bioregistry
v0.5.11
Getting Started
Reference
Alignment
Command Line Interface
bioregistry
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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
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
Symbols
--debug
bioregistry-web command line option
--host
bioregistry-web command line option
--paper
bioregistry-compare command line option
--port
bioregistry-web command line option
--skip-fairsharing
bioregistry-align command line option
--timeout
bioregistry-web 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_triples() (Collection method)
(Registry method)
align() (Aligner class method)
Aligner (class in bioregistry.align)
alt_key_match (Aligner attribute)
(FairsharingAligner attribute)
appears_in (Resource attribute)
as_context_jsonld() (Collection method)
as_prefix_map() (Collection method)
authors (Collection attribute)
availability (Registry attribute)
B
banana (Resource 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
--skip-fairsharing
bioregistry-compare command line option
--paper
bioregistry-web command line option
--debug
--host
--port
--timeout
--verbose
--with-gunicorn
--workers
-v
bioregistry.align
module
bioregistry.external
module
bioregistry_prefix (Registry 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)
contact (Registry attribute)
(Resource attribute)
context (Collection attribute)
contributor (Resource attribute)
contributor_extras (Resource attribute)
curation_header (BioContextAligner attribute)
(BiolinkAligner attribute)
(BioPortalAligner attribute)
(CellosaurusAligner attribute)
(ChemInfAligner attribute)
(FairsharingAligner attribute)
(GoAligner attribute)
(MiriamAligner attribute)
(N2TAligner attribute)
(NcbiAligner attribute)
(OBOFoundryAligner attribute)
(OLSAligner attribute)
(OntobeeAligner attribute)
(PrefixCommonsAligner attribute)
(UniProtAligner attribute)
(WikidataAligner attribute)
curie_from_iri() (in module bioregistry)
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)
E
example (Registry attribute)
(Resource attribute)
example_decoys (Resource attribute)
example_extras (Resource attribute)
F
fairsharing (Resource attribute)
FairsharingAligner (class in bioregistry.align)
from_path() (Manager class method)
G
get_appears_in() (in module bioregistry)
(Manager method)
get_banana() (in module bioregistry)
(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_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_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)
get_curation_row() (Aligner method)
(BioContextAligner method)
(BiolinkAligner method)
(BioPortalAligner method)
(CellosaurusAligner method)
(ChemInfAligner method)
(FairsharingAligner method)
(GoAligner method)
(MiriamAligner method)
(N2TAligner method)
(NcbiAligner method)
(OBOFoundryAligner method)
(OLSAligner method)
(OntobeeAligner method)
(PrefixCommonsAligner method)
(UniProtAligner method)
(WikidataAligner method)
get_curation_table() (Aligner method)
get_curie_pattern() (in module bioregistry)
(Manager method)
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)
(Resource method)
get_download_obo() (Resource method)
get_download_obograph() (Resource method)
get_download_owl() (Resource method)
get_example() (in module bioregistry)
(Manager method)
(Resource method)
get_external() (in module bioregistry)
(Manager method)
(Resource 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_has_canonical() (in module bioregistry)
(Manager method)
get_has_parts() (in module bioregistry)
(Manager method)
get_homepage() (in module bioregistry)
(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_internal_prefix_map() (Manager method)
get_iri() (in module bioregistry)
(Manager method)
get_json_download() (in module bioregistry)
get_license() (in module bioregistry)
(Resource method)
get_license_conflicts() (in module bioregistry)
(Manager method)
get_link() (in module bioregistry)
get_mapped_prefix() (Manager method)
(Resource method)
get_mappings() (in module bioregistry)
(Resource method)
get_miriam() (in module bioregistry.external)
get_miriam_curie() (Manager method)
get_miriam_iri() (Manager 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_download() (in module bioregistry)
get_obo_health_url() (in module bioregistry)
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_pattern() (in module bioregistry)
(Manager method)
(Resource method)
get_pattern_map() (in module bioregistry)
(Manager method)
get_pattern_re() (Resource method)
get_preferred_prefix() (in module bioregistry)
(Manager method)
(Resource method)
get_prefix_key() (Resource method)
get_prefix_list() (Manager method)
get_prefix_map() (in module bioregistry)
(Manager method)
