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CVTerm Class Reference

Detailed Description

Representation of MIRIAM-compliant controlled vocabulary annotation.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and biochemical entities, and (b) describing the creator of a model and the model's modification history. This SBML format is a concrete syntax that conforms to the guidelines of MIRIAM ("Minimum Information Requested in the Annotation of biochemical Models", Nature Biotechnology, vol. 23, no. 12, Dec. 2005). The format uses a subset of W3C RDF (Resource Description Format). In order to help application developers work with annotations in this format, libSBML provides several helper classes that provide higher-level interfaces to the data elements; these classes include CVTerm, ModelCreator, ModelHistory, RDFAnnotationParser, and Date.

Components of an SBML annotation

The SBML annotation format consists of RDF-based content placed inside an <annotation> element attached to an SBML component such as Species, Compartment, etc. The following template illustrates the different parts of SBML annotations in XML form:

<SBML_ELEMENT +++ metaid="meta id" +++>
  +++
  <annotation>
    +++
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
             xmlns:dc="http://purl.org/dc/elements/1.1/"
             xmlns:dcterm="http://purl.org/dc/terms/"
             xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"
             xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
             xmlns:bqmodel="http://biomodels.net/model-qualifiers/" >
      <rdf:Description rdf:about="#meta id">
        HISTORY
        <RELATION_ELEMENT>
          <rdf:Bag>
            <rdf:li rdf:resource="URI" />
            ...
          </rdf:Bag>
        </RELATION_ELEMENT>
        ...
      </rdf:Description>
      +++
    </rdf:RDF>
    +++
  </annotation>
  +++
</SBML_ELEMENT>

In the template above, the placeholder SBML_ELEMENT stands for the XML tag name of an SBML model component (e.g., model, reaction, etc.) and the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, the symbol +++ is a placeholder for either no content or valid XML content that is not defined by this annotation scheme, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element. The optional content HISTORY is a creation and modification history; in libSBML, this is stored using ModelHistory objects.

The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace "http://biomodels.net/model-qualifiers" (for model qualifiers) or "http://biomodels.net/biology-qualifiers" (for biological qualifier). The URI is a required data value that uniquely identifies a resource and data within that resource to which the annotation refers. (Since a URI is only a label, not an address, applications will often want a means of looking up the resource to which the URI refers. Providing the facilities for doing this is the purpose of MIRIAM Resources.)

The relation-resource pairs above are the "controlled vocabulary" terms that which CVTerm is designed to store and manipulate. The next section describes these parts in more detail. For more information about SBML annotations in general, please refer to Section 6 in the SBML Level 2 (Versions 2–4) or Level 3 specification documents.

The parts of a CVTerm

Annotations that refer to controlled vocabularies are managed in libSBML using CVTerm objects. A set of RDF-based annotations attached to a given SBML <annotation> element are read by RDFAnnotationParser and converted into a list of these CVTerm objects. Each CVTerm object instance stores the following components of an annotation:

  • The qualifier, which can be a BioModels.net "biological qualifier", a BioModels.net "model qualifier", or an unknown qualifier (as far as the CVTerm class is concerned). Qualifiers are used in MIRIAM to indicate the nature of the relationship between the object being annotated and the resource. In CVTerm, the qualifiers can be manipulated using the methods CVTerm::getQualifierType(), CVTerm::setQualifierType(), and related methods.

  • The resource, represented by a URI (which, we must remind developers, is not the same as a URL). In the CVTerm class, the resource component can be manipulated using the methods CVTerm::addResource() and CVTerm::removeResource().

Note that a CVTerm contains a single qualifier, but possibly more than one resource. This corresponds to the possibility of an annotation that points to multiple resources, all of which are qualified by the same BioModels.net qualifier. The CVTerm object class supports this by supporting a list of resources.

Detailed explanations of the qualifiers defined by BioModels.net can be found at http://biomodels.net/qualifiers.

Public Member Functions

int addResource (const std::string &resource)
 Adds a resource reference to this CVTerm object. More...
 
CVTermclone () const
 Creates and returns a deep copy of this CVTerm object. More...
 
 CVTerm (QualifierType_t type=UNKNOWN_QUALIFIER)
 Creates an empty CVTerm, optionally with the given QualifierType_t value type. More...
 
 CVTerm (const XMLNode node)
 Creates a new CVTerm from the given XMLNode. More...
 
 CVTerm (const CVTerm &orig)
 Copy constructor; creates a copy of a CVTerm object. More...
 
BiolQualifierType_t getBiologicalQualifierType ()
 Returns the biological qualifier type of this CVTerm object. More...
 
