Reference

This page includes the reference documentation for all user-facing code from the Bioregistry Python package.

Functions

add_resource(resource)	Add a resource.
add_to_collection(collection, resource)	Add a resource to the collection.
count_mappings()	Count the mappings for each registry.
curie_from_iri(iri, *[, use_preferred])	Generate a CURIE from an IRI via Manager.compress().
curie_to_str(prefix, identifier)	Combine a prefix and identifier into a CURIE string.
get_appears_in(prefix)	Return a list of resources that this resources (has been annotated to) depends on.
get_banana(prefix)	Get the optional redundant prefix to go before an identifier.
get_biocontext_uri_format(prefix)	Get the URI format for a BioContext entry.
get_bioportal_iri(prefix, identifier)	Get the Bioportal URL for the given CURIE.
get_bioportal_prefix(prefix)	Get the BioPortal prefix if available.
get_bioregistry_iri(prefix, identifier)	Get the bioregistry link.
get_canonical_for(prefix)	Get the prefixes for which this is annotated as canonical.
get_collection(...)	Get the collection entry for the given identifier.
get_collection_prefixes(-> list[str])	Get collection prefixes.
get_collection_resources(...)	Get collection resources.
get_contact(prefix)	Return the contact, if available.
get_contact_email(prefix)	Return the contact email, if available.
get_contact_github(prefix)	Return the contact GitHub, if available.
get_contact_name(prefix)	Return the contact name, if available.
get_contact_orcid(prefix)	Return the contact ORCiD, if available.
get_context(identifier)	Get the context for the given identifier.
get_converter(**kwargs)	Get a converter from this manager.
get_curie_pattern(prefix, *[, use_preferred])	Get the CURIE pattern for this resource.
get_default_converter()	Get a converter from this manager.
get_default_format(prefix)	Get the default, first-party URI prefix.
get_default_iri(prefix, identifier)	Get the default URL for the given CURIE.
get_depends_on(prefix)	Return a list of resources that this resources (has been annotated to) depends on.
get_description(prefix, *[, use_markdown])	Get the description for the given prefix, if available.
get_example(prefix)	Get an example identifier, if it's available.
get_external(prefix, metaprefix)	Get the external data for the entry.
get_fairsharing_prefix(prefix)	Get the FAIRSharing prefix if available.
get_has_canonical(prefix)	Get the canonical prefix.
get_has_parts(prefix)	Get children resources.
get_homepage(prefix)	Return the homepage, if available.
get_identifiers_org_curie(prefix, identifier)	Get the identifiers.org CURIE for the given CURIE.
get_identifiers_org_iri(prefix, identifier)	Get the identifiers.org URL for the given CURIE.
get_identifiers_org_prefix(prefix)	Get the identifiers.org prefix if available.
get_iri(prefix[, identifier, priority, ...])	Get the best link for the CURIE, if possible.
get_jskos_download(prefix)	Get the download link for the JSKOS JSON file.
get_json_download(prefix)	Get the download link for the latest OBOGraph JSON file.
get_keywords(prefix)	Return the keywords, if available.
get_license(prefix)	Get the license for the resource.
get_logo(prefix)	Get the logo for the resource, if it's available.
get_mailing_list(prefix)	Get the mailing list for the resource, if it's available.
get_mappings(prefix)	Get the mappings to external registries, if available.
get_miriam_uri_format(prefix, **kwargs)	Get the URI format for a MIRIAM entry.
get_miriam_uri_prefix(prefix, **kwargs)	Get the URI prefix for a MIRIAM entry.
get_n2t_iri(prefix, identifier)	Get the name-to-thing URL for the given CURIE.
get_n2t_prefix(prefix)	Get the name-to-thing prefix if available.
get_name(...)	Get the name for the given prefix, if it's available.
get_namespace_in_lui(...)	Check if the namespace should appear in the LUI.
get_obo_context_prefix_map([include_synonyms])	Get the OBO Foundry prefix map.
get_obo_download(prefix)	Get the download link for the latest OBO file.
get_obo_health_url(prefix)	Get the OBO community health badge.
get_obofoundry_iri(prefix, identifier)	Get the OBO Foundry URL if possible.
get_obofoundry_prefix(prefix)	Get the OBO Foundry prefix if available.
get_obofoundry_uri_format(prefix)	Get the OBO Foundry URI format for this entry, if possible.
get_obofoundry_uri_prefix(prefix)	Get the URI prefix for an OBO Foundry entry.
get_ols_iri(prefix, identifier)	Get the OLS URL if possible.
get_ols_prefix(prefix)	Get the OLS prefix if available.
get_ols_uri_format(prefix)	Get the URI format for an OLS entry.
get_ols_uri_prefix(prefix)	Get the URI format for an OLS entry.
get_organizations(prefix)	Get organizations for the prefix.
get_owl_download(prefix)	Get the download link for the latest OWL file.
get_part_of(prefix)	Get the parent resource.
get_parts_collections()	Group resources' prefixes based on their part_of entries.
get_pattern(prefix)	Get the pattern for the given prefix, if it's available.
get_pattern_map(*[, include_synonyms, ...])	Get a mapping from Bioregistry prefixes to their regular expression patterns.
get_preferred_prefix(prefix)	Get the preferred prefix (e.g., with stylization) if it exists.
get_prefix_map(*[, prefix_priority, ...])	Get a mapping from Bioregistry prefixes to their URI prefixes.
get_prefixcommons_uri_format(prefix)	Get the URI format for a Prefix Commons entry.
get_provided_by(prefix)	Get the resources that provide for the given prefix, or return none if the prefix can't be looked up.
get_providers(prefix, identifier)	Get all providers for the CURIE.
get_providers_list(prefix, identifier)	Get all providers for the CURIE.
get_provides_for(prefix)	Get the resource that the given prefix provides for, or return none if not a provider.
get_rdf_download(...)	Get the download link for the RDF file.
get_registry(...)	Get the metaregistry entry for the given prefix.
get_registry_description(metaprefix)	Get the description for the registry, if available.
get_registry_example(metaprefix)	Get an example for the registry, if available.
get_registry_homepage(metaprefix)	Get the URL for the registry, if available.
get_registry_invmap(metaprefix, **kwargs)	Get a mapping from the external registry prefixes to Bioregistry prefixes.
get_registry_map(metaprefix)	Get a mapping from the Bioregistry prefixes to prefixes in another registry.
get_registry_name(metaprefix)	Get the metaregistry name for the given prefix, if it's available.
get_registry_provider_uri_format(metaprefix, ...)	Get the URL for the resource inside registry, if available.
get_registry_short_name(metaprefix)	Get the metaregistry short name for the given prefix, if it's available.
get_registry_short_name_to_prefix(metaprefix)	Get a mapping from short names in an external registry to their associated prefixes in the external registry.
get_registry_uri(metaprefix, prefix, identifier)	Get the URL to resolve the given prefix/identifier pair with the given resolver.
get_repository(prefix)	Return the repository, if available.
get_repository_to_prefix()	Get a mapping from GitHub repository to Bioregistry prefix.
get_resource(...)	Get the Bioregistry entry for the given prefix.
get_skos_download(...)	Get the download link for the SKOS RDF file.
get_synonyms(prefix)	Get the synonyms for a given prefix, if available.
get_uri_format(prefix[, priority])	Get the URI format string for the given prefix, if it's available.
get_uri_prefix(-> str | None)	Get a well-formed URI prefix for usage in a prefix map.
get_version(prefix)	Get the version.
get_versions()	Get a map of prefixes to versions.
get_wikidata_prefix(prefix)	Get the wikidata prefix if available.
has_no_terms(prefix)	Check if the prefix is specifically noted to not have terms.
is_deprecated(prefix)	Return if the given prefix corresponds to a deprecated resource.
is_mismatch(bioregistry_prefix, ...)	Return if the triple is a mismatch.
is_novel(prefix)	Check if the prefix is novel to the Bioregistry, i.e., it has no external mappings.
is_obo_foundry(prefix)	Get if the prefix has an OBO Foundry link.
is_proprietary(prefix)	Get if the prefix is proprietary.
is_standardizable_curie(curie)	Check if a CURIE is validatable, but not necessarily standardized.
is_standardizable_identifier(prefix, identifier)	Check if the identifier is standardizable.
is_valid_curie(curie)	Check if a CURIE is standardized and valid.
is_valid_identifier(prefix, identifier)	Check if the pre-parsed CURIE is standardized valid.
miriam_standardize_identifier(prefix, identifier)	Normalize the identifier with the appropriate banana.
normalize_curie(-> str)	Normalize a CURIE.
normalize_parsed_curie(...)	Normalize a prefix/identifier pair.
normalize_prefix(-> str)	Get the normalized prefix, or return None if not registered.
parse_curie(...)	Parse a CURIE, normalizing the prefix and identifier if necessary.
parse_iri(...)	Parse a compact identifier from an IRI that wraps Manager.parse_uri().
read_collections()	Read the manually curated collections.
read_contexts()	Get a mapping from context keys to contexts.
read_contributors([direct_only])	Get a mapping from contributor ORCID identifiers to author objects.
read_mappings()	Read curated mappings as a nested dict data structure.
read_metaregistry()	Read the metaregistry.
read_mismatches()	Read the mismatches subset of curated mappings as a nested dictionary data structure.
read_registry()	Read the Bioregistry as JSON.
registries()	Get a list of registries in the Bioregistry.
resources()	Get a list of resources in the Bioregistry.
standardize_identifier(prefix, identifier)	Normalize an identifier.
write_collections(collections, *[, path])	Write the collections.
write_contexts(contexts)	Write to contexts.
write_registry(registry, *[, path])	Write to the Bioregistry.

