sbol3.collection

Classes

Collection

The Collection class is a class that groups together a set of

Experiment

The purpose of the Experiment class is to aggregate

Module Contents

class Collection(identity: str, *, members: List[str] = None, namespace: str = None, attachments: List[str] = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, type_uri: str = SBOL_COLLECTION)

Bases: sbol3.TopLevel

The Collection class is a class that groups together a set of TopLevel objects that have something in common.

Some examples of Collection objects:

  • Results of a query to find all Component objects in a repository that function as promoters.

  • A set of Component objects representing a library of genetic logic gates.

  • A “parts list” for Component with a complex design, containing both that component and all of the Component, Sequence, and Model objects used to provide its full specification.

Parameters:

  • identity – this object’s Uniform Resource Identifier (URI). this URI MUST be globally unique among all other Identified object URIs. See SBOL 3.0.1 specification section 5.1. This can also be a displayId, which will be concatenated to a default namespace automatically.

  • type_uri – the concrete type of this object, specified as a URI. These are typically in the SBOL3 namespace, like http://sbols.org/v3#Sequence or http://sbols.org/v3#Component. This can also be the type URI of an extension class.

  • name – A human-readable name for this object, for display purposes.

  • description – Per the SBOL 3.0.1 specification, “a more thorough text description” of this object.

  • derived_from – The URIs of one or more SBOL or non-SBOL objects from which this object was derived. This property is defined by the PROV-O ontology.

  • generated_by – The URIs of one or more prov:Activity objects that describe how this object was generated. This property is defined by the PROV-O ontology.

  • measures – The URIs of one or more om:Measure objects, each of which refers to a om:Measure object that describes measured parameters for this object. om:Measure objects are defined by the OM ontology

accept(visitor: Any) → Any

Invokes visit_collection on visitor with self as the only argument.

Parameters:

visitor (Any) – The visitor instance

Raises:

AttributeError – If visitor lacks a visit_collection method

Returns:

Whatever visitor.visit_collection returns

Return type:

Any

members
class Experiment(identity: str, *, members: List[str] = None, namespace: str = None, attachments: List[str] = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, type_uri: str = SBOL_EXPERIMENT)

Bases: Collection

The purpose of the Experiment class is to aggregate ExperimentalData objects for subsequent analysis, usually in accordance with an experimental design. Namely, the member properties of an Experiment MUST refer to ExperimentalData objects.

Parameters:

  • identity – this object’s Uniform Resource Identifier (URI). this URI MUST be globally unique among all other Identified object URIs. See SBOL 3.0.1 specification section 5.1. This can also be a displayId, which will be concatenated to a default namespace automatically.

  • type_uri – the concrete type of this object, specified as a URI. These are typically in the SBOL3 namespace, like http://sbols.org/v3#Sequence or http://sbols.org/v3#Component. This can also be the type URI of an extension class.

  • name – A human-readable name for this object, for display purposes.

  • description – Per the SBOL 3.0.1 specification, “a more thorough text description” of this object.

  • derived_from – The URIs of one or more SBOL or non-SBOL objects from which this object was derived. This property is defined by the PROV-O ontology.

  • generated_by – The URIs of one or more prov:Activity objects that describe how this object was generated. This property is defined by the PROV-O ontology.

  • measures – The URIs of one or more om:Measure objects, each of which refers to a om:Measure object that describes measured parameters for this object. om:Measure objects are defined by the OM ontology

accept(visitor: Any) → Any

Invokes visit_experiment on visitor with self as the only argument.

Parameters:

visitor (Any) – The visitor instance

Raises:

AttributeError – If visitor lacks a visit_experiment method

Returns:

Whatever visitor.visit_experiment returns

Return type:

Any