bioregistry
Getting Started
Reference
Alignment
Command Line Interface
Tabular Data Processing
Deploying the Bioregistry
Deploying a custom Bioregistry
Curation
bioregistry
Index
Index
Symbols
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
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_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)
not_notable (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)