API Reference

Idiomatic conversion between URIs and compact URIs (CURIEs).

Functions

chain(converters, *[, case_sensitive])	Chain several converters.
discover(uris, *[, delimiters, cutoff, ...])	Discover new URI prefixes and construct a converter with a unique dummy CURIE prefix for each.
discover_from_rdf(graph, *[, format])	Discover new URI prefixes from RDF content via rdflib.
filter_df_by_curies(df, *, column, curies)	Filter a dataframe based on CURIEs in a given column having a given prefix or set of prefixes.
filter_df_by_prefixes(df, *, column, prefixes)	Filter a dataframe based on CURIEs in a given column having a given prefix or set of prefixes.
get_bioregistry_converter([web])	Get the latest extended prefix map from the Bioregistry [hoyt2022].
get_go_converter()	Get the Prefix Commons-maintained GO context.
get_monarch_converter()	Get the Prefix Commons-maintained Monarch context.
get_obo_converter()	Get the latest OBO Foundry context.
get_prefixcommons_converter([name])	Get a Prefix Commons-maintained context.
get_version([with_git_hash])	Get the curies version string, including a git hash.
load_extended_prefix_map(records, **kwargs)	Get a converter from a list of dictionaries by creating records out of them.
load_jsonld_context(data, **kwargs)	Get a converter from a JSON-LD object, which contains a prefix map in its @context key.
load_prefix_map(prefix_map, **kwargs)	Get a converter from a simple prefix map.
load_shacl(data, **kwargs)	Get a converter from a JSON-LD object, which contains a prefix map in its @context key.
process(...)	Process multiple semantically processable instances.
remap_curie_prefixes(converter, remapping)	Apply CURIE prefix remappings.
remap_uri_prefixes(converter, remapping)	Apply URI prefix remappings.
rewire(converter, rewiring)	Apply URI prefix upgrades.
standardize(...)	Standardize an instance.
upgrade_prefix_map(prefix_map)	Convert a (potentially problematic) prefix map (i.e., not bijective) into a list of records.
write_extended_prefix_map(converter, path)	Write an extended prefix map as JSON to a file.
write_jsonld_context(converter, path, *[, ...])	Write the converter's bijective map as a JSON-LD context to a file.
write_shacl(converter, path, *[, ...])	Write the converter's bijective map as SHACL in turtle RDF to a file.
write_tsv(converter, path, *[, header])	Write a simple prefix map CSV file.

Classes

Converter([records, delimiter, strict])	A cached prefix map data structure.
DuplicatePrefixes(duplicates)	An error raised with constructing a converter with data containing duplicate prefixes.
DuplicateURIPrefixes(duplicates)	An error raised with constructing a converter with data containing duplicate URI prefixes.
DuplicateValueError(duplicates)	An error raised with constructing a converter with data containing duplicate values.
NamableReference(*, prefix, identifier[, name])	A reference, maybe with a name.
NamedReference(*, prefix, identifier, name)	A reference with a name.
PostprocessingRewrites(*, suffix, list[str]] =)	A model for post-processing based on the prefix parsed.
Prefix	A string that is validated by Pydantic as a CURIE prefix.
PrefixMap([root])	A simple prefix map.
PreprocessingBlocklists(*, full, ...)	A model for prefix and full blocklists.
PreprocessingConverter(*args, rules[, ...])	A converter with pre-processing rules.
PreprocessingRewrites(*, full, str] =, ...)	A model for prefix and full rewrites.
PreprocessingRules(*, blocklists, rewrites, ...)	A model for blocklists and rewrites.
Record(*, prefix, uri_prefix, ...)	A record of some prefixes and their associated URI prefixes.
Records([root])	A list of records.
Reference(*, prefix, identifier)	A reference to an entity in a given identifier space.
ReferenceTuple(prefix, identifier)	A pair of a prefix (corresponding to a semantic space) and a local unique identifier in that semantic space.
SemanticallyProcessable()	A class that can be processed with a converter.
SemanticallyStandardizable()	An object that can be standardized.
Triple(*, subject, predicate, object)	A Pydantic model for a subject-predicate-object triple.

