Index

Symbols

--base-url bioregistry-web command line option --collections bioregistry-web command line option --config bioregistry-web command line option --contexts bioregistry-web command line option --host bioregistry-web command line option --metaregistry bioregistry-web command line option --no-force bioregistry-align command line option --port bioregistry-web command line option --registry bioregistry-web command line option --skip-agroportal bioregistry-align command line option

--skip-bioportal bioregistry-align command line option --skip-fairsharing bioregistry-align command line option --skip-re3data bioregistry-align command line option --skip-slow bioregistry-align command line option --verbose bioregistry-web command line option --version bioregistry command line option --with-gunicorn bioregistry-web command line option --workers bioregistry-web command line option -v bioregistry-web command line option

A

aberowl (Resource attribute) add_triples() (Collection method) (Registry method) agroportal (Resource attribute) appears_in (Resource attribute)

as_context_jsonld() (Collection method) as_context_jsonld_str() (Collection method) as_prefix_map() (Collection method) authors (Collection attribute) availability (Registry attribute)

B

banana (Resource attribute) banana_peel (Resource attribute) bartoc (Resource attribute) bibtex (Registry attribute) biocontext (Resource attribute) biolink (Resource attribute) bioportal (Resource attribute) bioregistry command line option --version bioregistry-align command line option --no-force --skip-agroportal --skip-bioportal --skip-fairsharing --skip-re3data --skip-slow bioregistry-web command line option --base-url --collections --config --contexts --host --metaregistry --port --registry --verbose --with-gunicorn --workers -v

bioregistry.curation.bulk_import module bioregistry.curation.literature module bioregistry.external module bioregistry.pandas module bioregistry_prefix (Registry attribute) blacklist (Context attribute)

C

cellosaurus (Resource attribute) cheminf (Resource attribute) code (Provider attribute) comment (Resource attribute) compress() (Manager method) contact (Registry attribute) (Resource attribute) context (Collection attribute) contributor (Resource attribute) contributor_extras (Resource attribute)

converter (Manager attribute) count_mappings() (in module bioregistry) (Manager method) cropoct (Resource attribute) CurationRelevance (class in bioregistry.curation.literature) curie_from_iri() (in module bioregistry) curie_to_str() (in module bioregistry) curies_to_identifiers() (in module bioregistry.pandas) curies_to_iris() (in module bioregistry.pandas) custom_prefix_map (Context attribute)

D

DEFAULT_URI_FORMATTER_PRIORITY (Resource attribute) depends_on (Resource attribute) deprecated (Resource attribute) description (Collection attribute) (Context attribute) (Provider attribute) (Registry attribute) (Resource attribute)

download (Registry attribute) download_json (Resource attribute) download_obo (Resource attribute) download_owl (Resource attribute) download_rdf (Resource attribute)

E

ecoportal (Resource attribute) edam (Resource attribute) example (Registry attribute) (Resource attribute)

example_decoys (Resource attribute) example_extras (Resource attribute) existing (CurationRelevance attribute)

F

fairsharing (Resource attribute)

first_party (Provider attribute)

