Reference

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

Functions

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(identifier)	Get the collection entry for the given identifier.
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_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_license_conflicts()	Get license conflicts.
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(prefix, *[, provenance])	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_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(prefix)	Get the download link for the RDF file.
get_registry(metaprefix)	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)	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_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_resource(prefix)	Get the Bioregistry entry for the given prefix.
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(prefix[, priority])	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(curie, *[, sep, ...])	Normalize a CURIE.
normalize_parsed_curie(prefix, identifier, *)	Normalize a prefix/identifier pair.
normalize_prefix()	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_contexts(contexts)	Write to contexts.
write_registry(registry, *[, path])	Write to the Bioregistry.

Classes

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

Class Inheritance Diagram

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