ModelQualifierType_t getModelQualifierType ()
 Returns the model qualifier type of this CVTerm object. More...
 
unsigned int getNumResources ()
 Returns the number of resources for this CVTerm object. More...
 
QualifierType_t getQualifierType ()
 Returns the qualifier type of this CVTerm object. More...
 
XMLAttributesgetResources ()
 Returns the resource references for this CVTerm object. More...
 
const XMLAttributesgetResources () const
 Returns the resources for this CVTerm object. More...
 
std::string getResourceURI (unsigned int n)
 Returns the value of the nth resource for this CVTerm object. More...
 
bool hasRequiredAttributes ()
 Predicate returning true if all the required elements for this CVTerm object have been set. More...
 
CVTermoperator= (const CVTerm &rhs)
 Assignment operator for CVTerm. More...
 
int removeResource (std::string resource)
 Removes a resource URI from the set of resources stored in this CVTerm object. More...
 
int setBiologicalQualifierType (BiolQualifierType_t type)
 Sets the BiolQualifierType_t value of this CVTerm object. More...
 
int setBiologicalQualifierType (const std::string &qualifier)
 Sets the BiolQualifierType_t of this CVTerm object. More...
 
int setModelQualifierType (ModelQualifierType_t type)
 Sets the ModelQualifierType_t value of this CVTerm object. More...
 
int setModelQualifierType (const std::string &qualifier)
 Sets the ModelQualifierType_t value of this CVTerm object. More...
 
int setQualifierType (QualifierType_t type)
 Sets the QualifierType_t of this CVTerm object. More...
 
 ~CVTerm ()
 Destroys this CVTerm. More...
 

Constructor & Destructor Documentation

CVTerm::CVTerm ( QualifierType_t  type = UNKNOWN_QUALIFIER)

Creates an empty CVTerm, optionally with the given QualifierType_t value type.

The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and other entities, and (b) describing the creator of a model and the model's modification history. The annotation content is stored in <annotation> elements attached to individual SBML elements. The format for storing the content inside SBML <annotation> elements is a subset of W3C RDF (Resource Description Format) expressed in XML. The CVTerm class provides a programming interface for working directly with controlled vocabulary term ("CV term") objects without having to deal directly with the XML form. When libSBML reads in an SBML model containing RDF annotations, it parses those annotations into a list of CVTerm objects, and when writing a model, it parses the CVTerm objects back into the appropriate SBML <annotation> structure.

This method creates an empty CVTerm object. The possible qualifier types usable as values of type are MODEL_QUALIFIER and BIOLOGICAL_QUALIFIER. If an explicit value for type is not given, this method defaults to using UNKNOWN_QUALIFIER. The QualifierType_t value can be set later using the CVTerm::setQualifierType() method.

Different BioModels.net qualifier elements encode different types of relationships. Please refer to the SBML specification or the BioModels.net qualifiers web page for an explanation of the meaning of these different qualifiers.

Parameters
typea QualifierType_t value
CVTerm::CVTerm ( const XMLNode  node)

Creates a new CVTerm from the given XMLNode.

The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and other entities, and (b) describing the creator of a model and the model's modification history. The annotation content is stored in <annotation> elements attached to individual SBML elements. The format for storing the content inside SBML <annotation> elements is a subset of W3C RDF (Resource Description Format) expressed in XML. The CVTerm class provides a programming interface for working directly with controlled vocabulary term ("CV term") objects without having to deal directly with the XML form. When libSBML reads in an SBML model containing RDF annotations, it parses those annotations into a list of CVTerm objects, and when writing a model, it parses the CVTerm objects back into the appropriate SBML <annotation> structure.

This method creates a CVTerm object from the XMLNode object node. Recall that XMLNode is a node in an XML tree of elements, and each such element can be placed in a namespace. This constructor looks for the element to be in the XML namespaces "http://biomodels.net/model-qualifiers" (for model qualifiers) and "http://biomodels.net/biology-qualifiers" (for biological qualifier), and if they are, creates CVTerm objects for the result.

Parameters
nodean XMLNode representing a CVTerm.
Note
This method assumes that the given XMLNode object node is of the correct structural form.
CVTerm::~CVTerm ( )

Destroys this CVTerm.

CVTerm::CVTerm ( const CVTerm orig)

Copy constructor; creates a copy of a CVTerm object.

Parameters
origthe CVTerm instance to copy.
Exceptions
SBMLConstructorExceptionThrown if the argument orig is NULL.