G

get_appears_in() (in module bioregistry) (Manager method) get_banana() (in module bioregistry) (Resource method) get_banana_peel() (Resource method) get_bartoc() (in module bioregistry.external) get_bartoc_uri_format() (Resource method) get_biocontext() (in module bioregistry.external) get_biocontext_uri_format() (in module bioregistry) (Resource method) get_biolink() (in module bioregistry.external) get_bioportal() (in module bioregistry.external) get_bioportal_iri() (in module bioregistry) (Manager method) get_bioportal_prefix() (in module bioregistry) get_bioregistry_iri() (in module bioregistry) (Manager method) get_bioregistry_uri_format() (Resource method) get_bioschemas_jsonld() (Resource method) get_canonical_for() (in module bioregistry) (Manager method) get_cellosaurus() (in module bioregistry.external) get_cheminf() (in module bioregistry.external) get_code_link() (Registry method) get_collection() (in module bioregistry) get_collection_name() (Manager method) get_contact() (in module bioregistry) (Resource method) get_contact_email() (in module bioregistry) (Resource method) get_contact_github() (in module bioregistry) (Resource method) get_contact_name() (in module bioregistry) (Resource method) get_contact_orcid() (in module bioregistry) (Resource method) get_context() (in module bioregistry) (Manager method) get_context_artifacts() (Manager method) get_converter() (in module bioregistry) (Manager method) get_converter_from_context() (Manager method) get_curie() (Resource method) get_curie_pattern() (in module bioregistry) (Manager method) get_curies_records() (Manager method) get_default_converter() (in module bioregistry) get_default_format() (in module bioregistry) (Resource method) get_default_iri() (in module bioregistry) (Manager method) get_default_uri() (Resource method) get_depends_on() (in module bioregistry) (Manager method) get_description() (in module bioregistry) (Manager method) (Resource method) get_download_obo() (Resource method) get_download_obograph() (Resource method) get_download_owl() (Resource method) get_download_rdf() (Resource method) get_edam() (in module bioregistry.external) get_example() (in module bioregistry) (Manager method) (Resource method) get_example_curie() (Resource method) get_example_iri() (Resource method) get_examples() (Resource method) get_external() (in module bioregistry) (Manager method) (Resource method) get_external_mappings() (Manager method) get_extra_providers() (Resource method) get_fairsharing() (in module bioregistry.external) get_fairsharing_prefix() (in module bioregistry) get_formatted_iri() (Manager method) get_go() (in module bioregistry.external) get_goa_example() (in module bioregistry.pandas) get_has_canonical() (in module bioregistry) (Manager method) get_has_parts() (in module bioregistry) (Manager method) get_hl7() (in module bioregistry.external) get_homepage() (in module bioregistry) (Manager method) (Resource method) get_identifiers_org_curie() (in module bioregistry) get_identifiers_org_iri() (in module bioregistry) get_identifiers_org_prefix() (in module bioregistry) (Resource method) get_in_collections() (Manager method) get_integbio() (in module bioregistry.external) get_internal_prefix_map() (Manager method) get_iri() (in module bioregistry) (Manager method) get_json_download() (in module bioregistry) get_keywords() (in module bioregistry) (Manager method) (Resource method) get_legacy_alt_miriam_uri_format() (Resource method) get_legacy_miriam_uri_format() (Resource method) get_license() (in module bioregistry) (Resource method) get_license_conflicts() (in module bioregistry) (Manager method) get_license_url() (Resource method) get_link() (in module bioregistry) get_logo() (Resource method) get_lov() (in module bioregistry.external) get_mapped_prefix() (Manager method) (Resource method) get_mappings() (in module bioregistry) (Resource method) get_mastodon() (Resource method) get_mastodon_url() (Resource method) get_miriam() (in module bioregistry.external) get_miriam_curie() (Manager method) (Resource method) get_miriam_iri() (Manager method) get_miriam_prefix() (Resource method) get_miriam_uri_format() (in module bioregistry) (Resource method) get_miriam_uri_prefix() (in module bioregistry) (Resource method) get_n2t() (in module bioregistry.external) get_n2t_iri() (in module bioregistry) (Manager method) get_n2t_prefix() (in module bioregistry) get_n2t_uri_format() (Resource method) get_name() (in module bioregistry) (Manager method) (Resource method)

