| ▼Nsbol | |
| CActivity | A generated Entity is linked through a wasGeneratedBy relationship to an Activity, which is used to describe how different Agents and other entities were used. An Activity is linked through a qualifiedAssociation to Associations, to describe the role of agents, and is linked through qualifiedUsage to Usages to describe the role of other entities used as part of the activity. Moreover, each Activity includes optional startedAtTime and endedAtTime properties. When using Activity to capture how an entity was derived, it is expected that any additional information needed will be attached as annotations. This may include software settings or textual notes. Activities can also be linked together using the wasInformedBy relationship to provide dependency without explicitly specifying start and end times |
| CAgent | Examples of agents are person, organisation or software. These agents should be annotated with additional information, such as software version, needed to be able to run the same software again |
| CAssociation | An Association is linked to an Agent through the agent relationship. The Association includes the hadRole property to qualify the role of the Agent in the Activity |
| CAttachment | General container for data files, especially experimental data files. Attachment is a TopLevel object, and any other TopLevel object can refer to a list of attachments |
| CBuild | A Build is a realization of a Design. For practical purposes, a Build can represent a biological clone, a plasmid, or other laboratory sample. For a given Design, there may be multiple Builds realized in the lab. A Build represents the second step in libSBOL's formalized Design-Build-Test-Analyze workflow |
| CCollection | Class that groups together a set of TopLevel objects that have something in common |
| CCombinatorialDerivation | A ComponentDeriviation specifies the composition of a combinatorial design or variant library for common use cases in synthetic biology, such as tuning the performance of a genetic circuit or biosynthetic pathway through combinatorial DNA assembly and screening |
| CComponent | Used to compose ComponentDefinition objects into a structural hierarchy. For example, the ComponentDefinition of a gene could contain four Component objects: a promoter, RBS, CDS, and terminator. In turn, the ComponentDefinition of the promoter Component could contain Component objects defined as various operator sites |
| CComponentDefinition | Structural entities of a biological design |
| CConfig | A class which contains global configuration variables for the libSBOL environment. Intended to be used like a static class, configuration variables are accessed through the Config::setOptions and Config::getOptions methods |
| CCut | Location between two coordinates of a Sequence's elements. class Cut : public Location |
| CDateTimeProperty | Contains a DateTime string following XML Schema |
| CDesign | This class represents a biological Design. A Design is a conceptual representation of a biological system that a synthetic biologist intends to build. A Design is the first object created in libSBOL's formalized Design-Build-Test-Analysis workflow |
| ▼CDocument | Read and write SBOL using a Document class. The Document is a container for Components, Modules, and all other SBOLObjects |
| Citerator | Iterate through TopLevel objects in a Document |
| CExperiment | A generated Entity is linked through a wasGeneratedBy relationship to an Activity, which is used to describe how different Agents and other entities were used. An Activity is linked through a qualifiedAssociation to Associations, to describe the role of agents, and is linked through qualifiedUsage to Usages to describe the role of other entities used as part of the activity. Moreover, each Activity includes optional startedAtTime and endedAtTime properties. When using Activity to capture how an entity was derived, it is expected that any additional information needed will be attached as annotations. This may include software settings or textual notes. Activities can also be linked together using the wasInformedBy relationship to provide dependency without explicitly specifying start and end times |
| CExperimentalData | Set of links to experimental data files (Attachment objects) that are typically but not always associated with a single sample, experimental condition, and/or lab instrument |
| CFloatProperty | FloatProperty objects are used to contain floats |
| CFunctionalComponent | Used to specify the functional usage of a ComponentDefinition inside a ModuleDefinition. The ModuleDefinition describes how the that describes how the FunctionalComponent interacts with others and summarizes their aggregate function |
| CGenericLocation | GenericLocation class is included as a starting point for specifying regions on Sequence objects with encoding properties other than IUPAC and potentially nonlinear structure. This class can also be used to set the orientation of a SequenceAnnotation and any associated Component when their parent ComponentDefinition is a partial design that lacks a Sequence |
| CIdentified | All SBOL-defined classes are directly or indirectly derived from the Identified abstract class |
| CImplementation | An Implementation represents a real, physical instance of a synthetic biological construct which may be associated with a laboratory sample. An Implementation may be linked back to its original design (either a ModuleDefinition or ComponentDefinition) using the wasDerivedFrom property inherited from the Identified superclass |
| CInteraction | 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) |
| CIntProperty | IntProperty objects are used to contain integers |