Member Function Documentation

int CVTerm::addResource ( const std::string &  resource)

Adds a resource reference to this CVTerm object.

The SBML Level 2 and Level 3 specifications define a simple standardized format for annotating models with references to controlled vocabulary terms and database identifiers that define and describe biological or other entities. This annotation format consists of RDF-based content placed inside an <annotation> element attached to an SBML component such as Species, Compartment, etc.

The specific RDF element used in this SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element containing one or more <rdf:li> elements. Each such element refers to a data item in an external resource; the resource and data item are together identified uniquely using a URI. The following template illustrates the structure:

<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>

In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element. The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace "http://biomodels.net/model-qualifiers" (for model qualifiers) or "http://biomodels.net/biology-qualifiers" (for biological qualifier).

The resource URI is a required data value that uniquely identifies a resource and data within that resource to which the annotation refers. The present method allows callers to add a reference to a resource URI with the same relationship to the enclosing SBML object. (In other words, the argument to this method is a resource URI as shown in the XML fragment above.) Resources are stored in this CVTerm object within an XMLAttributes object.

The relationship of this CVTerm to the enclosing SBML object can be determined using the CVTerm methods such as getModelQualifierType() and getBiologicalQualifierType().

Parameters
resourcea string representing the URI of the resource and data item being referenced; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
integer value indicating success/failure of the call. The possible values returned by this function are:
See Also
getResources()
removeResource(std::string resource)
getQualifierType()
getModelQualifierType()
getBiologicalQualifierType()
CVTerm * CVTerm::clone ( ) const

Creates and returns a deep copy of this CVTerm object.

Returns
a (deep) copy of this CVTerm.
BiolQualifierType_t CVTerm::getBiologicalQualifierType ( )

Returns the biological qualifier type of this CVTerm object.

The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>
In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.

The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace "http://biomodels.net/model-qualifiers" (for model qualifiers) or "http://biomodels.net/biology-qualifiers" (for biological qualifier). Callers will typically use getQualifierType() to find out the type of qualifier relevant to this particular CVTerm object, then if it is a biological qualifier, use the present method to determine the specific qualifier. The set of known biological qualifiers is, at the time of this libSBML release, the following:

Any other BioModels.net qualifier found in the model is considered unknown by libSBML and reported as BQB_UNKNOWN.

Returns
the BiolQualifierType_t value of this object or BQB_UNKNOWN (the default).
ModelQualifierType_t CVTerm::getModelQualifierType ( )

Returns the model qualifier type of this CVTerm object.

The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>
In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.

The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace "http://biomodels.net/model-qualifiers" (for model qualifiers) or "http://biomodels.net/biology-qualifiers" (for biological qualifier). Callers will typically use getQualifierType() to find out the type of qualifier relevant to this particular CVTerm object, then if it is a model qualifier, use the present method to determine the specific qualifier. The set of known model qualifiers is, at the time of this libSBML release, the following:

Any other BioModels.net qualifier found in the model is considered unknown by libSBML and reported as BQM_UNKNOWN.

Returns
the ModelQualifierType_t value of this object or BQM_UNKNOWN (the default).
unsigned int CVTerm::getNumResources ( )

Returns the number of resources for this CVTerm object.

The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>
In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.

The fragment above illustrates that there can be more than one resource referenced by a given relationship annotation (i.e., the resource URI values associated with a particular RELATION_ELEMENT). The present method returns a count of the resources stored in this CVTerm object.

Returns
the number of resources in the set of XMLAttributes of this CVTerm.
See Also
getResources()
getResourceURI(unsigned int n)
QualifierType_t CVTerm::getQualifierType ( )

Returns the qualifier type of this CVTerm object.

The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>
In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.

The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace "http://biomodels.net/model-qualifiers" (for model qualifiers) or "http://biomodels.net/biology-qualifiers" (for biological qualifier). The present method returns a code identifying which one of these two relationship namespaces is being used; any other qualifier in libSBML is considered unknown (as far as the CVTerm class is concerned). Consequently, this method will return one of the following values:

The specific relationship of this CVTerm to the enclosing SBML object can be determined using the CVTerm methods such as getModelQualifierType() and getBiologicalQualifierType(). Callers will typically want to use the present method to find out which one of the other two methods to call to find out the specific relationship.

Returns
the QualifierType_t value of this object or UNKNOWN_QUALIFIER (the default).
See Also
getResources()
getModelQualifierType()
getBiologicalQualifierType()
XMLAttributes * CVTerm::getResources ( )

Returns the resource references for this CVTerm object.

The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>
In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.