Class Inheritance Diagram

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"DuplicateValueError" -> "DuplicatePrefixes" [arrowsize=0.5,style="setlinewidth(0.5)"]; "DuplicateURIPrefixes" [URL="api/curies.DuplicateURIPrefixes.html#curies.DuplicateURIPrefixes",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="An error raised with constructing a converter with data containing duplicate URI prefixes."]; "DuplicateValueError" -> "DuplicateURIPrefixes" [arrowsize=0.5,style="setlinewidth(0.5)"]; "DuplicateValueError" [URL="api/curies.DuplicateValueError.html#curies.DuplicateValueError",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="An error raised with constructing a converter with data containing duplicate values."]; "Generic" [URL="https://docs.python.org/3/library/typing.html#typing.Generic",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Abstract base class for generic types."]; "NamableReference" [URL="api/curies.NamableReference.html#curies.NamableReference",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A reference, maybe with a name."]; "Reference" -> "NamableReference" [arrowsize=0.5,style="setlinewidth(0.5)"]; "NamedReference" [URL="api/curies.NamedReference.html#curies.NamedReference",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A reference with a name."]; "NamableReference" -> "NamedReference" [arrowsize=0.5,style="setlinewidth(0.5)"]; "PostprocessingRewrites" [URL="api/curies.PostprocessingRewrites.html#curies.PostprocessingRewrites",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A model for post-processing based on the prefix parsed."]; "BaseModel" -> "PostprocessingRewrites" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Prefix" [URL="api/curies.Prefix.html#curies.Prefix",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A string that is validated by Pydantic as a CURIE prefix."]; "PrefixMap" [URL="api/curies.PrefixMap.html#curies.PrefixMap",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A simple prefix map."]; "RootModel[dict[Prefix, str]]" -> "PrefixMap" [arrowsize=0.5,style="setlinewidth(0.5)"]; "PreprocessingBlocklists" [URL="api/curies.PreprocessingBlocklists.html#curies.PreprocessingBlocklists",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A model for prefix and full blocklists."]; "BaseModel" -> "PreprocessingBlocklists" [arrowsize=0.5,style="setlinewidth(0.5)"]; "PreprocessingConverter" [URL="api/curies.PreprocessingConverter.html#curies.PreprocessingConverter",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A converter with pre-processing rules."]; "Converter" -> "PreprocessingConverter" [arrowsize=0.5,style="setlinewidth(0.5)"]; "PreprocessingRewrites" [URL="api/curies.PreprocessingRewrites.html#curies.PreprocessingRewrites",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A model for prefix and full rewrites."]; "BaseModel" -> "PreprocessingRewrites" [arrowsize=0.5,style="setlinewidth(0.5)"]; "PreprocessingRules" [URL="api/curies.PreprocessingRules.html#curies.PreprocessingRules",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A model for blocklists and rewrites."]; "BaseModel" -> "PreprocessingRules" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Record" [URL="api/curies.Record.html#curies.Record",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A record of some prefixes and their associated URI prefixes."]; "BaseModel" -> "Record" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Records" [URL="api/curies.Records.html#curies.Records",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A list of records."]; "RootModel[list[Record]]" -> "Records" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Reference" [URL="api/curies.Reference.html#curies.Reference",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A reference to an entity in a given identifier space."]; "BaseModel" -> "Reference" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ReferenceTuple" [URL="api/curies.ReferenceTuple.html#curies.ReferenceTuple",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A pair of a prefix (corresponding to a semantic space) and a local unique identifier in that semantic space."]; "RootModel" [URL="https://pydantic.dev/docs/validation/latest/api/pydantic/root_model/#pydantic.root_model.RootModel",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="!!! abstract \"Usage Documentation\""]; "BaseModel" -> "RootModel" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Generic" -> "RootModel" [arrowsize=0.5,style="setlinewidth(0.5)"]; "RootModel[dict[Prefix, str]]" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled"]; "RootModel" -> "RootModel[dict[Prefix, str]]" [arrowsize=0.5,style="setlinewidth(0.5)"]; "RootModel[list[Record]]" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled"]; "RootModel" -> "RootModel[list[Record]]" [arrowsize=0.5,style="setlinewidth(0.5)"]; "SemanticallyProcessable" [URL="api/curies.SemanticallyProcessable.html#curies.SemanticallyProcessable",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A class that can be processed with a converter."]; "ABC" -> "SemanticallyProcessable" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Generic" -> "SemanticallyProcessable" [arrowsize=0.5,style="setlinewidth(0.5)"]; "SemanticallyStandardizable" [URL="api/curies.SemanticallyStandardizable.html#curies.SemanticallyStandardizable",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="An object that can be standardized."]; "ABC" -> "SemanticallyStandardizable" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Triple" [URL="api/curies.Triple.html#curies.Triple",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A Pydantic model for a subject-predicate-object triple."]; "BaseModel" -> "Triple" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Dataframe operations.

Functions

filter_df_by_curies(df, *, column, curies)	Filter a dataframe based on CURIEs in a given column having a given prefix or set of prefixes.
filter_df_by_prefixes(df, *, column, prefixes)	Filter a dataframe based on CURIEs in a given column having a given prefix or set of prefixes.
get_df_curies_index(df, *[, column])	Get a dictionary from CURIEs that appear in the column to the row indexes where they appear.
get_df_prefixes_index(df, *[, column, ...])	Get a dictionary from prefixes that appear in the column to the row indexes where they appear.
get_df_unique_prefixes(df, *[, column, ...])	Get unique prefixes.
get_filter_df_by_curies_index(df, *[, column])	Get an index of CURIEs in the given column that are the given CURIE(s).
get_filter_df_by_prefixes_index(df, *[, ...])	Get an index of CURIEs in the given column that start with the prefix(es).