Definition of a CVTerm class for adding annotations to a Model. More...

Include dependency graph for CVTerm.h:

This graph shows which files directly or indirectly include this file:

Classes
class	CVTerm
	A MIRIAM-compliant controlled vocabulary term. More...

Enumerations
enum	BiolQualifierType_t { BQB_IS, BQB_HAS_PART, BQB_IS_PART_OF, BQB_IS_VERSION_OF, BQB_HAS_VERSION, BQB_IS_HOMOLOG_TO, BQB_IS_DESCRIBED_BY, BQB_IS_ENCODED_BY, BQB_ENCODES, BQB_OCCURS_IN, BQB_HAS_PROPERTY, BQB_IS_PROPERTY_OF, BQB_HAS_TAXON, BQB_UNKNOWN }
	Enumeration of possible biological qualifiers used for annotations. More...

enum	ModelQualifierType_t { BQM_IS, BQM_IS_DESCRIBED_BY, BQM_IS_DERIVED_FROM, BQM_IS_INSTANCE_OF, BQM_HAS_INSTANCE, BQM_UNKNOWN }
	Enumeration of possible model qualifiers used for annotations. More...

enum	QualifierType_t { MODEL_QUALIFIER, BIOLOGICAL_QUALIFIER, UNKNOWN_QUALIFIER }
	Enumeration used to indicate the type of BioModels.net qualifier in a given CVTerm object. More...

Functions
BiolQualifierType_t	BiolQualifierType_fromString (const char *s)
	This method takes a string and returns a biol qualifier representing the string. More...

const char *	BiolQualifierType_toString (BiolQualifierType_t type)
	This method takes a biol qualifier type code and returns a string representing the code. More...

ModelQualifierType_t	ModelQualifierType_fromString (const char *s)
	This method takes a string and returns a model qualifier representing the string. More...

const char *	ModelQualifierType_toString (ModelQualifierType_t type)
	This method takes a model qualifier type code and returns a string representing the code. More...

Detailed Description

Definition of a CVTerm class for adding annotations to a Model.

Author: Sarah Keating

Enumeration Type Documentation

enum BiolQualifierType_t

Enumeration of possible biological qualifiers used for annotations.

Annotations with this type of qualifier express a relationship between an annotation resource and the biological concept represented by a given object in the model. The diagram below illustrates the relationship in this case:

Relationship expressed by biological qualifiers

Enumerator
BQB_IS	The biological entity represented by the object in the model is identical to the subject of the referenced resource.
BQB_HAS_PART	The biological entity represented by the object in the model includes the subject of the referenced resource.
BQB_IS_PART_OF	The biological entity represented by the object in the model is a physical or logical part of the subject of the referenced resource. For example, this could be used to indicate that the molecular entity represented by a given object in the model is part of the referenced molecular complex.
BQB_IS_VERSION_OF	The biological entity represented by the object in the model is a version or an instance of the subject of the referenced resource.
BQB_HAS_VERSION	The subject of the referenced resource is a version or an instance of the biological entity represented by the model element.
BQB_IS_HOMOLOG_TO	The biological entity represented by the object in the model is homologous to the subject of the referenced resource.
BQB_IS_DESCRIBED_BY	The biological entity represented by the object in the model is described by the subject of the referenced resource. This could be used, for example, to link a species or a parameter to the literature that describes the concentration of that species or the value of that parameter.
BQB_IS_ENCODED_BY	The biological entity represented by the object in the model is encoded, directly or transitively, by the subject of the referenced resource.
BQB_ENCODES	The biological entity represented by the object in the model encodes directly or transitively the subject of the referenced resource.
BQB_OCCURS_IN	The biological entity represented by the object in the model is physically limited to a location. The location is the subject of the referenced resource.
BQB_HAS_PROPERTY	The subject of the referenced resource is a property of the biological entity represented by the model element.
BQB_IS_PROPERTY_OF	The biological entity represented by the object in the model is a property of the referenced resource.
BQB_HAS_TAXON	The biological entity represented by the object in the model is taxonomically restricted, where the restriction is the subject of the referenced resource. This relation may be used to ascribe a species restriction to a biochemical reaction.
BQB_UNKNOWN	The relationship is unknown.

enum ModelQualifierType_t

Enumeration of possible model qualifiers used for annotations.

