All Classes and Interfaces
Class
Description
A class to generated annotated OWL axioms from a mapping.
A class to generate OWL annotation assertion axioms from mappings.
A mapping slots visitor that converts mapping metadata to OWL annotations.
URL prefixes considered builtin by the SSSOM specification.
A helper object to compute cardinality values.
Represents some "well-known" mapping predicates for which we have built-in
knowledge on how to invert them.
A class to hold constant values that may be used throughout the library and
in client code.
Constant values used throughout the RDF support package.
Represents a metadata slot that holds the prefix (or curie) map used by a
mapping set.
Represents a metadata slot that holds a date.
Comparator for mapping objects.
A class to generate OWL axioms “directly”, that is without any external input
outside of the mappings themselves.
A class to transform mapping metadata slots into their corresponding IRIs
according to the SSSOM specification.
Represents a metadata slot that holds a numerical value.
Check that no two records in a set have the same record ID.
A helper class used by
SSSOMTOwlApplication and some of its
functions.An annotation to indicate that a SSSOM slot is an "entity reference".
Represents a metadata slot that is intended to hold an entity reference
(which is internally represented by a String).
Represents the type of an entity that is being mapped.
Represents a metadata slot that holds an entity type enumeration value.
A class to generate OWL equivalence axioms from mappings.
A basic implementation of the “Extended Prefix Map” concept promoted by the
Bioregistry.
Represents the definition of an extension slot.
Represents a metadata slot that holds a list of extension definitions
(describing the non-standard metadata slots in used within a mapping set).
Represents a metadata slot that holds all extension values (non-standard
metadata slots) for a SSSOM object.
A helper class to deal with non-standard metadata slots and their
definitions.
Represents the value of an extension slot.
An exception thrown when parsing an invalid “extractor expression”.
Represents the behaviour to adopt regarding non-standard metadata slots.
A set of filters.
Extracts the standard SSSOM hash for a mapping.
Represents a SSSOM/T format modifier function.
An interface to filter mappings according in a mapping set.
Represents a custom processing step that can be called when applying rules to
a mapping set.
A listener invoked by the
MappingProcessor engine when a rule is
applied to a mapping and results in the production of an object.Represents a single check for a possible post-parsing error that can make a
mapping set invalid.
An interface to transform a mapping into another object.
Represents a single check for a possible post-parsing error that can make an
individual mapping invalid.
An interface to transform a metadata slot into another object.
A visitor interface to visit the different metadata slot of a SSSOM Java
object.
A visitor interface to visit the different types of metadata slots of a SSSOM
object.
Represents a function in a SSSOM/Transform application.
Represents a specialised application of the SSSOM/Transform language.
Extracts an arbitrary piece of content from a mapping set object.
An interface for applying arbitrary treatments to a YAML-derived dictionary.
A YAML preprocessor to convert SSSOM-Py’s JSON-LD output into a normalised
form.
A parser to read a SSSOM mapping set from a JSON serialisation format.
A writer to serialise a SSSOM mapping set into a JSON format.
A YAML preprocessor to convert
literal* slots.Represents the cardinality of a mapping.
Represents a metadata slot that holds a mapping cardinality value.
A mapping transformer that applies arbitrary changes to a mapping.
Extracts the value of an extension slot from a mapping object.
Helper class to format mappings into strings.
Creates deterministic hash values from mappings.
This class represents an arbitrary treatment applied to a mapping.
An engine for applying
MappingProcessingRules to mappings.Extracts the value of an extension slot from a mapping set object.
Extracts the value of a slot from a mapping set object.
Extracts the value of a slot from a mapping object.
Base class for extractors that extract a value from a specific mapping
record.
A YAML preprocessor to convert a dictionary containing a
match_term_type metadata slot into its standardised equivalents.A YAML preprocessor to convert a dictionary containing a
match_type
metadata slot into its standardised equivalent.Represents various possible behaviours when merging a mapping set into
another.
Checks that a mapping has a mapping justification.
Checks that a mapping set has a license.
Checks that a mapping has an object.
Checks that a mapping has a predicate.
Checks that either all records in a set have a record ID, or none have one.
Checks that a mapping set has a set identifier.
Checks that a mapping has a subject.
A filter that has a string representation.
A processor callback that has a string representation.
A mapping transformer that has a string representation.
Generates OWL axioms from mappings.
A class of helper methods to work with OWL ontologies.
Modes of operation for the
OWLHelper.updateMappingSet(MappingSet, OWLOntology, String, boolean, EnumSet)
method.A value that modifies the meaning of a mapping predicate.
Represents a metadata slot that holds a predicate modifier enumeration value.
Checks that a mapping has a predicate with a suitable type.
Helper class to shorten/expand identifiers based on a prefix map.
An annotation to indicate that a SSSOM slot is "propagatable".
