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fix citation error detected by Cell Systems editors
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78 changes: 39 additions & 39 deletions evaluated_standards.tex
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\midrule
\endhead
\midrule
\small{SciPy optimize, ODE solver, etc.} &\small{Simulator} &\cite{virtanen2020scipy} &\small{2020} &\small{39.8} &\small{881.4} &\small{}\\
\small{SciPy optimize, ODE solver, etc.} &\small{Simulator} &\cite{virtanen2020scipy} &\small{2020} &\small{87.0} &\small{1355.3} &\small{}\\
\midrule
\small{FAIR} &\small{Modeling process guidelines} &\cite{Wilkinson2016TheStewardship.} &\small{2016} &\small{142.0} &\small{590.7} &\small{}\\
\small{FAIR} &\small{Modeling process guidelines} &\cite{Wilkinson2016TheStewardship.} &\small{2016} &\small{151.6} &\small{632.0} &\small{}\\
\midrule
\small{SBML} &\small{Modeling language} &\cite{Hucka2003TheModels} &\small{2003} &\small{50.0} &\small{183.8} &\small{69.5}\\
\small{SBML} &\small{Modeling language} &\cite{Hucka2003TheModels} &\small{2003} &\small{49.7} &\small{184.8} &\small{69.5}\\
\midrule
\small{COPASI} &\small{Modeling application} &\cite{Hoops2006COPASI--aSImulator} &\small{2006} &\small{} &\small{149.6} &\small{31.7}\\
\small{COPASI} &\small{Modeling application} &\cite{Hoops2006COPASI--aSImulator} &\small{2006} &\small{} &\small{151.3} &\small{31.7}\\
\midrule
\small{SBGN} &\small{Modeling visualization language} &\cite{Novere2009TheNotation} &\small{2009} &\small{} &\small{71.0} &\small{2.4}\\
\small{SBGN} &\small{Modeling visualization language} &\cite{Novere2009TheNotation} &\small{2009} &\small{} &\small{71.8} &\small{2.4}\\
\midrule
\small{COBRApy} &\small{Simulator} &\cite{ebrahim2013cobrapy} &\small{2013} &\small{22.2} &\small{59.6} &\small{11.3}\\
\small{COBRApy} &\small{Simulator} &\cite{ebrahim2013cobrapy} &\small{2013} &\small{22.6} &\small{60.8} &\small{11.3}\\
\midrule
\small{BioPAX} &\small{Biochemical data manager} &\cite{Demir2010TheSharing.} &\small{2010} &\small{24.8} &\small{56.5} &\small{}\\
\small{BioPAX} &\small{Biochemical data manager} &\cite{Demir2010TheSharing.} &\small{2010} &\small{24.5} &\small{56.8} &\small{}\\
\midrule
\small{BioModels} &\small{Model repository} &\cite{Li2010BioModelsModels} &\small{2010} &\small{17.3} &\small{52.1} &\small{33.3}\\
\small{BioModels} &\small{Model repository} &\cite{Li2010BioModelsModels} &\small{2010} &\small{17.1} &\small{52.3} &\small{33.3}\\
\midrule
\small{Pathway Tools} &\small{Biochemical data manager} &\cite{karp2002pathway} &\small{2002} &\small{} &\small{39.6} &\small{}\\
\small{InChI} &\small{Biochemical data standard} &\cite{Heller2015InChIIdentifier.} &\small{2015} &\small{15.7} &\small{41.2} &\small{}\\
\midrule
\small{InChI} &\small{Biochemical data standard} &\cite{Heller2015InChIIdentifier.} &\small{2015} &\small{15.6} &\small{38.5} &\small{}\\
\small{Pathway Tools} &\small{Biochemical data manager} &\cite{karp2002pathway} &\small{2002} &\small{} &\small{39.4} &\small{}\\
\midrule
\small{The ontology for biomedical investigations} &\small{Ontology} &\cite{Bandrowski2016TheInvestigations} &\small{2016} &\small{} &\small{33.4} &\small{}\\
\small{The ontology for biomedical investigations} &\small{Ontology} &\cite{Bandrowski2016TheInvestigations} &\small{2016} &\small{} &\small{34.9} &\small{}\\
\midrule
