libSBML C++ API
5.18.0
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Definition of a CVTerm class for adding annotations to a Model. More...
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... | |
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:
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:
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 | |
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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. |
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.
s | the string to translate to a BiolQualifierType_t value. |
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"
.
type | the BiolQualifierType_t value to translate. |
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.
s | the string to translate to a ModelQualifierType_t value. |
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"
.
type | the ModelQualifierType_t value to translate. |