Index

Symbols

--analytics bioregistry-web command line option --base-url bioregistry-web command line option --collections bioregistry-web command line option --config bioregistry-web command line option --context bioregistry-validate-jsonld command line option bioregistry-validate-linkml command line option bioregistry-validate-ttl command line option bioregistry-validate-virtuoso 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 --relax bioregistry-validate-jsonld command line option bioregistry-validate-linkml command line option bioregistry-validate-ttl command line option bioregistry-validate-virtuoso command line option --skip-agroportal bioregistry-align command line option

--skip-biodivportal 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 --tab bioregistry-web command line option --tablefmt bioregistry-validate-jsonld command line option bioregistry-validate-linkml command line option bioregistry-validate-ttl command line option bioregistry-validate-virtuoso command line option --use-preferred bioregistry-validate-jsonld command line option bioregistry-validate-linkml command line option bioregistry-validate-ttl command line option bioregistry-validate-virtuoso 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

add_collection() (Manager method) add_resource() (in module bioregistry) (Manager method) add_to_collection() (in module bioregistry) (Manager method)

add_triples() (Collection method) (Registry method) as_context_jsonld() (Collection method) as_context_jsonld_str() (Collection method) as_prefix_map() (Collection method) Author (class in bioregistry)

B

bioregistry command line option --version bioregistry-align command line option --no-force --skip-agroportal --skip-biodivportal --skip-bioportal --skip-fairsharing --skip-re3data --skip-slow bioregistry-curate-linkml command line option URL bioregistry-validate-jsonld command line option --context --relax --tablefmt --use-preferred LOCATION bioregistry-validate-linkml command line option --context --relax --tablefmt --use-preferred URL bioregistry-validate-ttl command line option --context --relax --tablefmt --use-preferred LOCATION

bioregistry-validate-virtuoso command line option --context --relax --tablefmt --use-preferred URL bioregistry-web command line option --analytics --base-url --collections --config --contexts --host --metaregistry --port --registry --tab --verbose --with-gunicorn --workers -v bioregistry.curation.add_linkml module bioregistry.curation.bulk_import module bioregistry.curation.literature module bioregistry.external module bioregistry.pandas module

C

Collection (class in bioregistry) compress() (Manager method) Context (class in bioregistry) converter (Manager attribute) count_mappings() (in module bioregistry) (Manager method)

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)

D

DEFAULT_URI_FORMATTER_PRIORITY (Resource attribute)

E

existing (CurationRelevance attribute)

F

format_messages() (in module bioregistry.validate)

G

get_annotated_prefixes() (Collection method) 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_biodivportal() (in module bioregistry.external) 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_charlie() (Author class method) get_cheminf() (in module bioregistry.external) get_code_link() (Registry method) get_collection() (in module bioregistry) get_collection_first_party() (Manager method) get_collection_indirect_dependencies() (Manager method) get_collection_name() (Manager method) get_collection_prefixes() (in module bioregistry) get_collection_resources() (in module bioregistry) 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_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_domain() (Resource method) get_download() (Resource method) get_download_jskos() (Resource method) get_download_obo() (Resource method) get_download_obograph() (Resource method) get_download_owl() (Resource method) get_download_rdf() (Resource method) get_download_skos() (Resource method) get_edam() (in module bioregistry.external) get_example() (in module bioregistry) (Manager method) (Resource method) get_example_curie() (Resource method) get_example_extras() (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_indirect_dependencies() (Manager method) get_integbio() (in module bioregistry.external) get_internal_prefix_map() (Manager method) get_iri() (in module bioregistry) (Manager method) get_jskos_download() (in module bioregistry) get_json_download() (in module bioregistry) get_keyword_to_resources() (Manager method) 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_url() (in module bioregistry) (Resource method) get_logo() (in module bioregistry) (Manager method) (Resource method) get_lov() (in module bioregistry.external) get_mailing_list() (in module bioregistry) (Manager method) (Resource method) 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) (Manager method) (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_config() (Resource method) 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_organizations() (in module bioregistry) get_owl_download() (in module bioregistry) get_owners() (Resource method) 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_prefixes() (Collection 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_short_name_to_prefix() (in module bioregistry) (Manager method) get_registry_uri() (in module bioregistry) (Manager method) get_repository() (in module bioregistry) (Resource method) get_repository_to_prefix() (in module bioregistry) get_resolver_uri_format() (Registry method) get_resource() (in module bioregistry) (Manager method) get_resource_from_linkml() (in module bioregistry.curation.add_linkml) get_resources_with_keyword() (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_skos_download() (in module bioregistry) get_synonyms() (in module bioregistry) (Manager method) (Resource method) get_tib_ts() (in module bioregistry.external) 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_entity() (Resource method) get_wikidata_prefix() (in module bioregistry) get_zazuko() (in module bioregistry.external)