Classes

Author(*, name, orcid[, email, github, wikidata])	Metadata for an author.
Collection(*, identifier, name, description, ...)	A collection of resources.
Context(*, name, description, maintainers, ...)	A prescriptive context.
Manager([registry, metaregistry, ...])	A manager for functionality related to a metaregistry.
NormalizedNamableReference(*, prefix, identifier)	Extends curies.NamableReference to normalize the prefix against the Bioregistry.
NormalizedNamedReference(*, prefix, identifier)	Extends curies.NamedReference to normalize the prefix against the Bioregistry.
NormalizedReference(*, prefix, identifier)	Extends curies.Reference to normalize the prefix against the Bioregistry.
Organization(*[, ror, wikidata, gnd, partnered])	Model for organizations.
Provider(*, code[, name, description, ...])	A provider.
Registry(*, prefix, name, description, ...)	Metadata about a registry.
Resource(*, prefix[, name, description, ...])	Metadata about an ontology, database, or other resource.
StandardNamableReference(*, prefix, identifier)	An extension to curies.NamableReference that automatically validates prefix and identifier.
StandardNamedReference(*, prefix, identifier)	An extension to curies.NamedReference that automatically validates prefix and identifier.
StandardReference(*, prefix, identifier)	An extension to curies.Reference that automatically validates prefix and identifier.

Class Inheritance Diagram

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