get_namespace_in_lui() (in module bioregistry) (Resource method) get_ncbi() (in module bioregistry.external) get_nt2_uri_prefix() (Resource method) get_obo_context_prefix_map() (in module bioregistry) get_obo_download() (in module bioregistry) get_obo_health_url() (in module bioregistry) (Manager method) get_obo_preferred_prefix() (Resource method) get_obofoundry() (in module bioregistry.external) get_obofoundry_iri() (in module bioregistry) (Manager method) get_obofoundry_prefix() (in module bioregistry) (Resource method) get_obofoundry_uri_format() (in module bioregistry) (Resource method) get_obofoundry_uri_prefix() (in module bioregistry) (Resource method) get_ols() (in module bioregistry.external) get_ols_iri() (in module bioregistry) (Manager method) get_ols_prefix() (in module bioregistry) (Resource method) get_ols_uri_format() (in module bioregistry) (Resource method) get_ols_uri_prefix() (in module bioregistry) (Resource method) get_ontobee() (in module bioregistry.external) get_owl_download() (in module bioregistry) get_part_of() (in module bioregistry) (Manager method) get_parts_collections() (in module bioregistry) (Manager method) get_pathguide() (in module bioregistry.external) get_pattern() (in module bioregistry) (Manager method) (Resource method) get_pattern_map() (in module bioregistry) (Manager method) get_pattern_re() (Resource method) get_pattern_re_with_banana() (Resource method) get_pattern_with_banana() (Resource method) get_preferred_prefix() (in module bioregistry) (Manager method) (Resource method) get_prefix_key() (Resource method) get_prefix_map() (in module bioregistry) (Manager method) get_prefixcommons() (in module bioregistry.external) get_prefixcommons_prefix() (Resource method) get_prefixcommons_uri_format() (in module bioregistry) (Resource method) get_priority_prefix() (Resource method) get_provided_by() (in module bioregistry) (Manager method) get_provider_functions() (Manager method) get_provider_uri_format() (Registry method) get_provider_uri_prefix() (Registry method) get_providers() (in module bioregistry) (Manager method) get_providers_list() (in module bioregistry) (Manager method) get_provides_for() (in module bioregistry) (Manager method) get_publications() (Resource method) get_quality_score() (Registry method) get_rdf_download() (in module bioregistry) get_rdf_uri() (Manager method) (Resource method) get_rdf_uri_format() (Resource method) get_rdf_uri_prefix() (Resource method) get_re3data() (in module bioregistry.external) get_registry() (in module bioregistry) (Manager method) get_registry_description() (in module bioregistry) (Manager method) get_registry_example() (in module bioregistry) get_registry_homepage() (in module bioregistry) (Manager method) get_registry_invmap() (in module bioregistry) (Manager method) get_registry_map() (in module bioregistry) (Manager method) get_registry_name() (in module bioregistry) (Manager method) get_registry_provider_uri_format() (in module bioregistry) (Manager method) get_registry_short_name() (in module bioregistry) (Manager method) get_registry_uri() (in module bioregistry) (Manager method) get_repository() (in module bioregistry) (Resource method) get_resolver_uri_format() (Registry method) get_resource() (in module bioregistry) (Manager method) get_reverse_prefix_map() (Manager method) get_rrid() (in module bioregistry.external) get_rrid_iri() (Manager method) get_rrid_uri_format() (Resource method) get_scholia_iri() (Manager method) get_scholia_prefix() (Resource method) get_short_description() (Resource method) get_short_name() (Registry method) get_synonyms() (in module bioregistry) (Manager method) (Resource method) get_togoid() (in module bioregistry.external) get_twitter() (Resource method) get_uniprot() (in module bioregistry.external) get_uri_format() (in module bioregistry) (Manager method) (Resource method) get_uri_formats() (Resource method) get_uri_prefix() (in module bioregistry) (Manager method) (Resource method) get_uri_prefixes() (Resource method) get_version() (in module bioregistry) (Resource method) get_versions() (in module bioregistry) (Manager method) get_wikidata() (in module bioregistry.external) get_wikidata_prefix() (in module bioregistry) get_zazuko() (in module bioregistry.external) github_request_issue (Resource attribute) go (Resource attribute) governance (Registry attribute)

H

has_canonical (Resource attribute) has_download() (Resource method) has_no_terms() (in module bioregistry) (Manager method)

has_permissive_license (Registry property) hl7 (Resource attribute) homepage (Provider attribute) (Registry attribute) (Resource attribute)