\small{Physiome} &\small{Model repository} &\cite{hunter2003integration} &\small{2003} &\small{4.9} &\small{32.8} &\small{}\\
\midrule
\small{SBO} &\small{Ontology} &\cite{Courtot2011ControlledBiology.} &\small{2011} &\small{} &\small{23.9} &\small{}\\
\small{KiSAO} &\small{Ontology} &\cite{Courtot2011ControlledBiology.} &\small{2011} &\small{} &\small{24.5} &\small{}\\
\midrule
\small{Data2Dynamics} &\small{Parameter estimation tool} &\cite{Raue2015Data2Dynamics:Systems} &\small{2015} &\small{7.8} &\small{23.7} &\small{1.1}\\
\small{SBO} &\small{Ontology} &\cite{Courtot2011ControlledBiology.} &\small{2011} &\small{} &\small{24.5} &\small{}\\
\midrule
\small{BioNetGen} &\small{Modeling language} &\cite{Harris2016BioNetGenModeling} &\small{2016} &\small{7.7} &\small{22.5} &\small{8.5}\\
\small{Data2Dynamics} &\small{Parameter estimation tool} &\cite{Raue2015Data2Dynamics:Systems} &\small{2015} &\small{7.7} &\small{24.1} &\small{1.1}\\
\midrule
\small{SED-ML} &\small{Simulation description language} &\cite{Waltemath2011ReproducibleLanguage} &\small{2011} &\small{8.2} &\small{20.6} &\small{}\\
\small{BioNetGen} &\small{Modeling language} &\cite{Harris2016BioNetGenModeling} &\small{2016} &\small{8.1} &\small{23.9} &\small{8.5}\\
\midrule
\small{JWS Online} &\small{Modeling application} &\cite{Olivier2004Web-basedOnline} &\small{2004} &\small{4.6} &\small{19.9} &\small{5.4}\\
\small{SED-ML} &\small{Simulation description language} &\cite{Waltemath2011ReproducibleLanguage} &\small{2011} &\small{8.2} &\small{21.1} &\small{}\\
\midrule
\small{PySB} &\small{Modeling language} &\cite{Lopez2013ProgrammingPySB} &\small{2013} &\small{6.3} &\small{19.6} &\small{6.5}\\
\small{JWS Online} &\small{Modeling application} &\cite{Olivier2004Web-basedOnline} &\small{2004} &\small{4.6} &\small{20.1} &\small{5.4}\\
\midrule
\small{CellML} &\small{Modeling language} &\cite{Cuellar2003AnLanguage} &\small{2003} &\small{} &\small{18.2} &\small{7.3}\\
\small{PySB} &\small{Modeling language} &\cite{Lopez2013ProgrammingPySB} &\small{2013} &\small{6.4} &\small{20.0} &\small{6.5}\\
\midrule
\small{VCell} &\small{Modeling application} &\cite{moraru2008virtual} &\small{2008} &\small{6.0} &\small{17.7} &\small{2.7}\\
\small{CellML} &\small{Modeling language} &\cite{Cuellar2003AnLanguage} &\small{2003} &\small{} &\small{18.5} &\small{7.3}\\
\midrule
\small{MIASE} &\small{Modeling process guidelines} &\cite{Waltemath2011MinimumMIASE} &\small{2011} &\small{3.3} &\small{12.4} &\small{}\\
\small{VCell} &\small{Modeling application} &\cite{moraru2008virtual} &\small{2008} &\small{6.0} &\small{17.8} &\small{2.7}\\
\midrule
\small{PROV} &\small{Reproducibility standard} &\cite{Moreau2015ThePROV} &\small{2015} &\small{} &\small{12.2} &\small{}\\
\small{MIASE} &\small{Modeling process guidelines} &\cite{Waltemath2011MinimumMIASE} &\small{2011} &\small{3.2} &\small{12.7} &\small{}\\
\midrule
\small{FAIRDOMHub} &\small{Model repository} &\cite{Wolstencroft2017FAIRDOMHub:Research.} &\small{2017} &\small{3.9} &\small{12.1} &\small{}\\
\midrule
\small{Memote} &\small{Validation tool} &\cite{Lieven2018Memote:Suite} &\small{2018} &\small{} &\small{12.1} &\small{}\\
\midrule
\small{libRoadRunner} &\small{Simulator} &\cite{Somogyi2015LibRoadRunner:Library.} &\small{2015} &\small{4.6} &\small{11.1} &\small{5.4}\\
\small{PROV} &\small{Reproducibility standard} &\cite{Moreau2015ThePROV} &\small{2015} &\small{} &\small{11.9} &\small{}\\
