bioregistry
v0.10.46
Getting Started
Reference
Alignment
Command Line Interface
Tabular Data Processing
Deploying the Bioregistry
Deploying a custom Bioregistry
bioregistry
Index
Edit on GitHub
Index
Symbols
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A
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B
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C
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D
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E
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F
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G
|
H
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I
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K
|
L
|
M
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N
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O
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P
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Q
|
R
|
S
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T
|
U
|
V
|
W
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-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)
AberOWLAligner (class in bioregistry.align)
add_triples() (Collection method)
(Registry method)
agroportal (Resource attribute)
AgroPortalAligner (class in bioregistry.align)
align() (Aligner class method)
Aligner (class in bioregistry.align)
alt_key_match (Aligner attribute)
(BartocAligner attribute)
(EDAMAligner attribute)
(FairsharingAligner attribute)
(HL7Aligner attribute)
(Re3dataAligner attribute)
(UniProtAligner attribute)
alt_keys_match (Aligner attribute)
(PrefixCommonsAligner 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)
BartocAligner (class in bioregistry.align)
bibtex (Registry attribute)
biocontext (Resource attribute)
BioContextAligner (class in bioregistry.align)
biolink (Resource attribute)
BiolinkAligner (class in bioregistry.align)
bioportal (Resource attribute)
BioPortalAligner (class in bioregistry.align)
bioregistry command line option
--version
bioregistry-align command line option
--no-force
--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.align
module
bioregistry.external
module
bioregistry.pandas
module
bioregistry_prefix (Registry attribute)
blacklist (Context attribute)
C
cellosaurus (Resource attribute)
CellosaurusAligner (class in bioregistry.align)
cheminf (Resource attribute)
ChemInfAligner (class in bioregistry.align)
cli() (Aligner class method)
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)
CropOCTAligner (class in bioregistry.align)
curation_header (AberOWLAligner attribute)
(BartocAligner attribute)
(BioContextAligner attribute)
(BiolinkAligner attribute)
(CellosaurusAligner attribute)
(ChemInfAligner attribute)
(CropOCTAligner attribute)
(EDAMAligner attribute)
(FairsharingAligner attribute)
(GoAligner attribute)
(HL7Aligner attribute)
(MiriamAligner attribute)
(N2TAligner attribute)
(NcbiAligner attribute)
(OBOFoundryAligner attribute)
(OLSAligner attribute)
(OntobeeAligner attribute)
(PrefixCommonsAligner attribute)
(Re3dataAligner attribute)
(UniProtAligner attribute)
(WikidataAligner attribute)
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)
EcoPortalAligner (class in bioregistry.align)
edam (Resource attribute)
EDAMAligner (class in bioregistry.align)
example (Registry attribute)
(Resource attribute)
example_decoys (Resource attribute)
example_extras (Resource attribute)
F
fairsharing (Resource attribute)
FairsharingAligner (class in bioregistry.align)
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_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_curation_row() (Aligner method)
(BioContextAligner method)
(BiolinkAligner method)
(NcbiAligner method)
(OntobeeAligner method)
(PrefixCommonsAligner method)
get_curation_table() (Aligner 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_extended_prefix_map() (in module bioregistry)
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_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_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_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_records_from_context() (Manager method)
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_scholia_iri() (Manager method)
get_scholia_prefix() (Resource method)
get_short_description() (Resource method)
get_short_name() (Registry method)
get_skip() (Aligner method)
(BioContextAligner method)
(BiolinkAligner method)
(CellosaurusAligner method)
(ChemInfAligner method)
(EDAMAligner method)
(GoAligner method)
(N2TAligner method)
(OBOFoundryAligner method)
(OLSAligner method)
(PrefixCommonsAligner method)
(WikidataAligner method)
get_synonyms() (in module bioregistry)
(Manager method)
(Resource method)
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)
getter() (AberOWLAligner method)
(AgroPortalAligner method)
(BartocAligner method)
