Package de.uni_halle.informatik.biodata.mp.annotation.bigg

Class BiGGSpeciesAnnotator

java.lang.Object

de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator

de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator

de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator<org.sbml.jsbml.Species>

de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator

All Implemented Interfaces:

IAnnotateSBases<org.sbml.jsbml.Species>, IReportDiffs, IReportStatus

public class BiGGSpeciesAnnotator
extends BiGGCVTermAnnotator<org.sbml.jsbml.Species>
implements IAnnotateSBases<org.sbml.jsbml.Species>

This class provides functionality to annotate a species in an SBML model using BiGG database identifiers. It extends the BiGGCVTermAnnotator class, allowing it to manage controlled vocabulary (CV) terms associated with the species. The class handles various aspects of species annotation including setting the species' name, SBO term, and additional annotations. It also sets the chemical formula and charge for the species using FBC (Flux Balance Constraints) extensions.

Field Summary

Fields inherited from class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator

bigg, biGGAnnotationParameters, registry

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	BiGGSpeciesAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, SBOParameters sboParameters, Registry registry)
protected	BiGGSpeciesAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, SBOParameters sboParameters, Registry registry, List<ProgressObserver> observers)

Method Summary

Modifier and Type	Method	Description
void	annotate(List<org.sbml.jsbml.Species> species)	Delegates annotation processing for all chemical species contained in the Model.
void	annotate(org.sbml.jsbml.Species species)	This method annotates a species with various details fetched from the BiGG Knowledgebase.
BiGGId	findBiGGId(org.sbml.jsbml.Species species)	Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
void	setName(org.sbml.jsbml.Species species, BiGGId biggId)	Updates the name of the species based on data retrieved from the BiGG Knowledgebase.

Methods inherited from class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator

getBiGGIdFromResources

Methods inherited from class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator

diffReport, getObservers, statusReport

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

BiGGSpeciesAnnotator

protected BiGGSpeciesAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters parameters,
 SBOParameters sboParameters,
 Registry registry)

BiGGSpeciesAnnotator

protected BiGGSpeciesAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters parameters,
 SBOParameters sboParameters,
 Registry registry,
 List<ProgressObserver> observers)

Method Details

annotate

public void annotate(List<org.sbml.jsbml.Species> species)
              throws SQLException

Delegates annotation processing for all chemical species contained in the Model. This method iterates over each species in the model and applies specific annotations.

Specified by:

annotate in interface IAnnotateSBases<org.sbml.jsbml.Species>

Throws:

SQLException

annotate

public void annotate(org.sbml.jsbml.Species species)
              throws SQLException

This method annotates a species with various details fetched from the BiGG Knowledgebase. It performs the following: 1. Sets the species name based on the BiGGId. If the species does not have a name, it uses the BiGGId as the name. 2. Assigns an SBO (Systems Biology Ontology) term to the species based on the BiGGId. 3. Adds additional annotations to the species, such as database cross-references.

The BiGGId used for these operations is either derived from the species' URI list or directly from its ID if available.

Specified by:

annotate in interface IAnnotateSBases<org.sbml.jsbml.Species>

Throws:

SQLException

findBiGGId

public BiGGId findBiGGId(org.sbml.jsbml.Species species)
                  throws SQLException

Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations. This method first tries to create a BiGGId from the species ID. If the species ID does not correspond to a known BiGGId in the database, it then searches through the species' annotations to find a valid BiGGId.

Specified by:

findBiGGId in class BiGGCVTermAnnotator<org.sbml.jsbml.Species>

Returns:

An Optional containing the BiGGId if a valid one is found or created, otherwise Optional.empty()

Throws:

SQLException

setName

public void setName(org.sbml.jsbml.Species species,
 BiGGId biggId)
             throws SQLException

Updates the name of the species based on data retrieved from the BiGG Knowledgebase. The species name is set only if it has not been previously set or if the current name follows a default format that combines the BiGGId abbreviation and compartment code. This method relies on the availability of a valid BiGGId for the species.

Parameters:

biggId - The BiGGId associated with the species, used to fetch the component name from the BiGG database.

Throws:

SQLException