\midrule
\small{FAIRDOMHub} &\small{Model repository} &\cite{Wolstencroft2017FAIRDOMHub:Research.} &\small{2017} &\small{3.2} &\small{10.6} &\small{}\\
\small{libRoadRunner} &\small{Simulator} &\cite{Somogyi2015LibRoadRunner:Library.} &\small{2015} &\small{4.7} &\small{11.5} &\small{5.4}\\
\midrule
\small{SEEK} &\small{Model repository} &\cite{Wolstencroft2015SEEK:Platform} &\small{2015} &\small{3.1} &\small{10.6} &\small{3.8}\\
\midrule
\small{SESSL} &\small{Simulation description language} &\cite{Ewald2014SESSL:Experiments} &\small{2014} &\small{0.0} &\small{10.6} &\small{}\\
\small{SESSL} &\small{Simulation description language} &\cite{Ewald2014SESSL:Experiments} &\small{2014} &\small{0.0} &\small{10.5} &\small{}\\
\midrule
\small{BioLab} &\small{Validation tool} &\cite{Clarke2008StatisticalPathway} &\small{2008} &\small{} &\small{10.1} &\small{}\\
\small{BioLab} &\small{Validation tool} &\cite{Clarke2008StatisticalPathway} &\small{2008} &\small{} &\small{10.0} &\small{}\\
\midrule
\small{COMBINE} &\small{Biochemical data format} &\cite{Bergmann2014COMBINEProject} &\small{2014} &\small{3.6} &\small{9.5} &\small{}\\
\small{COMBINE} &\small{Biochemical data format} &\cite{Bergmann2014COMBINEProject} &\small{2014} &\small{3.7} &\small{9.9} &\small{}\\
\midrule
\small{RightField} &\small{Model data annotation tool} &\cite{Wolstencroft2011RightField:Spreadsheets} &\small{2011} &\small{2.4} &\small{8.6} &\small{}\\
\midrule
\small{OpenCOR} &\small{Simulator} &\cite{garny2015opencor} &\small{2015} &\small{2.6} &\small{8.1} &\small{3.8}\\
\small{OpenCOR} &\small{Simulator} &\cite{garny2015opencor} &\small{2015} &\small{2.7} &\small{8.5} &\small{3.8}\\
\midrule
\small{MIRIAM} &\small{Modeling process guidelines} &\cite{Laibe2007MIRIAMBiology.} &\small{2007} &\small{3.1} &\small{7.9} &\small{}\\
\small{MIRIAM} &\small{Modeling process guidelines} &\cite{Laibe2007MIRIAMBiology.} &\small{2007} &\small{3.0} &\small{8.0} &\small{}\\
\midrule
\small{PyDREAM} &\small{Parameter estimation tool} &\cite{Shockley2018PyDREAM:Python} &\small{2018} &\small{2.5} &\small{7.9} &\small{}\\
\small{PyDREAM} &\small{Parameter estimation tool} &\cite{Shockley2018PyDREAM:Python} &\small{2018} &\small{3.5} &\small{7.8} &\small{}\\
\midrule
\small{SBML-PET} &\small{Parameter estimation tool} &\cite{Zi2006SBML-PET:Tool} &\small{2006} &\small{1.7} &\small{7.1} &\small{}\\
\small{StochSS} &\small{Simulator} &\cite{drawert2016stochastic} &\small{2016} &\small{2.9} &\small{7.2} &\small{}\\
\midrule
\small{StochSS} &\small{Simulator} &\cite{drawert2016stochastic} &\small{2016} &\small{2.7} &\small{7.0} &\small{}\\
\small{SBML-PET} &\small{Parameter estimation tool} &\cite{Zi2006SBML-PET:Tool} &\small{2006} &\small{1.6} &\small{7.0} &\small{}\\
\midrule
\small{Tellurium} &\small{Modeling application} &\cite{Choi2018Tellurium:Biology} &\small{2018} &\small{2.1} &\small{6.7} &\small{4.8}\\
\small{Tellurium} &\small{Modeling application} &\cite{Choi2018Tellurium:Biology} &\small{2018} &\small{2.0} &\small{6.7} &\small{4.8}\\
\midrule
\small{SBRML} &\small{Model data annotation tool} &\cite{Dada2010SBRML:Models} &\small{2010} &\small{1.7} &\small{6.2} &\small{}\\
\midrule
\small{PyBioNetFit} &\small{Validation tool} &\cite{Mitra2019PyBioNetFitLanguage} &\small{2019} &\small{2.1} &\small{5.0} &\small{}\\
