# -*- coding: utf-8 -*-
"""Resolvers for CURIE (e.g., pairs of prefix and identifier)."""
import warnings
from typing import Mapping, Optional, Sequence, Tuple
from .resolve import get_resource
from .resource_manager import manager
__all__ = [
"is_valid_curie",
"is_standardizable_curie",
"is_valid_identifier",
"is_standardizable_identifier",
"get_providers",
"get_providers_list",
"get_identifiers_org_iri",
"get_identifiers_org_curie",
"get_obofoundry_iri",
"get_ols_iri",
"get_bioportal_iri",
"get_n2t_iri",
"get_iri",
"get_link",
"get_bioregistry_iri",
"get_default_iri",
"standardize_identifier",
"miriam_standardize_identifier",
]
[docs]def is_valid_curie(curie: str) -> bool:
"""Check if a CURIE is standardized and valid.
:param curie: A compact URI of the form ``<prefix>:<local unique identifier>``.
:return:
If the CURIE is standardized in both syntax and semantics. This means that it uses the Bioregistry
canonical prefix, does not have a redundant prefix, and if available, matches the Bioregistry's
regular expression pattern for identifiers.
Standard CURIE
>>> is_valid_curie("go:0000001")
True
Not a standard CURIE (i.e., no colon)
>>> is_valid_curie("0000001")
False
>>> is_valid_curie("GO_0000001")
False
>>> is_valid_curie("PTM-0001")
False
Non-standardized prefix
>>> is_valid_curie("GO:0000001")
False
Incorrect identifier
>>> is_valid_curie("go:0001")
False
Banana scenario
>>> is_valid_curie("go:GO:0000001")
False
Unknown prefix
>>> is_valid_curie("xxx:yyy")
False
"""
return manager.is_valid_curie(curie)
[docs]def is_standardizable_curie(curie: str) -> bool:
"""Check if a CURIE is validatable, but not necessarily standardized.
:param curie: A compact URI
:return: If the CURIE can be standardized (e.g., prefix normalize and identifier normalized)
then validated.
Standard CURIE
>>> is_standardizable_curie("go:0000001")
True
Not a standard CURIE (i.e., no colon)
>>> is_standardizable_curie("0000001")
False
>>> is_standardizable_curie("GO_0000001")
False
>>> is_standardizable_curie("PTM-0001")
False
Non-standardized prefix
>>> is_standardizable_curie("GO:0000001")
True
Incorrect identifier
>>> is_standardizable_curie("go:0001")
False
Banana scenario
>>> is_standardizable_curie("go:GO:0000001")
True
Unknown prefix
>>> is_standardizable_curie("xxx:yyy")
False
"""
return manager.is_standardizable_curie(curie)
[docs]def is_valid_identifier(prefix: str, identifier: str) -> bool:
"""Check if the pre-parsed CURIE is standardized valid.
:param prefix: The prefix from a compact URI
:param identifier: The local unique identifer from a compact URI
:return:
If the CURIE is standardized in both syntax and semantics. This means that it uses the Bioregistry
canonical prefix, does not have a redundant prefix, and if available, matches the Bioregistry's
regular expression pattern for identifiers.
.. seealso:: The :func:`is_standardizable_identifier` performs normalization before checking validity
Standard CURIE
>>> is_valid_identifier("go", "0000001")
True
Non-standardized prefix
>>> is_valid_identifier("GO", "0000001")
False
Incorrect identifier
>>> is_valid_identifier("go", "0001")
False
Banana scenario
>>> is_valid_identifier("go", "GO:0000001")
False
Unknown prefix
>>> is_valid_identifier("xxx", "yyy")
False
"""
return manager.is_valid_identifier(prefix, identifier)
[docs]def is_standardizable_identifier(prefix: str, identifier: str) -> bool:
"""Check if the identifier is standardizable.
:param prefix: The prefix from a compact URI
:param identifier: The local unique identifer from a compact URI
:return:
If the CURIE can be standardized (e.g., prefix normalize and identifier normalized)
then validated.
