FAIRsharing Collection: Computational Modeling

Computational Modeling

A collection of the standards and databases covering all aspects of computational modelling. This collection also includes the standards found in the COMBINE Collection.

This record is maintained by: PeteMcQ ORCID

Record added: May 19, 2016, 11:41 a.m..
Record updated: Oct. 5, 2016, 11:06 a.m. by The FAIRsharing Team.

Taxonomic range

All

Scope and data types

Biomedical Science

Environmental Science

Life Science

Mathematical model

View as Graph (BETA)

26 records in view

Name	Abbreviation	Type	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
BioModels Ontology	BioModels	Standard	Enzymatic reaction Mathematical model Molecular entity Network model Ontology and terminology Plus 1 more...	All	BioModels	None	None	Computational Modeling
Biological Pathway eXchange	BioPAX	Standard	Bioinformatics tools and formats Data sharing Life Science Molecular interactions, pathways and networks Resource metadata	All	Reactome PC	GPML SBGN	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards
CellML	CellML	Standard	Cell Life Science Mathematical model Physiology XML	All	BioModels KiMoSys PMR	SED-ML MIRIAM SBML RDF FieldML Plus 2 more...	EMBO Press Recommended Databases and Data Standards	Computational Modeling (COMBINE) EMBO Press Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Chemical Markup Language	CML	Standard	Biochemistry Chemistry Life Science Mathematical model Molecular entity Plus 3 more...	All	Rhea CCD eCrystals	None	None	Computational Modeling
Computational Neuroscience Ontology	CNO	Standard	Life Science Neurobiology	Homo sapiens	None	None	None	Computational Modeling
Human Physiom Field Markup Language	FieldML	Standard	Physiology	Homo sapiens	PMR	CellML	None	Computational Modeling The NormSys Registry for Modeling Standards
General Formal Ontology	GFO	Standard	Biomedical Science Life Science Mathematical model	All	None	GFO-BIO	None	Computational Modeling
JWS Online	JWS Online	Database	Kinetic model Mathematical model Systems biology	All	BioModels SABIO-RK FAIRDOMHub BiGG Models	SED-ML SBML MIRIAM	EMBO Press Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition Rockefeller University Press - Journal Of Experimental Medicine - Data Deposition	EMBO Press Computational Modeling
Kinetic Simulation Algorithm Ontology	KiSAO	Standard	Algorithm Computer science General purpose Kinetic model Ontology and terminology	All	None	SBO MIASE MIRIAM SED-ML	None	Computational Modeling OBO Foundry FAIRDOM Community Standards
Mathematical Modelling Ontology	MAMO	Standard	Computational biology General purpose Mathematics Ontology and terminology Systems biology	All	BioModels	SBML SED-ML	None	Computational Modeling OBO Foundry
Minimal Information Required In the Annotation of Models	MIRIAM	Standard	Annotation Biochemistry Biomedical Science Chemical entity Enzymatic reaction Plus 4 more...	All	MIRIAM Registry BioModels YEASTNET: JWS Online BiGG Models	CellML SED-ML SBML SBO OMEX Plus 1 more...	EMBO Press Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition Rockefeller University Press - Journal Of Experimental Medicine - Data Deposition	EMBO Press Computational Modeling FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations
Neural Open Markup Language	NeuroML	Standard	Assay Brain Life Science Network model Neurobiology	Homo sapiens	OSB	None	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Numerical Markup Language	NuML	Standard	Computational biology Data sharing Kinetic model Mathematical model Reaction data Plus 2 more...	All	None	SBRML SED-ML	None	Computational Modeling
Open Modeling EXchange format	OMEX	Standard	Mathematical model	All	None	CellML SBGN SED-ML MIRIAM SBML Plus 1 more...	None	Computational Modeling
Pharmacometrics Markup Language	PharmML	Standard	Biochemistry Biomedical Science Reaction data	Vertebrata	ProbOnto	None	None	Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Physiome Model Repository	PMR	Database	Biomedical Science Life Science Mathematical model Mathematics Physiology Plus 1 more...	All	None	CellML FieldML SBML SED-ML	None	Computational Modeling
Ontology and Knowledge Base of Probability Distributions	ProbOnto	Database	Computational biology Mathematical model Mathematics Statistics and probability Systems biology	None	None	PharmML	None	Computational Modeling
Systems Biology Graphical Notation	SBGN	Standard	Enzymatic reaction Life Science Mathematical model Molecular entity Network model Plus 1 more...	All	MetaCrop 2.0 IPAVS SubtiWiki TopFIND BioModels Plus 1 more...	BioPAX SBML SBO OMEX	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Systems Biology Markup Language	SBML	Standard	Enzymatic reaction Life Science Mathematical model Molecular entity Network model Plus 1 more...	All	MetaCrop 2.0 IPAVS BRENDA BioModels Reactome Plus 10 more...	CellML SBGN SED-ML MIRIAM SBO Plus 2 more...	EMBO Press Recommended Databases and Data Standards	Computational Modeling (COMBINE) EMBO Press Computational Modeling H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards Plus 1 more...
Systems Biology Ontology	SBO	Standard	Life Science Mathematical model Molecular interactions, pathways and networks Pathway model Systems biology	All	None	SBGN SED-ML MIRIAM SBML TEDDY Plus 1 more...	None	Computational Modeling FAIRDOM Community Standards
Synthetic Biology Open Language	SBOL	Standard	DNA sequence data Life Science Nucleic acid design Sequence annotation Synthetic Biology	All	VPR	SBOL Visual	None	Computational Modeling (COMBINE) Computational Modeling The NormSys Registry for Modeling Standards
Synthetic Biology Open Language Visual	SBOL Visual	Standard	DNA sequence data Data visualization Life Science Nucleic acid design Sequence annotation Plus 1 more...	All	None	SBOL	None	Computational Modeling The NormSys Registry for Modeling Standards
Simulation Experiment Description Markup Language	SED-ML	Standard	Enzymatic reaction Life Science Mathematical model Simulation experiment Systems biology	All	BioModels WholeCellSimDB PMR JWS Online	MIRIAM MAMO KiSAO CellML SBML Plus 5 more...	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
TErminology for the Description of DYnamics	TEDDY	Standard	Life Science Simulation experiment Synthetic Biology Systems biology	All	None	SBO SED-ML	None	Computational Modeling FAIRDOM Community Standards
Tumor model repositories Markup Language	TumorML	Standard	Biomedical Science Cancer Data sharing Mathematical model	All	None	None	None	Computational Modeling
Virtual Parts Repository	VPR	Database	None	None	None	SBOL SBML	None	Computational Modeling

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