\small{SBtab} &\small{Biochemical data format} &\cite{Lubitz2016SBtab:Biology} &\small{2016} &\small{2.0} &\small{5.1} &\small{}\\
\midrule
\small{SBtab} &\small{Biochemical data format} &\cite{Lubitz2016SBtab:Biology} &\small{2016} &\small{1.8} &\small{5.0} &\small{}\\
\small{PyBioNetFit} &\small{Validation tool} &\cite{Mitra2019PyBioNetFitLanguage} &\small{2019} &\small{2.6} &\small{4.5} &\small{}\\
\midrule
\small{HDF} &\small{Data format} &\cite{Brown1993SoftwareManagement} &\small{1993} &\small{} &\small{2.5} &\small{}\\
\small{HDF} &\small{Data format} &\cite{Brown1993SoftwareManagement} &\small{1993} &\small{} &\small{2.6} &\small{}\\
\midrule
\small{SciUnit} &\small{Validation tool} &\cite{Omar2014CollaborativeValidation} &\small{2014} &\small{} &\small{2.3} &\small{}\\
\small{SciUnit} &\small{Validation tool} &\cite{Omar2014CollaborativeValidation} &\small{2014} &\small{} &\small{2.4} &\small{}\\
\midrule
\small{SEPIO} &\small{Ontology} &\cite{Brush2016SEPIO:Evidence} &\small{2016} &\small{} &\small{1.8} &\small{}\\
\midrule
\small{KiSAO} &\small{Ontology} &\cite{Zhukova2011KineticOntology} &\small{2007} &\small{} &\small{1.1} &\small{}\\
\midrule
\small{BpForms and BcForms} &\small{Biochemical data format} &\cite{Lang2019BpForms:Proteins} &\small{2019} &\small{} &\small{0.7} &\small{}\\
\small{BpForms and BcForms} &\small{Biochemical data format} &\cite{Lang2019BpForms:Proteins} &\small{2019} &\small{} &\small{1.3} &\small{}\\
\midrule
\small{ObjTables} &\small{Biochemical data format} &\cite{karr2020structured} &\small{2020} &\small{} &\small{0.0} &\small{}\\
\bottomrule\end{longtable}
92 changes: 46 additions & 46 deletions evaluated_standards.tsv
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Standard / tool Type of standard / tool Most cited paper Paper year PubMed (cites / yr) Scholar (cites / yr) Reported use (\%)
SciPy optimize, ODE solver, etc. Simulator \cite{virtanen2020scipy} 2020 39.8 881.4
FAIR Modeling process guidelines \cite{Wilkinson2016TheStewardship.} 2016 142.0 590.7
SBML Modeling language \cite{Hucka2003TheModels} 2003 50.0 183.8 69.5
COPASI Modeling application \cite{Hoops2006COPASI--aSImulator} 2006 149.6 31.7
SBGN Modeling visualization language \cite{Novere2009TheNotation} 2009 71.0 2.4
COBRApy Simulator \cite{ebrahim2013cobrapy} 2013 22.2 59.6 11.3
BioPAX Biochemical data manager \cite{Demir2010TheSharing.} 2010 24.8 56.5
BioModels Model repository \cite{Li2010BioModelsModels} 2010 17.3 52.1 33.3
Pathway Tools Biochemical data manager \cite{karp2002pathway} 2002 39.6
InChI Biochemical data standard \cite{Heller2015InChIIdentifier.} 2015 15.6 38.5
The ontology for biomedical investigations Ontology \cite{Bandrowski2016TheInvestigations} 2016 33.4
Physiome Model repository \cite{hunter2003integration} 2003 4.9 32.8
SBO Ontology \cite{Courtot2011ControlledBiology.} 2011 23.9
Data2Dynamics Parameter estimation tool \cite{Raue2015Data2Dynamics:Systems} 2015 7.8 23.7 1.1
BioNetGen Modeling language \cite{Harris2016BioNetGenModeling} 2016 7.7 22.5 8.5
SED-ML Simulation description language \cite{Waltemath2011ReproducibleLanguage} 2011 8.2 20.6
JWS Online Modeling application \cite{Olivier2004Web-basedOnline} 2004 4.6 19.9 5.4
PySB Modeling language \cite{Lopez2013ProgrammingPySB} 2013 6.3 19.6 6.5
CellML Modeling language \cite{Cuellar2003AnLanguage} 2003 18.2 7.3
VCell Modeling application \cite{moraru2008virtual} 2008 6.0 17.7 2.7
