SBML-utilities

convertSBMLID(str, toSBML)

CONVERTSBMLID converts the given str to a valid SBML ID USAGE:

convertedstr = convertSBMLID(str,toSBML)

INPUT:

str: The String to convert

OPTIONAL INPUT:

toSBML: Whether to convert to SBML format (or undo a

conversion) (default true, ie convert to SBML)

OUTPUT:

convertedstr: The converted String.

getBioQualifiers()

Get a list of possible bioqualifiers

USAGE:

annotationQualifiers = getBioQualifiers()

OUTPUT:

bioQualifiers: A cell array of bioqualifier strings in descending order. standardQualifiers: A n x 2 cell array with the first column representing the standard identifiers and the second column representing the alternative name.

getDataBases(Ressources, qualifier)

getDataBases extracts database and correspdoning id from a ressource string in an sbml USAGE:

[databases,ids,qualifiers] = getDataBases(Ressource,qualifier)

INPUT:

Ressources: The Ressource String(s) as a cell array qualifier: The bio-qualifier of the ressource

OUTPUT:

databases: The databases of the ressources ids: The identifiers of the ressource strings qualifier: The bio-qualifiers associated (the same as the input)

Note

Currently two different schemes are accepted: urn:miriam:DatabaeID:EntryID https://identifiers.org/databaseid/EntryID The correctness of the entries is NOT checked!

makeSBMLAnnotationString(model, id, fieldentries, position, mergeAnnotations)

makeSBMLAnnotationString gives the annotationString for an SBML based on the fields in the model

USAGE:

[annotationString, notes] = makeSBMLAnnotationString(model,id,fieldentries,position)

INPUT:

model: the model to extract the data id: the ID of the entity fieldentries: either a char indicating the field

(prot,met,rxn,comp,gene), or a cell array with X{:,1} being field IDs and X{:,2} being bioql qualiiers to annotate for the field.

position: the position in the model to extract the data.

OPTIONAL INPUTS:

mergeAnnotations: If multiple fields are given, merge the fields and

only produce one annotation.

OUTPUT:

annotationString: The annotation String to be put into the SBML. notes: A 2*x cell array of fields which did not contain

valid identifiers (according to the pattern check.

mapAnnotationsToFields(model, databases, identifiers, relations, field, relationSelection, inverseRelationSelection)

MAPANNOTATIONSTOFIELDS maps annotations in bioql/MIRIAM annotation from SBML to model fields.

USAGE:

mappedFields = mapAnnotationsToFields(model,databases,identifiers,relations,field,relationSelection, exclusiveSelection)

INPUT:

model: the COBRA model to annotate databases: a cell array of cell arrays containing databases identifiers: a cell array of cell arrays containing the identifiers

associated with the databases above

relations: a cell array of cell arrays containing the bioql relations

associated with the databases above

field: the model field (met/gene/rxn/protein/comp etc) to

annotate. Note that there is an s missing here.

OPTIONAL INPUT:

relationSelection: whether only a specific relation is choosen

and all others are ignored (default {})

inverseRelationSelection: whether the relation specified by

relationSelection is inverted (i.e. all other fields are used (default true))

OUTPUT:

mappedFields: a struct with fields for each encountered

annotation database (Known databases like e.g. HMDB will be mapped to their corresponding field metHMDBID, while unknown fields will be mapped to: [field relation convertSBMLID(database)]

parseCVTerms(CVTerms)

parseCVTerms extracts the annotations deposited in cvterms in an SBML struct

USAGE:

[databases, identifiers, relations] = parseCVTerms(CVTerms)

INPUT:

CVTerms: the CVTerms field of an SBML model field

OUTPUT:

databases: the databases stored in the ressources of the CVTerms. identifiers: The identifiers annotated for the databases. relations: The bio-qualifier relation encoded in the CVTerms.