The policy that defines how to propagate values between the mapping set level
and the level of individual mappings.
A helper class to convert SSSOM objects to and from a RDF model in the Rdf4J
API.
A parser to read a SSSOM mapping set from the RDF Turtle serialisation
format.
A writer to serialise a SSSOM mapping set into the RDF Turtle format.
A class providing helper methods to obtain SSSOM reader objects.
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.
A YAML preprocessor to convert a dictionary containing a
semantic_similarity_score or semantic_similarity_measure
metadata slot into its standardised equivalent.Represents a format able to serialise SSSOM data.
Helper object to merge one mapping set into another.
Extracts the canonical S-expression that represents a mapping.
Represents a metadata slot on a SSSOM object.
Common logic used by both the
MappingSetSlotExtractor and the
MappingSlotExtractor classes.A class to facilitate the manipulation of SSSOM slots.
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.
An annotation to indicate the URI associated with a SSSOM slot.
A default implementation of the
ISlotVisitor interface that does
nothing for every slot type.This exception is thrown when processing data that do not conform to the
SSSOM format specification.
Base class to read a mapping set from any of the supported serialisation
formats.
Represents the SSSOM/T-OWL generator function "annotate".
Deprecated.
Deprecated.
Maintained for backwards compatibility only; use
annotate(%{subject_id},Represents the SSSOM/T standard preprocessor function "assign".
Deprecated.
Maintained for backwards compatibility only.
Deprecated.
Maintained for backwards compatibility only.
Represents the SSSOM/T-OWL generator function "create_axiom".
Deprecated.
Maintained for backwards compatibility only; use
declare(CLASS[,...]) instead.Represents the SSSOM/T-OWL "declare" function.
Deprecated.
Maintained for backwards compatibility only; use
declare(PROPERY[,...], /type="object_property")
instead.Represents the SSSOM/T substitution modifier function "default".
Represents the SSSOM/T-OWL generator function "direct".
Represents the SSSOM/T filter function "is_duplicate".
Deprecated.
Maintained for backwards compatibility only.
Represents the SSSOM/T-OWL filter function "exists".
Represents the SSSOM/T modifier function "flatten".
Represents the SSSOM/T modifier function "format".
Represents the SSSOM/T filter function "has_extension".
A helper class intended to host some methods used throughout the SSSOM/T-OWL
code.
Represents the SSSOM/T standard callback function “infer_cardinality”.
Represents the SSSOM/T standard preprocessor function "invert".
Represents the SSSOM/T-OWL filter function "is_a".
Represents the SSSOM/T modifier function "list_item".
A specialised application of the SSSOM/Transform language to read mapping
processing rules that produce OWL axioms.
Deprecated.
Maintained for backwards compatibility only.
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.
A syntax error encountered when parsing a SSSOM/T ruleset.
A parser to read mapping processing rules in the SSSOM Transform language.
Represents the SSSOM/T standard preprocessor function "replace".
Represents the SSSOM/T standard callback function "set_var".
Represents the SSSOM/T standard directive function "set_var".
Represents the SSSOM/T substitution modifier function "short".
Represents the SSSOM/T standard preprocessor function "stop".
Represents the SSSOM/T filter function "uriexpr_contains".
Represents the SSSOM/T-OWL directive function "uriexpr_declare_format".
Represents the SSSOM/T-OWL substitution modifier function "uriexpr_expand".
Represents the SSSOM/T substitution modifier function "uriexpr_slot_value".
Represents the SSSOM/T preprocessor function "uriexpr_toext".
Helper methods for SSSOM.
Base class to serialise a mapping set.
A class to transform mapping metadata slots into into their mapped IRIs
according to the SSSOM specification.
Represents a metadata slot that is backed by a String-typed field.
A parser to read a SSSOM mapping set from the TSV serialisation format.
Defines what separator character the reader should expect when parsing the
TSV section.
A writer to serialise a SSSOM mapping set into the TSV format.
An annotation to indicate that a SSSOM slot is a URI.
Represents a “URI Expression ID”, a way to encode composed entities in a URI.
A basic registry of URI Expression schemas.
Represents a metadata slot that is intended to hold a URI (which is
internally represented by a string).
Represents all the post-parsing errors that can make a mapping set invalid.
Represents different levels of strictness when validating a mapping set.
Helper class to validate MappingSet and Mapping objects.
Builds
IValueExtractor instances from a string representation.Represents the type of an extension value.
A helper class to track variables that can have a different value
depending on the mapping that is currently being processed.
Represents a version of the SSSOM specification.
An annotation to provide information about the version of the SSSOM
specification a slot is compliant with.
Represents a metadata slot that holds a SSSOM version.
Extract mappings from cross-references (oboInOwl:hasDbXref annotations) in a
ontology.
A helper class to convert generic YAML dictionaries into SSSOM objects.
annotate(%{object_id},