| CLocation | Strand orientation of a Component and can be further extended by the Range, Cut, and GenericLocation classes |
| CMapsTo | The purpose of the MapsTo class is to make identity relationships between different ComponentInstances in functional and structural hierarchies more clear. For example, a MapsTo object may be used to connect outputs and inputs between different low-level ModuleDefinitions contained in a higher level Module Definition. A MapsTo object may also be used to override a generic Component in a low-level ModuleDefinition with an explicit Component in a high-level ModuleDefinition, for example mapping a generic gene to an explicit component with a name and sequence |
| CMeasurement | The purpose of the Measure class is to link a numerical value to a unit of measure |
| CModel | The purpose of the Model class is to serve as a placeholder for an external computational model and provide additional meta-data to enable better reasoning about the contents of this model |
| CModule | Submodule of a ModuleDefinition within a hierarchical design |
| CModuleDefinition | Grouping of structural and functional entities in a biological design. The primary usage of this class is to assert the molecular interactions and abstract function of its child entities |
| ▼COwnedObject | A container property that contains child objects |
| Citerator | Provides iterator functionality for SBOL properties that contain multiple objects |
| CParticipation | Each Participation represents how a particular FunctionalComponent behaves in its parent Interaction |
| CPartShop | A class which provides an API front-end for online bioparts repositories |
| CPlan | Examples of agents are person, organisation or software. These agents should be annotated with additional information, such as software version, needed to be able to run the same software again |
| ▼CProperty | Member properties of all SBOL objects are defined using a Property object |
| Citerator | Provides iterator functionality for SBOL properties that contain multiple values |
| CRange | A Range object specifies a region via discrete, inclusive start and end positions that correspond to indices for characters in the elements String of a Sequence. Note that the index of the first location is 1, as is typical practice in biology, rather than 0, as is typical practice in computer science |
| CReferencedObject | A reference to another SBOL object Contains a Uniform Resource Identifier (URI) that refers to an an associated object |
| CSampleRoster | A SampleRoster is a container used to group Builds that are included in an experiment together. A SampleRoster can be used to generate a Test in a Design-Build-Test-Learn workflow |
| CSBOLObject | An SBOLObject converts a C++ class data structure into an RDF triple store and contains methods for serializing and parsing RDF triples |
| CSearchQuery | A SearchQuery object is used to configure advanced searches for bioparts in a PartShop. Advanced searches are useful for matching values across multiple fields, or to specify multiple values in a single field |
| ▼CSearchResponse | A SearchResponse is a container of search records returned by a search request |
| Citerator | Provides iterator functionality for SBOL properties that contain multiple objects |
| CSequence | The primary structure (eg, nucleotide or amino acid sequence) of a ComponentDefinition object |
| CSequenceAnnotation | Describes one or more regions of interest on the Sequence objects referred to by its parent ComponentDefinition. In addition, SequenceAnnotation objects can describe the substructure of their parent ComponentDefinition through association with the Component objects contained by this ComponentDefinition |
| CSequenceConstraint | Can be used to assert restrictions on the relative, sequence-based positions of pairs of Component objects contained by the same parent ComponentDefinition. The primary purpose of this class is to enable the specification of partially designed ComponentDefinition objects, for which the precise positions or orientations of their contained Component objects are not yet fully determined |
| CTest | A Test is a container for experimental data. A Test is the product of the third step of libSBOL's formalized Design-Build-Test-Analyze workflow |
| CTextProperty | TextProperty objects are used to contain string literals |
| CTopLevel | All SBOL classes derived from TopLevel appear as top level nodes in the RDF/XML document tree and SBOL files. An abstract class |
| CURIProperty | A URIProperty may contain a restricted type of string that conforms to the specification for a Uniform Resource Identifier (URI), typically consisting of a namespace authority followed by an identifier |
| CUsage | How different entities are used in an Activity is specified with the Usage class, which is linked from an Activity through the qualifiedUsage relationship. A Usage is then linked to an Entity through the Entity’s URI and the role of this entity is qualified with the hadRole property. When the wasDerivedFrom property is used together with the full provenance described here, the entity pointed at by the wasDerivedFrom property MUST be included in a Usage |
| CVariableComponent | Can be used to specify a choice of ComponentDefinition objects for any new Component derived from a template Component in the template ComponentDefinition. This specification is made using the class properties variable, variants, variantCollections, and variantDerivations. While the variants, variantCollections, and variantDerivations properties are OPTIONAL, at least one of them MUST NOT be empty |
| CVersionProperty | Contains a version number for an SBOL object |
