All Classes

Class	Description
AnnotatedAxiomGenerator	A class to generated annotated OWL axioms from a mapping.
AnnotationAxiomGenerator	A class to generate OWL annotation assertion axioms from mappings.
AnnotationVisitor<T>	A mapping slots visitor that converts mapping metadata to OWL annotations.
BaseStringModifierFunction	Base class for format modifier functions that can act both on a single value and on a list of values, where all values in the list are to be processed in the same way as single values.
BuiltinPrefix	URL prefixes considered builtin by the SSSOM specification.
Cardinalizer	A helper object to compute cardinality values.
CommonPredicate	Represents some "well-known" mapping predicates for which we have built-in knowledge on how to invert them.
ConfidenceHelper	A helper class to work with confidence values and estimations.
Constants	A class to hold constant values that may be used throughout the library and in client code.
Constants	Constant values used throughout the RDF support package.
CurieMapSlot<T>	Represents a metadata slot that holds the prefix (or curie) map used by a mapping set.
DateSlot<T>	Represents a metadata slot that holds a date.
DefaultMappingComparator	Comparator for mapping objects.
DirectAxiomGenerator	A class to generate OWL axioms “directly”, that is without any external input outside of the mappings themselves.
DirectMetadataTransformer<T>	A class to transform mapping metadata slots into their corresponding IRIs according to the SSSOM specification.
DoubleSlot<T>	Represents a metadata slot that holds a numerical value.
DuplicatedRecordIdValidator	Check that no two records in a set have the same record ID.
EditableEntityChecker	A helper class used by SSSOMTOwlApplication and some of its functions.
EntityReference	An annotation to indicate that a SSSOM slot is an "entity reference".
EntityReferenceSlot<T>	Represents a metadata slot that is intended to hold an entity reference (which is internally represented by a String).
EntityType	Represents the type of an entity that is being mapped.
EntityTypeSlot<T>	Represents a metadata slot that holds an entity type enumeration value.
EquivalentAxiomGenerator	A class to generate OWL equivalence axioms from mappings.
ExtendedPrefixMap	A basic implementation of the “Extended Prefix Map” concept promoted by the Bioregistry.
ExtensionDefinition	Represents the definition of an extension slot.
ExtensionDefinitionSlot<T>	Represents a metadata slot that holds a list of extension definitions (describing the non-standard metadata slots in used within a mapping set).
ExtensionSlot<T>	Represents a metadata slot that holds all extension values (non-standard metadata slots) for a SSSOM object.
ExtensionSlotHelper	Helper class to work with extension slots.
ExtensionSlotManager	A helper class to deal with non-standard metadata slots and their definitions.
ExtensionValue	Represents the value of an extension slot.
ExtractorSyntaxException	An exception thrown when parsing an invalid “extractor expression”.
ExtraMetadataPolicy	Represents the behaviour to adopt regarding non-standard metadata slots.
FilterSet	A set of filters.
HashExtractor	Extracts the standard SSSOM hash for a mapping.
HashType	The type of hash that the MappingHasher class should produce.
IFormatModifierFunction	Represents a SSSOM/T format modifier function.
IMappingFilter	An interface to filter mappings according in a mapping set.
IMappingProcessorCallback	Represents a custom processing step that can be called when applying rules to a mapping set.
IMappingProcessorListener<T>	A listener invoked by the MappingProcessor engine when a rule is applied to a mapping and results in the production of an object.
IMappingSetValidator	Represents a single check for a possible post-parsing error that can make a mapping set invalid.
IMappingTransformer<T>	An interface to transform a mapping into another object.
IMappingValidator	Represents a single check for a possible post-parsing error that can make an individual mapping invalid.
IMetadataTransformer<T,V>	An interface to transform a metadata slot into another object.
ISimpleSlotVisitor<T,V>	A visitor interface to visit the different metadata slot of a SSSOM Java object.
ISlotVisitor<T>	A visitor interface to visit the different types of metadata slots of a SSSOM object.
ISSSOMTFunction<T>	Represents a function in a SSSOM/Transform application.
ISSSOMTransformApplication<T>	Represents a specialised application of the SSSOM/Transform language.
IValueExtractor	Extracts an arbitrary piece of content from a mapping set object.
IYAMLPreprocessor	An interface for applying arbitrary treatments to a YAML-derived dictionary.
JsonLDConverter	A YAML preprocessor to convert SSSOM-Py’s JSON-LD output into a normalised form.
JSONReader	A parser to read a SSSOM mapping set from a JSON serialisation format.
JSONWriter	A writer to serialise a SSSOM mapping set into a JSON format.
LiteralProfileConverter	A YAML preprocessor to convert literal* slots.
Mapping	Represents a mapping object.
Mapping.MappingBuilder
MappingCardinality	Represents the cardinality of a mapping.
MappingCardinalitySlot<T>	Represents a metadata slot that holds a mapping cardinality value.
MappingEditor	A mapping transformer that applies arbitrary changes to a mapping.
MappingExtensionExtractor	Extracts the value of an extension slot from a mapping object.