.. seealso:: The :func:`is_valid_identifier` does not perform normalization before checking validity
Standard CURIE
>>> is_standardizable_identifier("go", "0000001")
True
Non-standardized prefix
>>> is_standardizable_identifier("GO", "0000001")
True
Incorrect identifier
>>> is_standardizable_identifier("go", "0001")
False
Banana scenario
>>> is_standardizable_identifier("go", "GO:0000001")
True
Unknown prefix
>>> is_standardizable_identifier("xxx", "yyy")
False
"""
return manager.is_standardizable_identifier(prefix, identifier)
[docs]def standardize_identifier(prefix: str, identifier: str) -> str:
"""Normalize an identifier."""
resource = get_resource(prefix)
if resource is None:
return identifier # nothing we can do
return resource.standardize_identifier(identifier)
[docs]def miriam_standardize_identifier(prefix: str, identifier: str) -> Optional[str]:
"""Normalize the identifier with the appropriate banana.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE
:return: A normalize identifier, possibly with banana/redundant prefix added.
Returns none if the prefix doesn't map to MIRIAM.
Examples with explicitly annotated bananas:
>>> import bioregistry as br
>>> assert "VariO" == br.get_banana('vario')
>>> miriam_standardize_identifier('vario', '0376')
'VariO:0376'
>>> miriam_standardize_identifier('vario', 'VariO:0376')
'VariO:0376'
Examples with bananas from OBO:
>>> import bioregistry as br
>>> assert "GO" == br.get_banana('go')
>>> miriam_standardize_identifier('go', '0000001')
'GO:0000001'
>>> miriam_standardize_identifier('go', 'GO:0000001')
'GO:0000001'
>>> assert "VariO" == br.get_banana('vario')
>>> miriam_standardize_identifier('vario', '0000001')
'VariO:0000001'
>>> miriam_standardize_identifier('vario', 'VariO:0000001')
'VariO:0000001'
Examples from OBO Foundry:
>>> miriam_standardize_identifier('chebi', '1234')
'CHEBI:1234'
>>> miriam_standardize_identifier('chebi', 'CHEBI:1234')
'CHEBI:1234'
Examples outside of OBO:
>>> miriam_standardize_identifier('mgi', '6017782')
'MGI:6017782'
>>> miriam_standardize_identifier('mgi', 'MGI:6017782')
'MGI:6017782'
>>> miriam_standardize_identifier('swisslipid', '000000341')
'SLM:000000341'
>>> miriam_standardize_identifier('swisslipid', 'SLM:000000341')
'SLM:000000341'
Special cases with underscore-delimited bananas
>>> miriam_standardize_identifier('cellosaurus', '0001')
'CVCL_0001'
>>> miriam_standardize_identifier('cellosaurus', 'CVCL_0001')
'CVCL_0001'
>>> miriam_standardize_identifier('ro', '0000001')
'RO_0000001'
>>> miriam_standardize_identifier('ro', 'RO_0000001')
'RO_0000001'
>>> miriam_standardize_identifier('geogeo', '000000001')
'GEO_000000001'
>>> miriam_standardize_identifier('geogeo', 'GEO_000000001')
'GEO_000000001'
>>> miriam_standardize_identifier('biomodels.kisao', '0000057')
'KISAO_0000057'
>>> miriam_standardize_identifier('biomodels.kisao', 'KISAO_0000057')
'KISAO_0000057'
Standard:
>>> import bioregistry as br
>>> assert br.get_banana('pdb') is None
>>> assert not br.get_namespace_in_lui('pdb')
>>> miriam_standardize_identifier('pdb', '00000020')
'00000020'
"""
resource = get_resource(prefix)
if resource is None:
return identifier # nothing we can do
return resource.miriam_standardize_identifier(identifier)
[docs]def get_default_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get the default URL for the given CURIE.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE
:return: A IRI string corresponding to the default provider, if available.
>>> get_default_iri('chebi', '24867')
'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867'
"""
return manager.get_default_iri(prefix, identifier)
[docs]def get_providers(prefix: str, identifier: str) -> Mapping[str, str]:
"""Get all providers for the CURIE."""
return manager.get_providers(prefix, identifier)
[docs]def get_providers_list(prefix: str, identifier: str) -> Sequence[Tuple[str, str]]:
"""Get all providers for the CURIE."""
return manager.get_providers_list(prefix, identifier)
[docs]def get_identifiers_org_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get the identifiers.org URL for the given CURIE.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE
:return: A IRI string corresponding to the Identifiers.org, if the prefix exists and is
mapped to MIRIAM.
>>> get_identifiers_org_iri('chebi', '24867')
'https://identifiers.org/CHEBI:24867'
>>> get_identifiers_org_iri("interpro", "IPR016380")
'https://identifiers.org/interpro:IPR016380'
>>> get_identifiers_org_iri("cellosaurus", "0001")
'https://identifiers.org/cellosaurus:CVCL_0001'
>>> get_identifiers_org_iri("biomodels.kisao", "0000057")
'https://identifiers.org/biomodels.kisao:KISAO_0000057'
"""
return manager.get_miriam_iri(prefix, identifier)
[docs]def get_n2t_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get the name-to-thing URL for the given CURIE.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE
:return: A IRI string corresponding to the N2T resolve, if the prefix exists and is
mapped to N2T.