MIASE Modeling process guidelines \cite{Waltemath2011MinimumMIASE} 2011 3.3 12.4
PROV Reproducibility standard \cite{Moreau2015ThePROV} 2015 12.2
Memote Validation tool \cite{Lieven2018Memote:Suite} 2018 12.1
libRoadRunner Simulator \cite{Somogyi2015LibRoadRunner:Library.} 2015 4.6 11.1 5.4
FAIRDOMHub Model repository \cite{Wolstencroft2017FAIRDOMHub:Research.} 2017 3.2 10.6
SEEK Model repository \cite{Wolstencroft2015SEEK:Platform} 2015 3.1 10.6 3.8
SESSL Simulation description language \cite{Ewald2014SESSL:Experiments} 2014 0.0 10.6
BioLab Validation tool \cite{Clarke2008StatisticalPathway} 2008 10.1
COMBINE Biochemical data format \cite{Bergmann2014COMBINEProject} 2014 3.6 9.5
RightField Model data annotation tool \cite{Wolstencroft2011RightField:Spreadsheets} 2011 2.4 8.6
OpenCOR Simulator \cite{garny2015opencor} 2015 2.6 8.1 3.8
MIRIAM Modeling process guidelines \cite{Laibe2007MIRIAMBiology.} 2007 3.1 7.9
PyDREAM Parameter estimation tool \cite{Shockley2018PyDREAM:Python} 2018 2.5 7.9
SBML-PET Parameter estimation tool \cite{Zi2006SBML-PET:Tool} 2006 1.7 7.1
StochSS Simulator \cite{drawert2016stochastic} 2016 2.7 7.0
Tellurium Modeling application \cite{Choi2018Tellurium:Biology} 2018 2.1 6.7 4.8
SBRML Model data annotation tool \cite{Dada2010SBRML:Models} 2010 1.7 6.2
PyBioNetFit Validation tool \cite{Mitra2019PyBioNetFitLanguage} 2019 2.1 5.0
SBtab Biochemical data format \cite{Lubitz2016SBtab:Biology} 2016 1.8 5.0
HDF Data format \cite{Brown1993SoftwareManagement} 1993 2.5
SciUnit Validation tool \cite{Omar2014CollaborativeValidation} 2014 2.3
SEPIO Ontology \cite{Brush2016SEPIO:Evidence} 2016 1.8
KiSAO Ontology \cite{Zhukova2011KineticOntology} 2007 1.1
BpForms and BcForms Biochemical data format \cite{Lang2019BpForms:Proteins} 2019 0.7
ObjTables Biochemical data format \cite{karr2020structured} 2020 0.0
Standard / tool Type of standard / tool Most cited paper Paper year PubMed (cites / yr) Scholar (cites / yr) Reported use (\%)
SciPy optimize, ODE solver, etc. Simulator \cite{virtanen2020scipy} 2020 87.0 1355.3
FAIR Modeling process guidelines \cite{Wilkinson2016TheStewardship.} 2016 151.6 632.0
SBML Modeling language \cite{Hucka2003TheModels} 2003 49.7 184.8 69.5
COPASI Modeling application \cite{Hoops2006COPASI--aSImulator} 2006 151.3 31.7
SBGN Modeling visualization language \cite{Novere2009TheNotation} 2009 71.8 2.4
COBRApy Simulator \cite{ebrahim2013cobrapy} 2013 22.6 60.8 11.3
BioPAX Biochemical data manager \cite{Demir2010TheSharing.} 2010 24.5 56.8
BioModels Model repository \cite{Li2010BioModelsModels} 2010 17.1 52.3 33.3
InChI Biochemical data standard \cite{Heller2015InChIIdentifier.} 2015 15.7 41.2
Pathway Tools Biochemical data manager \cite{karp2002pathway} 2002 39.4
The ontology for biomedical investigations Ontology \cite{Bandrowski2016TheInvestigations} 2016 34.9
Physiome Model repository \cite{hunter2003integration} 2003 4.9 32.8
KiSAO Ontology \cite{Courtot2011ControlledBiology.} 2011 24.5
SBO Ontology \cite{Courtot2011ControlledBiology.} 2011 24.5
Data2Dynamics Parameter estimation tool \cite{Raue2015Data2Dynamics:Systems} 2015 7.7 24.1 1.1
BioNetGen Modeling language \cite{Harris2016BioNetGenModeling} 2016 8.1 23.9 8.5
SED-ML Simulation description language \cite{Waltemath2011ReproducibleLanguage} 2011 8.2 21.1
JWS Online Modeling application \cite{Olivier2004Web-basedOnline} 2004 4.6 20.1 5.4