MappingFormatter	Helper class to format mappings into strings.
MappingHasher	Creates deterministic hash values from mappings.
MappingProcessingRule<T>	This class represents an arbitrary treatment applied to a mapping.
MappingProcessor<T>	An engine for applying MappingProcessingRules to mappings.
MappingRegistry	Represents a mapping registry object.
MappingRegistry.MappingRegistryBuilder
MappingSet	Represents a mapping set object.
MappingSet.MappingSetBuilder
MappingSetExtensionExtractor	Extracts the value of an extension slot from a mapping set object.
MappingSetReference	Represents a mapping set reference object.
MappingSetReference.MappingSetReferenceBuilder
MappingSetSlotExtractor	Extracts the value of a slot from a mapping set object.
MappingSlotExtractor	Extracts the value of a slot from a mapping object.
MappingValueExtractor	Base class for extractors that extract a value from a specific mapping record.
MatchTermTypeConverter	A YAML preprocessor to convert a dictionary containing a match_term_type metadata slot into its standardised equivalents.
MatchTypeConverter	A YAML preprocessor to convert a dictionary containing a match_type metadata slot into its standardised equivalent.
MergeOption	Represents various possible behaviours when merging a mapping set into another.
MissingJustificationValidator	Checks that a mapping has a mapping justification.
MissingLicenseValidator	Checks that a mapping set has a license.
MissingObjectValidator	Checks that a mapping has an object.
MissingPredicateValidator	Checks that a mapping has a predicate.
MissingRecordIdValidator	Checks that either all records in a set have a record ID, or none have one.
MissingReviewerValidator	Checks that a mapping record that has a review_date or a reviewer_agreement also has either a reviewer_id or a reviewer_label.
MissingSetIdValidator	Checks that a mapping set has a set identifier.
MissingSubjectValidator	Checks that a mapping has a subject.
NamedFilter	A filter that has a string representation.
NamedMappingProcessorCallback	A processor callback that has a string representation.
NamedMappingTransformer<T>	A mapping transformer that has a string representation.
OWLGenerator	Generates OWL axioms from mappings.
OWLHelper	A class of helper methods to work with OWL ontologies.
OWLHelper.UpdateMode	Modes of operation for the OWLHelper.updateMappingSet(MappingSet, OWLOntology, String, boolean, EnumSet) method.
PredicateModifier	A value that modifies the meaning of a mapping predicate.
PredicateModifierSlot<T>	Represents a metadata slot that holds a predicate modifier enumeration value.
PredicateTypeValidator	Checks that a mapping has a predicate with a suitable type.
PrefixManager	Helper class to shorten/expand identifiers based on a prefix map.
Propagatable	An annotation to indicate that a SSSOM slot is "propagatable".
PropagationPolicy	The policy that defines how to propagate values between the mapping set level and the level of individual mappings.
RDFConverter	A helper class to convert SSSOM objects to and from a RDF model in the Rdf4J API.
RDFReader	A parser to read a SSSOM mapping set from the RDF Turtle serialisation format.
RDFWriter	A writer to serialise a SSSOM mapping set into the RDF Turtle format.
ReaderFactory	A class providing helper methods to obtain SSSOM reader objects.
RedefinedBuiltinPrefixValidator	Checks that the curie map embedded in a mapping set does not redefine any of the prefixes that are considered “builtin” by the SSSOM specification.
SemanticSimilarityConverter	A YAML preprocessor to convert a dictionary containing a semantic_similarity_score or semantic_similarity_measure metadata slot into its standardised equivalent.
SerialisationFormat	Represents a format able to serialise SSSOM data.
SetMerger	Helper object to merge one mapping set into another.
SExpressionExtractor	Extracts the canonical S-expression that represents a mapping.
SimpleStringModifierFunction	Represents a simple format modifier function that does not take any argument.
Slot<T>	Represents a metadata slot on a SSSOM object.
SlotExtractor<T>	Common logic used by both the MappingSetSlotExtractor and the MappingSlotExtractor classes.
SlotHelper<T>	A class to facilitate the manipulation of SSSOM slots.
SlotPropagator	A helper class to implement the propagation of slots from the mapping set level to the level of individual mappings and the other way round.
SlotURI	An annotation to indicate the URI associated with a SSSOM slot.
SlotVisitorBase<T>	A default implementation of the ISlotVisitor interface that does nothing for every slot type.
SSSOMFormatException	This exception is thrown when processing data that do not conform to the SSSOM format specification.
SSSOMReader	Base class to read a mapping set from any of the supported serialisation formats.
SSSOMTAnnotateFunction	Represents the SSSOM/T-OWL generator function "annotate".
SSSOMTAssignFunction	Represents the SSSOM/T standard preprocessor function "assign".
SSSOMTConfidenceFilterFunction	Represents the SSSOM/T filter function "confidence".
SSSOMTCreateAxiomFunction	Represents the SSSOM/T-OWL generator function "create_axiom".
SSSOMTDeclareFunction	Represents the SSSOM/T-OWL "declare" function.
