Language URNs

The following languages have to our knowledge so far been used with SED-ML. To specify the language of a model in the Model class, please use the according URN given. The general scheme for a language URN in SED-ML is urn:sedml:language:{ language name and version }.

Language URN Specification
Abstract Petri net notation (APNN) (generic) urn:sedml:language:apnn
Berkeley Logic Interchange Format (BLIF) (generic) urn:sedml:language:bngl
BioNetGen Language (BNGL) (generic) urn:sedml:language:bngl
BoolNet (generic) urn:sedml:language:boolnet
BooleanNet (generic) urn:sedml:language:booleannet
CNET (generic) urn:sedml:language:cnet
CellML (generic) urn:sedml:language:cellml
CellML 1.0 urn:sedml:language:cellml.1_0
CellML 1.1 urn:sedml:language:cellml.1_1
CellML 2.0 urn:sedml:language:cellml.2_0
GENESIS (generic) urn:sedml:language:genesis
GINsim Markup Language (GINML) (generic) urn:sedml:language:ginml https//
Genetic Network Analyzer (GNA) (generic) urn:sedml:language:gna
High Order Calculator (HOC) (generic) urn:sedml:language:hoc
Integrated Net Analyzer (INA) (generic) urn:sedml:language:ina
Kappa (generic) urn:sedml:language:kappa
Low Entropy Model Specification (LEMS) (generic) urn:sedml:language:lems
MaBoSS (generic) urn:sedml:language:maboss
Mass Action Stoichiometric Simulation (MASS) (generic) urn:sedml:language:mass
Morpheus Markup Language (MorpheusML) (generic) urn:sedml:language:morpheusml
NEURON MODeling Language (generic) urn:sedml:language:nmodl
Neocortical Simulator (NCS) (generic) urn:sedml:language:ncs
NeuroML (generic) urn:sedml:language:neuroml
NeuroML Version 1.8.1 Level 1 urn:sedml:language:neuroml.version-1_8_1.level-1
NeuroML Version 1.8.1 Level 2 urn:sedml:language:neuroml.version-1_8_1.level-2
NeuroML Version 1.8.1 Level 3 urn:sedml:language:neuroml.version-1_8_1.level-3
NeuroML Version 2.1 urn:sedml:language:neuroml.version-2_1
NuSMV (generic) urn:sedml:language:nusmv
Petri Net Markup Language (PNML) (generic) urn:sedml:language:pnml
Pharmacometrics Markup Language (pharmML) (generic) urn:sedml:language:pharmml
Pint (generic) urn:sedml:language:pint
Resource Balance Analysis (RBA) (generic) urn:sedml:language:rba
SBML Level 1 Version 1 urn:sedml:language:sbml.level-1.version-1
SBML Level 1 Version 2 urn:sedml:language:sbml.level-1.version-2
SBML Level 2 Version 1 urn:sedml:language:sbml.level-2.version-1
SBML Level 2 Version 2 urn:sedml:language:sbml.level-2.version-2
SBML Level 2 Version 3 urn:sedml:language:sbml.level-2.version-3
SBML Level 2 Version 4 urn:sedml:language:sbml.level-2.version-4
SBML Level 2 Version 5 urn:sedml:language:sbml.level-2.version-5
SBML Level 3 Version 1 urn:sedml:language:sbml.level-3.version-1
SBML Level 3 Version 2 urn:sedml:language:sbml.level-3.version-2
SLI (generic) urn:sedml:language:sli
Smoldyn (generic) urn:sedml:language:smoldyn
Systems Biology Markup Language (SBML) (generic) urn:sedml:language:sbml
TruthTable (generic) urn:sedml:language:truthtable
Virtual Cell Markup Language (VCML) (generic) urn:sedml:language:vcml
XPP ODE (generic) urn:sedml:language:xpp
Zipped GINsim Markup Language (ZGINML) (generic) urn:sedml:language:zginml https//
boolSim (generic) urn:sedml:language:boolsim

Data Format URNs

To specify the format of a resource please use the according URN given. The general scheme for a format URN in SED-ML is urn:sedml:format:{ format name }.

Data Format URN More information
CSV urn:sedml:format:csv
HDF (generic) urn:sedml:format:hdf
HDF5 urn:sedml:format:hdf.version-5
JSON (generic) urn:sedml:format:json
NuML (generic) urn:sedml:format:numl
NuML Level 1 Version 1 urn:sedml:format:numl.level-1.version-1
TSV urn:sedml:format:tsv
XLSX (Generic) urn:sedml:format:xlsx
XML (Generic) urn:sedml:format:xml
YAML (Generic) urn:sedml:format:yaml

Predefined Symbols

As described in the SED-ML specification some modeling languages use predefined symbols or implicit variables. In order to handle such variables the SED-ML introduced symbol URNs. The general scheme for a symbol URN in SED-ML is urn:sedml:symbol:{ symbolName }.

Language URN Definition
SBML urn:sedml:symbol:time Time in SBML is an intrinsic model variable that is addressable in model equations via a csymbol 'time'.

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