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evaluated_standards.tex
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evaluated_standards.tex
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\begin{longtable}{L{2.2cm}L{4cm}L{1cm}L{0.8cm}R{1.1cm}R{1cm}R{1cm}}
%% Obtain caption from the file 'evaluated_standards_caption.txt'
\caption{--Caption goes here.--}\\
% header for first page
\toprule
\textbf{\scriptsize{Standard / tool}} &\textbf{\scriptsize{Type of standard / tool}} &\textbf{\scriptsize{Most cited paper}} &\textbf{\scriptsize{Paper year}} &\textbf{\scriptsize{PubMed (cites / yr)}} &\textbf{\scriptsize{Scholar (cites / yr)}} &\textbf{\scriptsize{Reported use (\%)}}\\
\endfirsthead
% same header for subsequent pages
\toprule
\textbf{\scriptsize{Standard / tool}} &\textbf{\scriptsize{Type of standard / tool}} &\textbf{\scriptsize{Most cited paper}} &\textbf{\scriptsize{Paper year}} &\textbf{\scriptsize{PubMed (cites / yr)}} &\textbf{\scriptsize{Scholar (cites / yr)}} &\textbf{\scriptsize{Reported use (\%)}}\\
\midrule
\endhead
\midrule
\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{151.6} &\small{632.0} &\small{}\\
\midrule
\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{151.3} &\small{31.7}\\
\midrule
\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{22.6} &\small{60.8} &\small{11.3}\\
\midrule
\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{17.1} &\small{52.3} &\small{33.3}\\
\midrule
\small{InChI} &\small{Biochemical data standard} &\cite{Heller2015InChIIdentifier.} &\small{2015} &\small{15.7} &\small{41.2} &\small{}\\
\midrule
\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{34.9} &\small{}\\
\midrule
\small{Physiome} &\small{Model repository} &\cite{hunter2003integration} &\small{2003} &\small{4.9} &\small{32.8} &\small{}\\
\midrule
\small{KiSAO} &\small{Ontology} &\cite{Courtot2011ControlledBiology.} &\small{2011} &\small{} &\small{24.5} &\small{}\\
\midrule
\small{SBO} &\small{Ontology} &\cite{Courtot2011ControlledBiology.} &\small{2011} &\small{} &\small{24.5} &\small{}\\
\midrule
\small{Data2Dynamics} &\small{Parameter estimation tool} &\cite{Raue2015Data2Dynamics:Systems} &\small{2015} &\small{7.7} &\small{24.1} &\small{1.1}\\
\midrule
\small{BioNetGen} &\small{Modeling language} &\cite{Harris2016BioNetGenModeling} &\small{2016} &\small{8.1} &\small{23.9} &\small{8.5}\\
\midrule
\small{SED-ML} &\small{Simulation description language} &\cite{Waltemath2011ReproducibleLanguage} &\small{2011} &\small{8.2} &\small{21.1} &\small{}\\
\midrule
\small{JWS Online} &\small{Modeling application} &\cite{Olivier2004Web-basedOnline} &\small{2004} &\small{4.6} &\small{20.1} &\small{5.4}\\
\midrule
\small{PySB} &\small{Modeling language} &\cite{Lopez2013ProgrammingPySB} &\small{2013} &\small{6.4} &\small{20.0} &\small{6.5}\\
\midrule
\small{CellML} &\small{Modeling language} &\cite{Cuellar2003AnLanguage} &\small{2003} &\small{} &\small{18.5} &\small{7.3}\\
\midrule
\small{VCell} &\small{Modeling application} &\cite{moraru2008virtual} &\small{2008} &\small{6.0} &\small{17.8} &\small{2.7}\\
\midrule
\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{PROV} &\small{Reproducibility standard} &\cite{Moreau2015ThePROV} &\small{2015} &\small{} &\small{11.9} &\small{}\\
\midrule
\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{10.5} &\small{}\\
\midrule
\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{3.7} &\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{2.7} &\small{8.5} &\small{3.8}\\
\midrule
\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{3.5} &\small{7.8} &\small{}\\
\midrule
\small{StochSS} &\small{Simulator} &\cite{drawert2016stochastic} &\small{2016} &\small{2.9} &\small{7.2} &\small{}\\
\midrule
\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{2.0} &\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{SBtab} &\small{Biochemical data format} &\cite{Lubitz2016SBtab:Biology} &\small{2016} &\small{2.0} &\small{5.1} &\small{}\\
\midrule
\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{2.6} &\small{}\\
\midrule
\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{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}