SSSOMTDefaultModifierFunction	Represents the SSSOM/T substitution modifier function "default".
SSSOMTDirectFunction	Represents the SSSOM/T-OWL generator function "direct".
SSSOMTDuplicateFunction	Represents the SSSOM/T filter function "is_duplicate".
SSSOMTExistsFunction	Represents the SSSOM/T-OWL filter function "exists".
SSSOMTFlattenFunction	Represents the SSSOM/T modifier function "flatten".
SSSOMTFormatFunction	Represents the SSSOM/T modifier function "format".
SSSOMTHasExtensionFunction	Represents the SSSOM/T filter function "has_extension".
SSSOMTHelper	A helper class intended to host some methods used throughout the SSSOM/T-OWL code.
SSSOMTInferCardinalityFunction	Represents the SSSOM/T standard callback function “infer_cardinality”.
SSSOMTInvertFunction	Represents the SSSOM/T standard preprocessor function "invert".
SSSOMTIsAFunction	Represents the SSSOM/T-OWL filter function "is_a".
SSSOMTListItemFunction	Represents the SSSOM/T modifier function "list_item".
SSSOMTOwlApplication	A specialised application of the SSSOM/Transform language to read mapping processing rules that produce OWL axioms.
SSSOMTPrefixFunction	Represents the SSSOM/T modifier function "prefix".
SSSOMTransformApplication<T>	Represents a SSSOM/Transform application, that is, a specialisation of the SSSOM/Transform language (also called a “SSSOM/Transform dialect”) with its own functions and that produces its own type of mapping-derived objects.
SSSOMTransformError	A syntax error encountered when parsing a SSSOM/T ruleset.
SSSOMTransformReader<T>	A parser to read mapping processing rules in the SSSOM Transform language.
SSSOMTReplaceFunction	Represents the SSSOM/T standard preprocessor function "replace".
SSSOMTReplaceModifierFunction	Represents the SSSOM/T modifier function "replace".
SSSOMTSetvarCallbackFunction	Represents the SSSOM/T standard callback function "set_var".
SSSOMTSetvarFunction	Represents the SSSOM/T standard directive function "set_var".
SSSOMTShortFunction	Represents the SSSOM/T substitution modifier function "short".
SSSOMTStopFunction	Represents the SSSOM/T standard preprocessor function "stop".
SSSOMTSuffixFunction	Represents the SSSOM/T modifier function "suffix".
SSSOMTUriExpressionContainsFunction<T>	Represents the SSSOM/T filter function "uriexpr_contains".
SSSOMTUriExpressionDeclareFormatFunction	Represents the SSSOM/T-OWL directive function "uriexpr_declare_format".
SSSOMTUriExpressionExpandFunction	Represents the SSSOM/T-OWL substitution modifier function "uriexpr_expand".
SSSOMTUriExpressionSlotValueFunction	Represents the SSSOM/T substitution modifier function "uriexpr_slot_value".
SSSOMTUriExpressionToExtFunction<T>	Represents the SSSOM/T preprocessor function "uriexpr_toext".
SSSOMUtils	Helper methods for SSSOM.
SSSOMWriter	Base class to serialise a mapping set.
StandardMapMetadataTransformer<T>	A class to transform mapping metadata slots into into their mapped IRIs according to the SSSOM specification.
StringSlot<T>	Represents a metadata slot that is backed by a String-typed field.
TSVReader	A parser to read a SSSOM mapping set from the TSV serialisation format.
TSVReader.SeparatorMode	Defines what separator character the reader should expect when parsing the TSV section.
TSVWriter	A writer to serialise a SSSOM mapping set into the TSV format.
URI	An annotation to indicate that a SSSOM slot is a URI.
UriExpression	Represents a “URI Expression ID”, a way to encode composed entities in a URI.
UriExpressionRegistry	A basic registry of URI Expression schemas.
URISlot<T>	Represents a metadata slot that is intended to hold a URI (which is internally represented by a string).
ValidationError	Represents all the post-parsing errors that can make a mapping set invalid.
ValidationLevel	Represents different levels of strictness when validating a mapping set.
Validator	Helper class to validate MappingSet and Mapping objects.
ValueExtractorFactory	Builds IValueExtractor instances from a string representation.
ValueType	Represents the type of an extension value.
VariableManager	A helper class to track variables that can have a different value depending on the mapping that is currently being processed.
Version	Represents a version of the SSSOM specification.
Versionable	An annotation to provide information about the version of the SSSOM specification a slot is compliant with.
VersionComplianceVisitor<T>	Helper visitor to determine the minimum version of the SSSOM specification is required by a mapping or a mapping set.
VersionEnforcerVisitor<T>	Helper object to forcibly remove from a set or a mapping all slots or slot values that are incompatible with a given version of the SSSOM specification.
VersionSlot<T>	Represents a metadata slot that holds a SSSOM version.
XrefExtractor	Extract mappings from cross-references (oboInOwl:hasDbXref annotations) in a ontology.
YAMLConverter	A helper class to convert generic YAML dictionaries into SSSOM objects.