libSBOL  2.3.3
Public Attributes | Public Member Functions | Protected Member Functions | List of all members
Interaction Class Reference

Detailed Description

The Interaction class provides more detailed descriptionof how the FunctionalComponents are intended to work together. For example, this class can be used to represent different forms of genetic regulation (e.g., transcriptional activation or repression), processes from the central dogma of biology (e.g. transcription and translation), and other basic molecular interactions (e.g., non-covalent binding or enzymatic phosphorylation).

Public Attributes

URIProperty types
 The types property is a REQUIRED set of URIs that describes the behavior represented by an Interaction. More...
 
OwnedObject< Participationparticipations
 The participations property is an OPTIONAL and MAY contain a set of Participation objects, each of which identifies the roles that its referenced FunctionalComponent plays in the Interaction. Even though an Interaction generally contains at least one Participation, the case of zero Participation objects is allowed because it is plausible that a designer might want to specify that an Interaction will exist, even if its participants have not yet been determined.
 
OwnedObject< Measurementmeasurements
 The measurements property links an Interaction to parameters or measurements and their associated units. For example, an Interaction that represents a chemical reaction may have parameters added to it and each Participation it contains to capture its chemical kinetic rate and the stoichiometries of its reactants and products.
 
URIProperty persistentIdentity
 The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.
 
TextProperty displayId
 The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.
 
VersionProperty version
 If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters “.” and “-” and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.
 
URIProperty wasDerivedFrom
 The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain “ A was derived from B and B was derived from A” is cyclical.
 
ReferencedObject wasGeneratedBy
 An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.
 
TextProperty name
 The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the object’s displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.
 
TextProperty description
 The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.
 
URIProperty identity
 The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified object’s identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.
 

Public Member Functions

 Interaction (std::string uri="example", std::string interaction_type=SBO_INTERACTION)
 Construct an Interaction. More...
 
 Interaction (rdf_type type, std::string uri, std::string interaction_type)
 Constructor used for defining extension classes. More...
 
virtual rdf_type getTypeURI ()
 
std::string getClassName (std::string type)
 
SBOLObjectfind (std::string uri)
 Search this object recursively to see if an object or any child object with URI already exists. More...
 
SBOLObjectfind_property (std::string uri)
 Search this object recursively to see if it contains a member property with the given RDF type. More...
 
std::vector< SBOLObject * > find_property_value (std::string uri, std::string value, std::vector< SBOLObject *> matches={})
 Search this object recursively to see if it contains a member property with the given RDF type and indicated property value. More...
 
std::vector< SBOLObject * > find_reference (std::string uri)
 Search this object recursively to see if it contains a member property with the given RDF type and indicated property value. More...
 
int compare (SBOLObject *comparand)
 Compare two SBOL objects or Documents. More...
 
std::string getPropertyValue (std::string property_uri)
 Get the value of a custom annotation property by its URI. More...
 
std::vector< std::string > getPropertyValues (std::string property_uri)
 Get all values of a custom annotation property by its URI. More...
 
std::vector< std::string > getProperties ()
 Gets URIs for all properties contained by this object. More...
 
void setPropertyValue (std::string property_uri, std::string val)
 Set and overwrite the value for a user-defined annotation property. More...
 
void addPropertyValue (std::string property_uri, std::string val)
 Append a value to a user-defined annotation property. More...
 
void setAnnotation (std::string property_uri, std::string val)
 Set the value for a user-defined annotation property. More...
 
std::string getAnnotation (std::string property_uri)
 Get the value of a custom annotation property by its URI. More...
 
virtual void close ()
 Use this method to destroy an SBOL object that is not contained by a parent Document. More...
 

Protected Member Functions

Identifiedcopy (Document *target_doc=NULL, std::string ns="", std::string version="")
 Copy an object and automatically increment its version. More...
 
template<class ExtensionClass >
void register_extension_class (std::string ns, std::string ns_prefix, std::string class_name)
 Register an extension class and its namespace, so custom data can be embedded into and read from SBOL files. More...
 

Constructor & Destructor Documentation

◆ Interaction() [1/2]

Interaction ( std::string  uri = "example",
std::string  interaction_type = SBO_INTERACTION 
)
inline

Construct an Interaction.

Parameters
uriA full URI including a scheme, namespace, and identifier. If SBOLCompliance configuration is enabled, then this argument is simply the displayId for the new object and a full URI will automatically be constructed.
interaction_typeA Systems Biology Ontology term that describes a biochemical interaction

◆ Interaction() [2/2]

Interaction ( rdf_type  type,
std::string  uri,
std::string  interaction_type 
)
inline

Constructor used for defining extension classes.

Parameters
rdf_typeThe RDF type for an extension class derived from this one

Member Function Documentation

◆ addPropertyValue()

void addPropertyValue ( std::string  property_uri,
std::string  val 
)
inherited

Append a value to a user-defined annotation property.

Either a literal or URI value

◆ close()

void close ( )
virtualinherited

Use this method to destroy an SBOL object that is not contained by a parent Document.

If the object does have a parent Document, instead use doc.close() with the object's URI identity as an argument. Recurse through child objects and delete them.

◆ compare()

int compare ( SBOLObject comparand)
inherited

Compare two SBOL objects or Documents.

The behavior is currently undefined for objects with custom annotations or extension classes.

Parameters
comparandA pointer to the object being compared to this one.
Returns
1 if the objects are identical, 0 if they are different

◆ copy()

Identified& copy ( Document target_doc = NULL,
std::string  ns = "",
std::string  version = "" 
)
protectedinherited

Copy an object and automatically increment its version.