Annotations with this type of qualifier express a relationship between an annotation resource and the modeling concept represented by a given object in the model. The diagram below illustrates the relationship in this case:

Relationship expressed by model qualifiers

Enumerator
BQM_IS	The modeling entity represented by the object in the model is identical to the subject of the referenced resource.
BQM_IS_DESCRIBED_BY	The modeling entity represented by the object in the model is described by the subject of the referenced resource. For example, this relationship could be used to link a model element to a document (such as a paper published in the literature) describing the element.
BQM_IS_DERIVED_FROM	The modeling entity represented by the object in the model is derived from or adapted from the referenced resource. This relation could be used, for instance, to express a refinement or adaptation in usage of a model component located elsewere.
BQM_IS_INSTANCE_OF	The modeling entity represented by the object in the model is is an instance of the subject of the referenced resource. For instance, this qualifier might be used to link a specific model with its generic form.
BQM_HAS_INSTANCE	The modeling entity represented by the object in the model has for instance (is a class of) the subject of the referenced resource. For instance, this qualifier might be used to link a generic model with its specific forms.
BQM_UNKNOWN	The relationship is unknown.

enum QualifierType_t

Enumeration used to indicate the type of BioModels.net qualifier in a given CVTerm object.

The qualification of an annotation is important to convey the relationship between a given model component and the resource used to annotate it. This relationship is rarely one-to-one, and the information content of an annotation is greatly increased if one knows what it represents (as opposed to knowing merely that the two "are related somehow").

In the SBML/MIRIAM/BioModels.net scheme of things, there are currently two kinds of qualifiers. They are used for different purposes. One purpose is in the refinement of the relationship between an annotation resource and the modeling concept represented by a model element. The second purpose is in the refinement of the relationship between an annotation resource and the biological object represented by a model element. In libSBML, each of these two categories of qualifiers have their own enumerations: ModelQualifierType_t for the former type, and BiolQualifierType_t for the latter.

One can view the annotation of a model component as a statement in the form of a triple. The resource used in the annotation is the object, while the qualifier is the predicate. In situations where a model qualifier is used, the subject of the relation is the modeling concept represented by the model component referenced by the annotation. The modeling concept may be the model itself, a mathematical construct, or a hypothesis that is proposed, changing the way we previously understood the model, etc. Conversely, in situations where a biology qualifier is used, the subject of the relation is the biological or biochemical object represented by the enclosing model element.

Enumerator
MODEL_QUALIFIER	The qualifier is a model qualifier.
BIOLOGICAL_QUALIFIER	The qualifier is a biological qualifier.
UNKNOWN_QUALIFIER	The qualifier has not been set or is unknown.

Function Documentation

BiolQualifierType_t BiolQualifierType_fromString ( const char * s )

This method takes a string and returns a biol qualifier representing the string.

This method takes a string as argument and returns a biol qualifier type corresponding to that string. For example, passing it the string "hasVersion" will return the qualifier BQB_HAS_VERSION.

Parameters

s	the string to translate to a BiolQualifierType_t value.

Returns: a libSBML qualifier enumeration value for the given human readable qualifier name.

const char* BiolQualifierType_toString ( BiolQualifierType_t type )

This method takes a biol qualifier type code and returns a string representing the code.

This method takes a biol qualifier type as argument and returns a string name corresponding to that code. For example, passing it the qualifier BQB_HAS_VERSION will return the string "hasVersion".

Parameters

type	the BiolQualifierType_t value to translate.

Returns: a human readable qualifier name for the given type.

Note: The caller does not own the returned string and is therefore not allowed to modify it.

ModelQualifierType_t ModelQualifierType_fromString ( const char * s )

This method takes a string and returns a model qualifier representing the string.

This method takes a string as argument and returns a model qualifier type corresponding to that string. For example, passing it the string "isDescribedBy" will return the qualifier BQM_IS_DESCRIBED_BY.

Parameters

s	the string to translate to a ModelQualifierType_t value.

Returns: a libSBML qualifier enumeration value for the given human readable qualifier name.

const char* ModelQualifierType_toString ( ModelQualifierType_t type )

This method takes a model qualifier type code and returns a string representing the code.

This method takes a model qualifier type as argument and returns a string name corresponding to that code. For example, passing it the qualifier BQM_IS_DESCRIBED_BY will return the string "isDescribedBy".

Parameters

type	the ModelQualifierType_t value to translate.

Returns: a human readable qualifier name for the given qualifier type.

Note: The caller does not own the returned string and is therefore not allowed to modify it.

Classes

Enumerations

Functions

Detailed Description

Enumeration Type Documentation

Function Documentation