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()

Outputs

• 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)

Inputs

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

Outputs

• 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)

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

Usage

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

Inputs

• 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.

Outputs

• 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)

Inputs

• 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 inputs

• 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

Outputs

• 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.