Name: Computational Modeling
Published: 2016-05-19 11:41:54
License: https://creativecommons.org/licenses/by-sa/4.0/. Please link to https://fairsharing.org and https://fairsharing.org/static/img/home/svg/FAIRsharing-logo.svg for attribution.

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 Sciences

Life Science

Mathematical model

View as Graph

26 records in view

Name	Abbreviation	Type	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Biological Pathway eXchange	BioPAX	Standard	Bioinformatics tools and formats Data sharing Life Science Pathway model Resource metadata Plus 1 more...	All	Reactome PC	SBGN GPML	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards
BioModels Ontology	BioModels	Standard	Enzymatic reaction Mathematical model Molecular entity Network model Ontology and terminology Plus 1 more...	All	BioModels	None	None	Computational Modeling
CellML	CellML	Standard	Cell Life Science Mathematical model Physiology	All	BioModels KiMoSys PMR	SED-ML MIRIAM MathML RDF FieldML Plus 3 more...	EMBO Press Recommended Databases and Data Standards	Computational Modeling (COMBINE) 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	XML	None	Computational Modeling Chemistry
Computational Neuroscience Ontology	CNO	Standard	Life Science Neurobiology	Homo sapiens	None	None	None	Computational Modeling
General Formal Ontology	GFO	Standard	Biomedical Science Life Science Mathematical model	All	None	GFO-BIO	None	Computational Modeling
Human Physiome Field Markup Language	FieldML	Standard	Anatomy Bioengineering Biomedical Science Modeling and simulation Physiology Plus 2 more...	Homo sapiens	PMR	CellML XML	None	Computational Modeling The NormSys Registry for Modeling Standards
JWS Online	JWS Online	Database	Kinetic model Mathematical model Systems biology	All	BioModels SABIO-RK FAIRDOMHub BiGG Models	SBML SED-ML MIRIAM	EMBO Press Recommended Databases and Data Standards Rockefeller University Press - Journal Of Experimental Medicine - Data Deposition Rockefeller University Press - Journal Of Cell Biology - Data Deposition	Computational Modeling
Kinetic Simulation Algorithm Ontology	KiSAO	Standard	Algorithm Computer science General purpose Kinetic model Ontology and terminology	All	OBO	SED-ML MIRIAM MIASE SBO	None	OBO Foundry Computational Modeling FAIRDOM Community Standards
Mathematical Modelling Ontology	MAMO	Standard	Computational biology General purpose Mathematics Ontology and terminology Systems biology	All	BioModels OBO	SED-ML	None	OBO Foundry Computational Modeling
Minimal Information Required In the Annotation of Models	MIRIAM	Standard	Annotation Biochemistry Biomedical Science Chemical entity Enzymatic reaction Plus 4 more...	All	Identifiers.org BioModels YEASTNET JWS Online BiGG Models	CellML SED-ML SBOL SBML SBOL Visual Plus 4 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	Computational Modeling FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations Chemistry
Neural Open Markup Language	NeuroML	Standard	Assay Brain Life Science Network model Neurobiology	Homo sapiens	OSB	XML	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Numerical Markup Language	NuML	Standard	Computational biology Computer science Data sharing Kinetic model Mathematical model Plus 3 more...	All	None	SED-ML SBRML XML	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
Open Modeling EXchange format	OMEX	Standard	Mathematical model	All	None	CellML SBGN SED-ML MIRIAM MIASE Plus 1 more...	None	Computational Modeling
Pharmacometrics Markup Language	PharmML	Standard	Biochemistry Biomedical Science Reaction data	Vertebrata	ProbOnto	XML	None	Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards Chemistry
Physiome Model Repository	PMR	Database	Biomedical Science Life Science Mathematical model Mathematics Physiology Plus 1 more...	All	None	FieldML SBML SED-ML CellML	None	Computational Modeling
Simulation Experiment Description Markup Language	SED-ML	Standard	Enzymatic reaction Life Science Mathematical model Modeling and simulation Systems biology	All	BioModels WholeCellSimDB PMR JWS Online	CellML MIRIAM SBML NuML OMEX Plus 6 more...	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Synthetic Biology Open Language	SBOL	Standard	DNA sequence data Life Science Nucleic acid design Sequence annotation Synthetic Biology	All	VPR	MIRIAM 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	MIRIAM SBOL	None	The NormSys Registry for Modeling Standards 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 2 more...	All	MetaCrop 2.0 IPAVS BRENDA BioModels Reactome Plus 10 more...	CellML SED-ML SBGN MIRIAM OFSMR Plus 3 more...	EMBO Press Recommended Databases and Data Standards	Computational Modeling (COMBINE) Computational Modeling H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Systems Biology Ontology	SBO	Standard	Life Science Mathematical model Molecular interaction Pathway model Systems biology	All	None	SBGN TEDDY SED-ML MIRIAM KiSAO Plus 1 more...	None	FAIRDOM Community Standards Computational Modeling
TErminology for the Description of DYnamics	TEDDY	Standard	Life Science Modeling and simulation Synthetic Biology Systems biology	All	None	SED-ML SBO	None	Computational Modeling FAIRDOM Community Standards
Tumor model repositories Markup Language	TumorML	Standard	Biomedical Science Cancer Data sharing Mathematical model Tumor	All	None	XML	None	Computational Modeling
Virtual Parts Repository	VPR	Database	None	None	None	SBML SBOL	None	Computational Modeling

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