H

has_download() (Resource method) has_no_terms() (in module bioregistry) (Manager method) has_organization() (Collection method) (Resource method)

has_organization_with_ror() (Collection method) (Resource method) has_permissive_license (Registry attribute)

I

identifiers_to_curies() (in module bioregistry.pandas) identifiers_to_iris() (in module bioregistry.pandas) import_from_linkml() (in module bioregistry.curation.add_linkml) iris_to_curies() (in module bioregistry.pandas) irrelevant_other (CurationRelevance attribute) is_deprecated() (in module bioregistry) (Manager method) (Resource method) is_known_inactive() (Provider method) is_lookup (Registry attribute) is_mismatch() (in module bioregistry) is_novel() (in module bioregistry) (Manager method)

is_obo_foundry() (in module bioregistry) is_prefix_provider (Registry attribute) is_proprietary() (in module bioregistry) is_resolver (Registry attribute) 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)

L

link (Organization attribute) LOCATION bioregistry-validate-jsonld command line option bioregistry-validate-ttl command line option

lookup_from() (Manager method)

M

make_preferred() (Manager method) Manager (class in bioregistry) matches_reference() (Organization method) Message (class in bioregistry.validate) miriam_standardize_identifier() (in module bioregistry) (Resource method) model_config (Author attribute) (Collection attribute) (Context attribute) (Message attribute) (NormalizedNamableReference attribute) (NormalizedNamedReference attribute) (NormalizedReference attribute) (Organization attribute) (Provider attribute) (Registry attribute) (Resource attribute) (StandardNamableReference attribute) (StandardNamedReference attribute) (StandardReference attribute)

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

N

new_prefix (CurationRelevance attribute) new_provider (CurationRelevance attribute) new_publication (CurationRelevance attribute) non_resource_paper (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) NormalizedNamableReference (class in bioregistry) NormalizedNamedReference (class in bioregistry) NormalizedReference (class in bioregistry) not_identifiers_resource (CurationRelevance attribute) not_notable (CurationRelevance attribute)

O

Organization (class in bioregistry)

P

parse_curie() (in module bioregistry) (Manager method)

parse_iri() (in module bioregistry) parse_uri() (Manager method) Provider (class in bioregistry)

R

rasterize() (Manager method) rasterized_resource() (Manager method) read_collections() (in module bioregistry) read_contexts() (in module bioregistry) read_contributors() (in module bioregistry) (Manager method) read_mappings() (in module bioregistry) read_metaregistry() (in module bioregistry)

read_mismatches() (in module bioregistry) read_registry() (in module bioregistry) reference (Organization attribute) registries() (in module bioregistry) Registry (class in bioregistry) resolve() (Provider method) (Registry method) Resource (class in bioregistry) resources() (in module bioregistry)

S

score() (Registry method) standardize_identifier() (in module bioregistry) (Resource method)

StandardNamableReference (class in bioregistry) StandardNamedReference (class in bioregistry) StandardReference (class in bioregistry)

T

tabulate_messages() (in module bioregistry.validate)

U

unclear (CurationRelevance attribute) URI_FORMATTERS (Resource attribute) URL bioregistry-curate-linkml command line option bioregistry-validate-linkml command line option bioregistry-validate-virtuoso command line option

V

validate_curies() (in module bioregistry.pandas) validate_identifier() (NormalizedReference class method) (StandardReference class method) validate_identifiers() (in module bioregistry.pandas) validate_jsonld() (in module bioregistry.validate)

validate_linkml() (in module bioregistry.validate) validate_prefix_map() (in module bioregistry.validate) validate_prefixes() (in module bioregistry.pandas) validate_ttl() (in module bioregistry.validate) validate_virtuoso() (in module bioregistry.validate)

W

without_name() (NormalizedNamableReference method) (StandardNamableReference method) write_collections() (in module bioregistry) (Manager method)

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