PySB Modeling language \cite{Lopez2013ProgrammingPySB} 2013 6.4 20.0 6.5
CellML Modeling language \cite{Cuellar2003AnLanguage} 2003 18.5 7.3
VCell Modeling application \cite{moraru2008virtual} 2008 6.0 17.8 2.7
MIASE Modeling process guidelines \cite{Waltemath2011MinimumMIASE} 2011 3.2 12.7
FAIRDOMHub Model repository \cite{Wolstencroft2017FAIRDOMHub:Research.} 2017 3.9 12.1
Memote Validation tool \cite{Lieven2018Memote:Suite} 2018 12.1
PROV Reproducibility standard \cite{Moreau2015ThePROV} 2015 11.9
libRoadRunner Simulator \cite{Somogyi2015LibRoadRunner:Library.} 2015 4.7 11.5 5.4
SEEK Model repository \cite{Wolstencroft2015SEEK:Platform} 2015 3.1 10.6 3.8
SESSL Simulation description language \cite{Ewald2014SESSL:Experiments} 2014 0.0 10.5
BioLab Validation tool \cite{Clarke2008StatisticalPathway} 2008 10.0
COMBINE Biochemical data format \cite{Bergmann2014COMBINEProject} 2014 3.7 9.9
RightField Model data annotation tool \cite{Wolstencroft2011RightField:Spreadsheets} 2011 2.4 8.6
OpenCOR Simulator \cite{garny2015opencor} 2015 2.7 8.5 3.8
MIRIAM Modeling process guidelines \cite{Laibe2007MIRIAMBiology.} 2007 3.0 8.0
PyDREAM Parameter estimation tool \cite{Shockley2018PyDREAM:Python} 2018 3.5 7.8
StochSS Simulator \cite{drawert2016stochastic} 2016 2.9 7.2
SBML-PET Parameter estimation tool \cite{Zi2006SBML-PET:Tool} 2006 1.6 7.0
Tellurium Modeling application \cite{Choi2018Tellurium:Biology} 2018 2.0 6.7 4.8
SBRML Model data annotation tool \cite{Dada2010SBRML:Models} 2010 1.7 6.2
SBtab Biochemical data format \cite{Lubitz2016SBtab:Biology} 2016 2.0 5.1
PyBioNetFit Validation tool \cite{Mitra2019PyBioNetFitLanguage} 2019 2.6 4.5
HDF Data format \cite{Brown1993SoftwareManagement} 1993 2.6
SciUnit Validation tool \cite{Omar2014CollaborativeValidation} 2014 2.4
SEPIO Ontology \cite{Brush2016SEPIO:Evidence} 2016 1.8
BpForms and BcForms Biochemical data format \cite{Lang2019BpForms:Proteins} 2019 1.3
ObjTables Biochemical data format \cite{karr2020structured} 2020 0.0
24 changes: 11 additions & 13 deletions guidelines_4_repro_models_2020__curated_standards.bib
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Expand Up @@ -604,19 +604,6 @@ @article{Wolstencroft2017FAIRDOMHub:Research.
year = {2017}
}

@article{Zhukova2011KineticOntology,
author = {Zhukova, Anna and Zhukova, Anna and Waltemath, Dagmar and Juty, Nick and Laibe, Camille and Le Nov{\`{e}}re, Nicolas},
doi = {10.1038/npre.2011.6330.1},
issn = {1756-0357},
journal = {Nature Precedings},
keywords = {Bioinformatics, Data Standards},
month = {9},
publisher = {Nature Publishing Group},
title = {Kinetic simulation algorithm ontology},
url = {http://precedings.nature.com/doifinder/10.1038/npre.2011.6330.1},
year = {2011}
}

@article{Zi2006SBML-PET:Tool,
author = {Zi, Z. and Klipp, E.},
doi = {10.1093/bioinformatics/btl443},
Expand Down Expand Up @@ -675,3 +662,14 @@ @misc{karr2020structured
archivePrefix={arXiv},
primaryClass={cs.DB}
}

@article{courtot2011controlled,
title={Controlled vocabularies and semantics in systems biology},
author={Courtot, M{\'e}lanie and Juty, Nick and Kn{\"u}pfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Dr{\"a}ger, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and others},
journal={Molecular systems biology},
volume={7},
number={1},
pages={543},
year={2011},
publisher={John Wiley \& Sons, Ltd Chichester, UK}
}

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