If the optional version argument is specified, it will be used instead of incrementing the copied object's version. An object may also be copied into a new document and a new namespace, assuming compliant URIs.

Template Parameters
SBOLClassThe type of SBOL object being copied
Parameters
new_docThe new copies will be attached to this Document. NULL by default.
nsThis namespace will be substituted for the current namespace (as configured by setHomespace) in all SBOL-compliat URIs.
versionA new version
Returns
The full URI of the created object.

◆ find()

SBOLObject * find ( std::string  uri)
inherited

Search this object recursively to see if an object or any child object with URI already exists.

Parameters
uriThe URI to search for.
Returns
A pointer to theobject with this URI if it exists, NULL otherwise

◆ find_property()

SBOLObject * find_property ( std::string  uri)
inherited

Search this object recursively to see if it contains a member property with the given RDF type.

Parameters
uriThe RDF type of the property to search for.
Returns
A pointer to the object that contains a member property with the specified RDF type, NULL otherwise

◆ find_property_value()

vector< SBOLObject * > find_property_value ( std::string  uri,
std::string  value,
std::vector< SBOLObject *>  matches = {} 
)
inherited

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

Parameters
uriThe RDF type of the property to search for.
valueThe property value to match
Returns
A vector containing all objects found that contain a member property with the specified RDF type

◆ find_reference()

vector< SBOLObject * > find_reference ( std::string  uri)
inherited

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

Parameters
uriA URI, either an ontology term or an object reference, to search for
Returns
A vector containing all objects found that contain the URI in a property value

◆ getAnnotation()

std::string getAnnotation ( std::string  property_uri)
inherited

Get the value of a custom annotation property by its URI.

Synonymous with getPropertyValue

Parameters
property_uriThe URI for the property
Returns
The value of the property or SBOL_ERROR_NOT_FOUND

◆ getClassName()

std::string getClassName ( std::string  type)
inherited
Returns
Parses a local class name from the RDF-type of this SBOL Object

◆ getProperties()

std::vector< std::string > getProperties ( )
inherited

Gets URIs for all properties contained by this object.

This includes SBOL core properties as well as custom annotations. Use this to find custom extension data in an SBOL file.

Returns
A vector of URIs that identify the properties contained in this object

◆ getPropertyValue()

std::string getPropertyValue ( std::string  property_uri)
inherited

Get the value of a custom annotation property by its URI.

Parameters
property_uriThe URI for the property
Returns
The value of the property or SBOL_ERROR_NOT_FOUND

◆ getPropertyValues()

std::vector< std::string > getPropertyValues ( std::string  property_uri)
inherited

Get all values of a custom annotation property by its URI.

Parameters
property_uriThe URI for the property
Returns
A vector of property values or SBOL_ERROR_NOT_FOUND

◆ getTypeURI()

rdf_type getTypeURI ( )
virtualinherited
Returns
The uniform resource identifier that describes the RDF-type of this SBOL Object

◆ register_extension_class()

void register_extension_class ( std::string  ns,
std::string  ns_prefix,
std::string  class_name 
)
protectedinherited

Register an extension class and its namespace, so custom data can be embedded into and read from SBOL files.

Template Parameters
ExtensionClassThe new class
Parameters
nsThe extension namespace, eg, http://myhome.org/my_extension#. It's important that the namespace ends in a forward-slash or hash
ns_prefixA shorthand symbol for the full namespace as it will appear in the output file, eg, my_extension

◆ setAnnotation()

void setAnnotation ( std::string  property_uri,
std::string  val 
)
inherited

Set the value for a user-defined annotation property.

Synonymous with setPropertyValue If the value is a URI, it should be surrounded by angle brackets, else it will be interpreted as a literal value

◆ setPropertyValue()

void setPropertyValue ( std::string  property_uri,
std::string  val 
)
inherited

Set and overwrite the value for a user-defined annotation property.

Either a literal or URI value

Member Data Documentation

◆ types

URIProperty types

The types property is a REQUIRED set of URIs that describes the behavior represented by an Interaction.

The types property MUST contain one or more URIs that MUST identify terms from appropriate ontologies. It is RECOMMENDED that at least one of the URIs contained by the types property refer to a term from the occurring entity branch of the Systems Biology Ontology (SBO). (See http://www.ebi.ac.uk/sbo/main/) The following table provides a list of possible SBO terms for the types property and their corresponding URIs.

Type URI for SBO Term LibSBOL symbol
Biochemical Reaction http://identifiers.org/biomodels.sbo/SBO:0000176 SBO_BIOCHEMICAL_REACTION
Inhibition http://identifiers.org/biomodels.sbo/SBO:0000169 SBO_INHIBITION
Stimulation http://identifiers.org/biomodels.sbo/SBO:0000170 SBO_STIMULATION
Genetic Production http://identifiers.org/biomodels.sbo/SBO:0000589 SBO_GENETIC_PRODUCTION
Non-Covalent Binding http://identifiers.org/biomodels.sbo/SBO:0000177 SBO_NONCOVALENT_BINDING
Degradation http://identifiers.org/biomodels.sbo/SBO:0000179 SBO_DEGRADATION
Control http://identifiers.org/biomodels.sbo/SBO:0000168 SBO_CONTROL

The documentation for this class was generated from the following file:
Inheritance diagram for Interaction:
Inheritance graph