RAVEN Model Structure

The Specification of the RAVEN Model Structure

In order to successfully run RAVEN functions, the model must contain the fields as shown in the table below. Mandatory fields are written in bold. Note that the RAVEN structure is different from COBRA. Use ravenCobraWrapper to interconvert between RAVEN and COBRA structures.

Field name	Subfield name	Data type	Description	Example	Comments
id		String	Model ID	iAL1006	If missing during the model export, it is exported as 'blankID'
name		String	Model name	Penicillium chrysogenum genome-scale model	If missing during the model export, it is exported as 'blankName'
version		String	Model version	1.3.2	Not (yet) stored & retrieved from SBML
date		String	Date model file was written	2021-04-08	Not (yet) stored & retrieved from SBML
annotation		Struct	Additional information about the model
	defaultLB	Double	Default lower bound values for reactions	-1000	This value is used only if lower bound and upper bound values are not defined
	defaultUB	Double	Default upper bound values for reactions	1000	This value is used only if lower bound and upper bound values are not defined
	givenName	String	The name of the main model author	Rasmus
	familyName	String	The surname of the main model author	Agren
	authors	String	List of authors / contributors	Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas	Not (yet) stored & retrieved from SBML
	email	String	An e-mail address of the main model author	[email protected]
	organization	String	The organization of the main model author	Chalmers University of Technology
	taxonomy	String	The taxonomy ID for the target species	taxonomy/5076
	note	String	Additional comments about the model	This is a reconstruction of the biochemical network of the filamentous fungi Penicillium chrysogenum
	sourceUrl	String	Link to the repository where the model is maintained	https://github.com/org/repo	Not (yet) stored & retrieved from SBML
rxns		Column Cell Array of Strings	Reaction IDs	r0003
mets		Column Cell Array of Strings	Metabolite IDs	LLACb
S		Sparse or Full Matrix of Double	Stoichiometric (S) matrix
lb		Column Vector of Doubles	Reaction lower bounds	-1000
ub		Column Vector of Doubles	Reaction upper bounds	1000
rev		Column Vector of Doubles	Reaction reversibility vector (1-reversible, 0-irreversible)	1
c		Column Vector of Doubles	Coefficients for objective function
b		Column Vector of Doubles	Equality constraints for metabolite equations
comps		Column Cell Array of Strings	Compartment IDs	p
compNames		Column Cell Array of Strings	Compartment names	Peroxisome
compOutside		Column Cell Array of Strings	Compartment ID for compartment surrounding each of the compartments	c
compMiriams		Struct	Structure with MIRIAM information about the compartments		If there are multiple miriams, name indexes must match value indexes
	name	Column Cell Array of Strings	The name of MIRIAM prefix	go
	value	Column Cell Array of Strings	The ID for particular MIRIAM entry	GO:0005777
rxnNames		Column Cell Array of Strings	Reaction description	D-glucose 1-epimerase
rxnComps		Column Vector of Doubles	Reaction compartments	1	Shows the index of affiliated compartment in comps, not the compartment abbreviation
grRules		Column Cell Array of Strings	The name of MIRIAM prefix	(Pc20g08410 or Pc20g09570 or Pc13g14400)
rxnGeneMat		Sparse or Full Matrix of Double	Reaction-to-gene mapping in sparse matrix form
subSystems		Column Struct of Cell Array of Strings	Subsystem names for each reaction	Glycolysis / Gluconeogenesis
eccodes		Column Cell Array of Strings	EC-codes for the reactions	5.1.3.3
rxnMiriams		Struct	Structure with MIRIAM information about the reactions		If there are multiple miriams, name indexes must match value indexes
	name	Column Cell Array of Strings	The name of MIRIAM prefix	kegg.reaction
	value	Column Cell Array of Strings	The ID for particular MIRIAM entry	R01602
rxnNotes		Column Cell Array of Strings	Notes for each reaction	Was added during manual curation
rxnReferences		Column Cell Array of Strings	Non-PubMed references for each reaction	Agren et al 2013	Non-Pubmed references should be written here. PubMed references should be included in rxnMiriams instead
rxnConfidenceScores		Column Vector of Doubles	Confidence scores for each reaction (5 - best, 1 - worst)	3
rxnDeltaG		Column Vector of Doubles	Gibbs free energy under biochemical standard conditions	-24	In kJ/mol. Unknown Gibbs free energies must be set as NaN
genes		Column Cell Array of Strings	List of all genes
geneComps		Column Cell Array of Strings	Compartments for genes	1	This information is required for SBML Level 1-2, not for SBML Level 3
geneMiriams		Struct	Structure with MIRIAM information about the genes		If there are multiple miriams, name indexes must match value indexes
	name	Column Cell Array of Strings	The name of MIRIAM prefix	uniprot
	value	Column Cell Array of Strings	The ID for particular MIRIAM entry	P12345
geneShortNames		Column Cell Array of Strings	Gene alternative names (e.g. ERG10)	ERG10
metNames		Column Cell Array of Strings	Metabolite names	alpha-D-glucose
metComps		Column Vector of Doubles	Compartments for metabolites	1	Shows the index of affiliated compartment in comps, not the compartment abbreviation
inchis		Column Cell Array of Strings	InChI-codes for metabolites	1/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
metFormulas		Column Cell Array of Strings	Chemical formulas for metabolites	C6H12O6
metMiriams		Struct	Structure with MIRIAM information about the metabolites		If there are multiple miriams, name indexes must match value indexes
	name	Column Cell Array of Strings	The name of MIRIAM prefix	kegg.compound
	value	Column Cell Array of Strings	The ID for particular MIRIAM entry	C00267
metCharges		Column Vector of Doubles	Charge information for metabolites	0	Unknown charges must be set as NaN
metDeltaG		Column Vector of Doubles	Gibbs free energy of formation under biochemical standard conditions	-5	In kJ/mol. Unknown Gibbs free energies must be set as NaN
unconstrained		Column Vector of Doubles	Binary vector, positive for exchange (boundary) metabolites	0	This field is removed if boundary metabolites are deleted during the model import
rxnFrom		Column Cell Array of Strings	The name of template model from which particular reaction was taken	iTO977	This field is needed during the models merging procedure