I

identifier (Collection attribute) identifiers_to_curies() (in module bioregistry.pandas) identifiers_to_iris() (in module bioregistry.pandas) include_synonyms (Context attribute) integbio (Resource attribute) iris_to_curies() (in module bioregistry.pandas) irrelevant_other (CurationRelevance attribute) is_deprecated() (in module bioregistry) (Manager method) (Resource method) is_lookup (Registry property) is_mismatch() (in module bioregistry) is_novel() (in module bioregistry) (Manager method)

is_prefix_provider (Registry property) is_proprietary() (in module bioregistry) is_resolver (Registry property) is_standardizable_curie() (in module bioregistry) (Manager method) is_standardizable_identifier() (in module bioregistry) (Manager method) (Resource method) is_valid_curie() (in module bioregistry) (Manager method) is_valid_identifier() (in module bioregistry) (Manager method) (Resource method)

K

keywords (Resource attribute)

L

license (Registry attribute) (Resource attribute) logo (Resource attribute)

logo_url (Registry attribute) lookup_from() (Manager method) lov (Resource attribute)

M

maintainers (Context attribute) Manager (class in bioregistry) mappings (Resource attribute) mastodon (Resource attribute) miriam (Resource attribute) miriam_standardize_identifier() (in module bioregistry) (Resource method)

model_post_init() (Resource method) module bioregistry.curation.bulk_import bioregistry.curation.literature bioregistry.external bioregistry.pandas

N

n2t (Resource attribute) name (Collection attribute) (Context attribute) (Provider attribute) (Registry attribute) (Resource attribute) namespace_in_lui (Resource attribute) ncbi (Resource attribute) new_prefix (CurationRelevance attribute) new_provider (CurationRelevance attribute) new_publication (CurationRelevance attribute)

no_own_terms (Resource attribute) no_website (CurationRelevance attribute) normalize_curie() (in module bioregistry) (Manager method) normalize_curies() (in module bioregistry.pandas) normalize_parsed_curie() (in module bioregistry) (Manager method) normalize_prefix() (in module bioregistry) (Manager method) normalize_prefixes() (in module bioregistry.pandas) not_identifiers_resource (CurationRelevance attribute)

O

obofoundry (Resource attribute) ols (Resource attribute)

ontobee (Resource attribute) orcid (Author attribute) owners (Resource attribute)

P

parse_curie() (in module bioregistry) (Manager method) parse_iri() (in module bioregistry) parse_uri() (Manager method) part_of (Resource attribute) pathguide (Resource attribute) pattern (Resource attribute) preferred_prefix (Resource attribute) prefix (Registry attribute) (Resource attribute)

prefix_priority (Context attribute) prefix_remapping (Context attribute) prefixcommons (Resource attribute) proprietary (Resource attribute) provider_uri_format (Registry attribute) providers (Resource attribute) provides (Resource attribute) publications (Provider attribute) (Resource attribute)

Q

qualities (Registry attribute)

R

rasterize() (Manager method) rasterized_resource() (Manager method) rdf_uri_format (Resource attribute) re3data (Resource attribute) read_collections() (in module bioregistry) read_contexts() (in module bioregistry) read_contributors() (in module bioregistry) (Manager method) read_metaregistry() (in module bioregistry) read_mismatches() (in module bioregistry) read_registry() (in module bioregistry)

references (Collection attribute) (Resource attribute) registries() (in module bioregistry) repository (Resource attribute) resolve() (Provider method) (Registry method) resolver_type (Registry attribute) resolver_uri_format (Registry attribute) resources (Collection attribute) resources() (in module bioregistry) reviewer (Resource attribute) rrid (Resource attribute)

S

score() (Registry method) search_uri_format (Registry attribute) short_name (Registry attribute)

standardize_identifier() (in module bioregistry) (Resource method) synonyms (Resource attribute)

T

togoid (Resource attribute)

twitter (Resource attribute)

U

unclear (CurationRelevance attribute) uniprot (Resource attribute) uri_format (Provider attribute) (Resource attribute)

uri_format_resolvable (Resource attribute) URI_FORMATTERS (Resource attribute) uri_prefix_priority (Context attribute)

V

validate_curies() (in module bioregistry.pandas) validate_identifiers() (in module bioregistry.pandas)

validate_prefixes() (in module bioregistry.pandas) version (Resource attribute)

W

wikidata (Resource attribute) write_contexts() (in module bioregistry)

write_registry() (in module bioregistry) (Manager method)

Z

zazuko (Resource attribute)