get_prefixcommons() (in module bioregistry.external)
get_prefixcommons_uri_format() (in module bioregistry)
(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_registry() (in module bioregistry)
get_registry_description() (in module bioregistry)
get_registry_example() (in module bioregistry)
get_registry_homepage() (in module bioregistry)
get_registry_invmap() (in module bioregistry)
(Manager method)
get_registry_map() (in module bioregistry)
(Manager method)
get_registry_name() (in module bioregistry)
get_registry_provider_uri_format() (in module bioregistry)
get_registry_short_name() (in module bioregistry)
get_registry_uri() (in module bioregistry)
get_repository() (in module bioregistry)
(Resource method)
get_resolver_uri_format() (Registry method)
get_resource() (in module bioregistry)
(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)
(GoAligner method)
(N2TAligner method)
(OBOFoundryAligner method)
(OLSAligner 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_prefix() (in module bioregistry)
(Manager method)
(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() (BioContextAligner method)
(BiolinkAligner method)
(BioPortalAligner method)
(CellosaurusAligner method)
(ChemInfAligner method)
(FairsharingAligner method)
(GoAligner method)
(MiriamAligner method)
(N2TAligner method)
(NcbiAligner method)
(OBOFoundryAligner method)
(OLSAligner method)
(OntobeeAligner method)
(PrefixCommonsAligner method)
(UniProtAligner method)
(WikidataAligner method)
getter_kwargs (Aligner attribute)
(NcbiAligner attribute)
go (Resource attribute)
GoAligner (class in bioregistry.align)
governance (Registry attribute)
H
has_canonical (Resource attribute)
has_no_terms() (in module bioregistry)
(Manager method)
homepage (Provider attribute)
(Registry attribute)
(Resource attribute)
I
identifier (Collection attribute)
include_new (Aligner attribute)
(MiriamAligner attribute)
(OBOFoundryAligner attribute)
(OLSAligner attribute)
(PrefixCommonsAligner attribute)
include_synonyms (Context attribute)
internal_registry (Aligner attribute)
is_canonical_identifier() (Resource method)
is_deprecated() (in module bioregistry)
(Manager method)
(Resource method)
is_known_identifier() (in module bioregistry)
(Resource method)
is_mismatch() (in module bioregistry)
is_proprietary() (in module bioregistry)
K
key (BioContextAligner attribute)
(BiolinkAligner attribute)
(BioPortalAligner attribute)
(CellosaurusAligner attribute)
(ChemInfAligner attribute)
(FairsharingAligner attribute)
(GoAligner attribute)
(MiriamAligner attribute)
(N2TAligner attribute)
(NcbiAligner attribute)
(OBOFoundryAligner attribute)
(OLSAligner attribute)
(OntobeeAligner attribute)
(PrefixCommonsAligner attribute)
(UniProtAligner attribute)
(WikidataAligner attribute)
L
license (Registry attribute)
(Resource attribute)
logo_url (Registry attribute)
lookup_from() (Manager method)
M
maintainers (Context attribute)
Manager (class in bioregistry)
mappings (Resource attribute)
miriam (Resource attribute)
miriam_standardize_identifier() (Resource method)
MiriamAligner (class in bioregistry.align)
module
bioregistry.align
bioregistry.external
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_parsed_curie() (in module bioregistry)
(Manager method)
normalize_prefix() (in module bioregistry)
(Manager method)
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)
P
parse_curie() (in module bioregistry)
(Manager method)
parse_iri() (in module bioregistry)
parse_obolibrary_purl() (in module bioregistry)
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)
(BioPortalAligner method)
(GoAligner method)
(WikidataAligner method)
print_curation_table() (Aligner method)
proprietary (Resource attribute)
provider_uri_format (Registry attribute)
providers (Resource attribute)
provides (Resource attribute)
R
rasterize() (Manager method)
read_collections() (in module bioregistry)
read_contexts() (in module bioregistry)
read_contributors() (in module bioregistry)
read_metaregistry() (in module bioregistry)
read_mismatches() (in module bioregistry)
read_registry() (in module bioregistry)
references (Resource attribute)
repository (Resource attribute)
resolve() (Provider method)
(Registry method)
resolver_type (Registry attribute)
resolver_uri_format (Registry attribute)
resources (Collection attribute)
reviewer (Resource attribute)
S
score() (Registry method)
short_name (Registry attribute)
skip_deprecated (Aligner attribute)
(FairsharingAligner attribute)
standardize_identifier() (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)
use_preferred (Context attribute)
V
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)
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