

Pedrosa Mendes, P, Büchel, F, Rodriguez, N, Swainston, N, Wrzodek, C, Czauderna, T, Keller, R, Mittag, F, Schubert, M, Glont, M, Golebiewski, M, van Iersel, M, Keating, S, Rall, M, Wybrow, M, Hermjakob, H, Hucka, M, Kell, DB, Müller, W, Mendes, P, Zell, A, Chaouiya, C, Saez-Rodriguez, J, Schreiber, F, Laibe, C, Dräger, A & Le Novère, N 2013, 'Path2Models: Large-scale generation of computational models from biochemical pathway maps', BMC Systems Biology, vol. 7, 116. https://doi.org/10.1186/1752-0509-7-116

TY - JOUR

T1 - Path2Models: Large-scale generation of computational models from biochemical pathway maps

AU - Pedrosa Mendes, Pedro

AU - Büchel, Finja

AU - Rodriguez, Nicolas

AU - Swainston, Neil

AU - Wrzodek, Clemens

AU - Czauderna, Tobias

AU - Keller, Roland

AU - Mittag, Florian

AU - Schubert, Michael

AU - Glont, Mihai

AU - Golebiewski, Martin

AU - van Iersel, Martijn

AU - Keating, Sarah

AU - Rall, Matthias

AU - Wybrow, Michael

AU - Hermjakob, Henning

AU - Hucka, Michael

AU - Kell, Douglas B.

AU - Müller, Wolfgang

AU - Mendes, Pedro

AU - Zell, Andreas

AU - Chaouiya, Claudine

AU - Saez-Rodriguez, Julio

AU - Schreiber, Falk

AU - Laibe, Camille

AU - Dräger, Andreas

AU - Le Novère, Nicolas

N1 - NS and PM acknowledge support from the European Union FP7 project UNICELLSYS (grant number: 201142). MvI and PM received financial aid from the EU project BioPreDyn (ECFP7-KBBE-2011-5 Grant number 289434). PM acknowledges support from the BBSRC (grant number BB/J019259/1).All models generated by the project are availaible from BioModels Database.

PY - 2013/11/1

Y1 - 2013/11/1

N2 - 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. © 2013 Büchel et al.; licensee BioMed Central Ltd.

AB - 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. © 2013 Büchel et al.; licensee BioMed Central Ltd.

KW - Constraint based models

KW - Logical models

KW - Modular rate law

KW - SBGN

KW - SBML

U2 - 10.1186/1752-0509-7-116

DO - 10.1186/1752-0509-7-116

M3 - Article

C2 - 24180668

SN - 1752-0509

VL - 7

JO - BMC Systems Biology

JF - BMC Systems Biology

M1 - 116

ER -

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

Abstract

Keywords

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