%0 Journal Article %1 Buchel2013Path2Models %A Buchel, Finja %A Rodriguez, Nicolas %A Swainston, Neil %A Wrzodek, Clemens %A Czauderna, Tobias %A Keller, Roland %A Mittag, Florian %A Schubert, Michael %A Glont, Mihai %A Golebiewski, Martin %A van Iersel, Martijn %A Keating, Sarah %A Rall, Matthias %A Wybrow, Michael %A Hermjakob, Henning %A Hucka, Michael %A Kell, Douglas %A Muller, Wolfgang %A Mendes, Pedro %A Zell, Andreas %A Chaouiya, Claudine %A Rodriguez, Julio S. %A Schreiber, Falk %A Laibe, Camille %A Drager, Andreas %A Le Novere, Nicolas %D 2013 %J BMC Systems Biology %K curation genome-scale metabolic-networks tool %N 1 %P 116+ %R 10.1186/1752-0509-7-116 %T Path2Models: large-scale generation of computational models from biochemical pathway maps %U http://dx.doi.org/10.1186/1752-0509-7-116 %V 7 %X 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 webcite. 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.

@article{Buchel2013Path2Models, 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 webcite. 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.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Buchel, 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 and Rall, Matthias and Wybrow, Michael and Hermjakob, Henning and Hucka, Michael and Kell, Douglas and Muller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya, Claudine and Rodriguez, Julio S. and Schreiber, Falk and Laibe, Camille and Drager, Andreas and Le Novere, Nicolas}, biburl = {https://www.bibsonomy.org/bibtex/29eb253f6fa3c9840e49997aa46f77c60/karthikraman}, citeulike-article-id = {12750414}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-0509-7-116}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/24180668}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=24180668}, doi = {10.1186/1752-0509-7-116}, interhash = {376477bd983b2f02a3a1bcdcd212d6d1}, intrahash = {9eb253f6fa3c9840e49997aa46f77c60}, issn = {1752-0509}, journal = {BMC Systems Biology}, keywords = {curation genome-scale metabolic-networks tool}, number = 1, pages = {116+}, pmid = {24180668}, posted-at = {2013-11-04 10:35:13}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {{Path2Models}: large-scale generation of computational models from biochemical pathway maps}, url = {http://dx.doi.org/10.1186/1752-0509-7-116}, volume = 7, year = 2013 }