The resource URI values shown in the template above are stored internally in CVTerm objects using an XMLAttributes object. Each attribute stored inside the XMLAttributes will have the same name (specifically, "rdf:resource") but a different value, and the value will be a resource URI shown in the XML template above.

A valid CVTerm entity must always have at least one resource and a value for the relationship qualifier.

Returns
the XMLAttributes that store the resources of this CVTerm.
See Also
getQualifierType()
addResource(const std::string& resource)
getResourceURI(unsigned int n)
const XMLAttributes * CVTerm::getResources ( ) const

Returns the resources for this CVTerm object.

The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>
In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.

The resource URI values shown in the template above are stored internally in CVTerm objects using an XMLAttributes object. Each attribute stored inside the XMLAttributes will have the same name (specifically, "rdf:resource") but a different value, and the value will be a resource URI shown in the XML template above.

A valid CVTerm entity must always have at least one resource and a value for the relationship qualifier.

Returns
the XMLAttributes that store the resources of this CVTerm.
See Also
getQualifierType()
addResource(const std::string& resource)
getResourceURI(unsigned int n)
std::string CVTerm::getResourceURI ( unsigned int  n)

Returns the value of the nth resource for this CVTerm object.

The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
<rdf:Description rdf:about="#meta id">
  HISTORY
  <RELATION_ELEMENT>
    <rdf:Bag>
      <rdf:li rdf:resource="resource URI" />
      ...
    </rdf:Bag>
  </RELATION_ELEMENT>
  ...
</rdf:Description>
In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.

The fragment above illustrates that there can be more than one resource referenced by a given relationship annotation (i.e., the resource URI values associated with a particular RELATION_ELEMENT). LibSBML stores all resource URIs in a single CVTerm object for a given relationship. Callers can use getNumResources() to find out how many resources are stored in this CVTerm object, then call this method to retrieve the nth resource URI.

Parameters
nthe index of the resource to query
Returns
string representing the value of the nth resource in the set of XMLAttributes of this CVTerm.
See Also
getNumResources()
getQualifierType()
bool CVTerm::hasRequiredAttributes ( )

Predicate returning true if all the required elements for this CVTerm object have been set.

Note
The required attributes for a CVTerm are:
  • a qualifier type, which can be either a model qualifier or a biological qualifier
  • at least one resource
CVTerm & CVTerm::operator= ( const CVTerm rhs)

Assignment operator for CVTerm.

Parameters
rhsThe object whose values are used as the basis of the assignment.
Exceptions
SBMLConstructorExceptionThrown if the argument rhs is NULL.
int CVTerm::removeResource ( std::string  resource)

Removes a resource URI from the set of resources stored in this CVTerm object.

Parameters
resourcea string representing the resource URI to remove; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
addResource(const std::string& resource)
int CVTerm::setBiologicalQualifierType ( BiolQualifierType_t  type)

Sets the BiolQualifierType_t value of this CVTerm object.

Parameters
typethe BiolQualifierType_t value.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
If the Qualifier Type of this object is not BIOLOGICAL_QUALIFIER, then the BiolQualifierType_t value will default to BQB_UNKNOWN.
See Also
getQualifierType()
setQualifierType()
int CVTerm::setBiologicalQualifierType ( const std::string &  qualifier)

Sets the BiolQualifierType_t of this CVTerm object.

Parameters
qualifierthe string representing a biology qualifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
If the Qualifier Type of this object is not BIOLOGICAL_QUALIFIER, then the BiolQualifierType_t value will default to BQB_UNKNOWN.
See Also
getQualifierType()
setQualifierType()
int CVTerm::setModelQualifierType ( ModelQualifierType_t  type)

Sets the ModelQualifierType_t value of this CVTerm object.

Parameters
typethe ModelQualifierType_t value
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
If the Qualifier Type of this object is not MODEL_QUALIFIER, then the ModelQualifierType_t value will default to BQM_UNKNOWN.
See Also
getQualifierType()
setQualifierType()
int CVTerm::setModelQualifierType ( const std::string &  qualifier)

Sets the ModelQualifierType_t value of this CVTerm object.

Parameters
qualifierthe string representing a model qualifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
If the Qualifier Type of this object is not MODEL_QUALIFIER, then the ModelQualifierType_t value will default to BQM_UNKNOWN.
See Also
getQualifierType()
setQualifierType()
int CVTerm::setQualifierType ( QualifierType_t  type)

Sets the QualifierType_t of this CVTerm object.

Parameters
typethe QualifierType_t value. The possible values returned by this function are:
See Also
getQualifierType()