(BioContextAligner method)
(BiolinkAligner method)
(BioPortalAligner method)
(CellosaurusAligner method)
(ChemInfAligner method)
(CropOCTAligner method)
(EcoPortalAligner method)
(EDAMAligner method)
(FairsharingAligner method)
(GoAligner method)
(HL7Aligner method)
(MiriamAligner method)
(N2TAligner method)
(NcbiAligner method)
(OBOFoundryAligner method)
(OLSAligner method)
(OntobeeAligner method)
(PrefixCommonsAligner method)
(Re3dataAligner method)
(UniProtAligner method)
(WikidataAligner method)
getter_kwargs (Aligner attribute)
(NcbiAligner attribute)
github_request_issue (Resource attribute)
go (Resource attribute)
GoAligner (class in bioregistry.align)
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)
HL7Aligner (class in bioregistry.align)
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_new (Aligner attribute)
(MiriamAligner attribute)
(OBOFoundryAligner attribute)
(OLSAligner attribute)
(PrefixCommonsAligner attribute)
include_synonyms (Context attribute)
internal_registry (Aligner attribute)
iris_to_curies() (in module bioregistry.pandas)
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
key (AberOWLAligner attribute)
(AgroPortalAligner attribute)
(BartocAligner attribute)
(BioContextAligner attribute)
(BiolinkAligner attribute)
(BioPortalAligner attribute)
(CellosaurusAligner attribute)
(ChemInfAligner attribute)
(CropOCTAligner attribute)
(EcoPortalAligner attribute)
(EDAMAligner attribute)
(FairsharingAligner attribute)
(GoAligner attribute)
(HL7Aligner attribute)
(MiriamAligner attribute)
(N2TAligner attribute)
(NcbiAligner attribute)
(OBOFoundryAligner attribute)
(OLSAligner attribute)
(OntobeeAligner attribute)
(PrefixCommonsAligner attribute)
(Re3dataAligner attribute)
(UniProtAligner attribute)
(WikidataAligner attribute)
keywords (Resource attribute)
L
license (Registry attribute)
(Resource attribute)
logo (Resource attribute)
logo_url (Registry attribute)
lookup_from() (Manager method)
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)
MiriamAligner (class in bioregistry.align)
model_post_init() (Resource method)
module
bioregistry.align
bioregistry.external
bioregistry.pandas
N
n2t (Resource attribute)
N2TAligner (class in bioregistry.align)
name (Collection attribute)
(Context attribute)
(Provider attribute)
(Registry attribute)
(Resource attribute)
namespace_in_lui (Resource attribute)
ncbi (Resource attribute)
NcbiAligner (class in bioregistry.align)
no_own_terms (Resource attribute)
normalize_curie() (in module bioregistry)
(Manager method)
normalize_curies() (in module bioregistry.pandas)
normalize_invmap (Aligner attribute)
(OBOFoundryAligner attribute)
normalize_parsed_curie() (in module bioregistry)
(Manager method)
normalize_prefix() (in module bioregistry)
(Manager method)
normalize_prefixes() (in module bioregistry.pandas)
O
obofoundry (Resource attribute)
OBOFoundryAligner (class in bioregistry.align)
ols (Resource attribute)
OLSAligner (class in bioregistry.align)
ontobee (Resource attribute)
OntobeeAligner (class in bioregistry.align)
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)
pattern (Resource attribute)
preferred_prefix (Resource attribute)
prefix (Registry attribute)
(Resource attribute)
prefix_priority (Context attribute)
prefix_remapping (Context attribute)
prefixcommons (Resource attribute)
PrefixCommonsAligner (class in bioregistry.align)
prepare_external() (Aligner method)
(BioContextAligner method)
(BiolinkAligner method)
(GoAligner method)
print_curation_table() (Aligner method)
proprietary (Resource attribute)
provider_uri_format (Registry attribute)
providers (Resource attribute)
provides (Resource attribute)
publications (Resource attribute)
Q
qualities (Registry attribute)
R
rasterize() (Manager method)
rasterized_resource() (Manager method)
rdf_uri_format (Resource attribute)
re3data (Resource attribute)
Re3dataAligner (class in bioregistry.align)
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)
Resource.Config (class in bioregistry)
resources (Collection attribute)
resources() (in module bioregistry)
reviewer (Resource attribute)
S
score() (Registry method)
search_uri_format (Registry attribute)
short_name (Registry attribute)
skip_deprecated (Aligner attribute)
(FairsharingAligner attribute)
standardize_identifier() (in module bioregistry)
(Resource method)
subkey (Aligner attribute)
synonyms (Resource attribute)
T
twitter (Resource attribute)
U
uniprot (Resource attribute)
UniProtAligner (class in bioregistry.align)
uri_format (Provider attribute)
(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)
WikidataAligner (class in bioregistry.align)
write_contexts() (in module bioregistry)
write_curation_table() (Aligner method)
write_registry() (Aligner method)
(in module bioregistry)
(Manager method)
Read the Docs
v: v0.10.46
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