SED-ML URNs

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 https://ls4-www.cs.tu-dortmund.de/APNN-TOOLBOX/
Berkeley Logic Interchange Format (BLIF) (generic) urn:sedml:language:bngl http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.115.9222
BioNetGen Language (BNGL) (generic) urn:sedml:language:bngl https://bionetgen.org
BoolNet (generic) urn:sedml:language:boolnet https://cran.r-project.org/web/packages/BoolNet/index.html
BooleanNet (generic) urn:sedml:language:booleannet https://github.com/ialbert/booleannet
CNET (generic) urn:sedml:language:cnet https://people.kth.se/~dubrova/bns.html
CellML (generic) urn:sedml:language:cellml http://www.cellml.org/specifications/
CellML 1.0 urn:sedml:language:cellml.1_0 http://www.cellml.org/specifications/cellml_1.0
CellML 1.1 urn:sedml:language:cellml.1_1 https://www.cellml.org/specifications/cellml_1.1
CellML 2.0 urn:sedml:language:cellml.2_0 https://www.cellml.org/specifications/cellml_2.0
GINsim Markup Language (GINML) (generic) urn:sedml:language:ginml https//ginsim.org
Genetic Network Analyzer (GNA) (generic) urn:sedml:language:gna http://ibis.inrialpes.fr/people/dejong/GNA/user/ch03.html
High Order Calculator (HOC) (generic) urn:sedml:language:hoc https://www.neuron.yale.edu/neuron/static/new_doc/programming/hoc.html
Integrated Net Analyzer (INA) (generic) urn:sedml:language:ina https://www2.informatik.hu-berlin.de/~starke/ina.html
Kappa (generic) urn:sedml:language:kappa https://kappalanguage.org/
Low Entropy Model Specification (LEMS) (generic) urn:sedml:language:lems https://github.com/LEMS/LEMS
MaBoSS (generic) urn:sedml:language:maboss https://maboss.curie.fr/
Mass Action Stoichiometric Simulation (MASS) (generic) urn:sedml:language:mass https://masspy.readthedocs.io/en/stable/tutorials/reading_writing_models.html
Morpheus Markup Language (MorpheusML) (generic) urn:sedml:language:morpheusml https://morpheus.gitlab.io/
NeuroML (generic) urn:sedml:language:neuroml https://docs.neuroml.org/Userdocs/Specification.html
NeuroML Version 1.8.1 Level 1 urn:sedml:language:neuroml.version-1_8_1.level-1 https://docs.neuroml.org/Userdocs/NeuroMLv1.html
NeuroML Version 1.8.1 Level 2 urn:sedml:language:neuroml.version-1_8_1.level-2 https://docs.neuroml.org/Userdocs/NeuroMLv1.html
NeuroML Version 1.8.1 Level 3 urn:sedml:language:neuroml.version-1_8_1.level-3 https://docs.neuroml.org/Userdocs/NeuroMLv1.html
NeuroML Version 2.1 urn:sedml:language:neuroml.version-2_1 https://docs.neuroml.org/Userdocs/NeuroMLv2.html
NuSMV (generic) urn:sedml:language:nusmv https://nusmv.fbk.eu/NuSMV/userman/index-v2.html
Petri Net Markup Language (PNML) (generic) urn:sedml:language:pnml https://www.pnml.org/
Pharmacometrics Markup Language (pharmML) (generic) urn:sedml:language:pharmml http://www.pharmml.org/
Pint (generic) urn:sedml:language:pint https://loicpauleve.name/pint/
Resource Balance Analysis (RBA) (generic) urn:sedml:language:rba https://rba.inrae.fr/
SBML Level 1 Version 1 urn:sedml:language:sbml.level-1.version-1 http://sbml.org/Special/specifications/sbml-level-1/version-1/html/
SBML Level 1 Version 2 urn:sedml:language:sbml.level-1.version-2 http://sbml.org/Special/specifications/sbml-level-1/version-2/html/
SBML Level 2 Version 1 urn:sedml:language:sbml.level-2.version-1 http://www.sbml.org/specifications/sbml-level-2/version-1/html/
SBML Level 2 Version 2 urn:sedml:language:sbml.level-2.version-2 http://www.sbml.org/specifications/sbml-level-2/version-2/revision-1/sbml-level-2-version-2-rev1.pdf
SBML Level 2 Version 3 urn:sedml:language:sbml.level-2.version-3 http://www.sbml.org/specifications/sbml-level-2/version-3/release-1/sbml-level-2-version-3-rel-1.pdf
SBML Level 2 Version 4 urn:sedml:language:sbml.level-2.version-4 http://precedings.nature.com/documents/2715/version/1
SBML Level 2 Version 5 urn:sedml:language:sbml.level-2.version-5 http://co.mbine.org/specifications/sbml.level-2.version-5.release-1
SBML Level 3 Version 1 urn:sedml:language:sbml.level-3.version-1 http://precedings.nature.com/documents/4123/version/1
SBML Level 3 Version 2 urn:sedml:language:sbml.level-3.version-2 http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-1-rc2/sbml-level-3-version-2-core.pdf
Smoldyn (generic) urn:sedml:language:smoldyn http://www.smoldyn.org/
Systems Biology Markup Language (SBML) (generic) urn:sedml:language:sbml http://sbml.org/Special/specifications/
TruthTable (generic) urn:sedml:language:truthtable http://colomoto.org/formats/truthtable.html
Virtual Cell Markup Language (VCML) (generic) urn:sedml:language:vcml https://vcell.org
XPP ODE (generic) urn:sedml:language:xpp http://www.math.pitt.edu/~bard/xpp/xpp.html
Zipped GINsim Markup Language (ZGINML) (generic) urn:sedml:language:zginml https//ginsim.org
boolSim (generic) urn:sedml:language:boolsim https://www.vital-it.ch/research/software/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 https://portal.hdfgroup.org/display/support/Documentation
HDF5 urn:sedml:format:hdf.version-5 https://portal.hdfgroup.org/display/HDF5/HDF5
JSON (generic) urn:sedml:format:json https://www.json.org/
NuML (generic) urn:sedml:format:numl https://github.com/NuML/NuML
NuML Level 1 Version 1 urn:sedml:format:numl.level-1.version-1 https://github.com/NuML/NuML/raw/master/numl-spec-l1v1.pdf
TSV urn:sedml:format:tsv
XLSX (Generic) urn:sedml:format:xlsx https://www.ecma-international.org/publications-and-standards/standards/ecma-376/
XML (Generic) urn:sedml:format:xml https://www.w3.org/XML/
YAML (Generic) urn:sedml:format:yaml https://yaml.org/

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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