>>> get_n2t_iri('chebi', '24867')
'https://n2t.net/chebi:24867'
"""
return manager.get_n2t_iri(prefix, identifier)
[docs]def get_bioportal_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get the Bioportal URL for the given CURIE.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE
:return: A link to the Bioportal page
>>> get_bioportal_iri('chebi', '24431')
'https://bioportal.bioontology.org/ontologies/CHEBI/?p=classes&conceptid=http://purl.obolibrary.org/obo/CHEBI_24431'
"""
return manager.get_bioportal_iri(prefix, identifier)
[docs]def get_identifiers_org_curie(prefix: str, identifier: str) -> Optional[str]:
"""Get the identifiers.org CURIE for the given CURIE."""
return manager.get_miriam_curie(prefix, identifier)
[docs]def get_obofoundry_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get the OBO Foundry URL if possible.
:param prefix: The prefix
:param identifier: The identifier
:return: The OBO Foundry URL if the prefix can be mapped to an OBO Foundry entry
>>> get_obofoundry_iri('chebi', '24431')
'http://purl.obolibrary.org/obo/CHEBI_24431'
For entries where there's a preferred prefix, it is respected.
>>> get_obofoundry_iri('fbbt', '00007294')
'http://purl.obolibrary.org/obo/FBbt_00007294'
"""
return manager.get_obofoundry_iri(prefix, identifier)
[docs]def get_ols_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get the OLS URL if possible."""
return manager.get_ols_iri(prefix, identifier)
def get_scholia_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get a Scholia IRI, if possible.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE
:return: A link to the Scholia page
>>> get_scholia_iri("pubmed", "1234")
'https://scholia.toolforge.org/pubmed/1234'
>>> get_scholia_iri("pdb", "1234")
None
"""
return manager.get_scholia_iri(prefix, identifier)
[docs]def get_bioregistry_iri(prefix: str, identifier: str) -> Optional[str]:
"""Get the bioregistry link.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE
:return: A link to the bioregistry resolver
>>> get_bioregistry_iri('pdb', '1234')
'https://bioregistry.io/pdb:1234'
Redundant prefix (OBO)
>>> get_bioregistry_iri('go', 'GO:0120212')
'https://bioregistry.io/go:0120212'
>>> get_bioregistry_iri('go', 'go:0120212')
'https://bioregistry.io/go:0120212'
>>> get_bioregistry_iri('go', '0120212')
'https://bioregistry.io/go:0120212'
Redundant prefix (banana; OBO)
>>> get_bioregistry_iri('fbbt', 'fbbt:00007294')
'https://bioregistry.io/fbbt:00007294'
>>> get_bioregistry_iri('fbbt', 'fbbt:00007294')
'https://bioregistry.io/fbbt:00007294'
>>> get_bioregistry_iri('fbbt', '00007294')
'https://bioregistry.io/fbbt:00007294'
Redundant prefix (banana; explicit)
>>> get_bioregistry_iri('go.ref', 'GO_REF:1234')
'https://bioregistry.io/go.ref:1234'
>>> get_bioregistry_iri('go.ref', '1234')
'https://bioregistry.io/go.ref:1234'
"""
return manager.get_bioregistry_iri(prefix=prefix, identifier=identifier)
[docs]def get_iri(
prefix: str,
identifier: Optional[str] = None,
*,
priority: Optional[Sequence[str]] = None,
prefix_map: Optional[Mapping[str, str]] = None,
use_bioregistry_io: bool = True,
provider: Optional[str] = None,
) -> Optional[str]:
"""Get the best link for the CURIE, if possible.
:param prefix: The prefix in the CURIE
:param identifier: The identifier in the CURIE. If identifier is given as None, then this function will
assume that the first argument (``prefix``) is actually a full CURIE.
:param priority: A user-defined priority list. In addition to the metaprefixes in the Bioregistry
corresponding to resources that are resolvers/lookup services, you can also use ``default``
to correspond to the first-party IRI and ``custom`` to refer to the custom prefix map.
The default priority list is:
1. Custom prefix map (``custom``)
1. First-party IRI (``default``)
2. Identifiers.org / MIRIAM (``miriam``)
3. Ontology Lookup Service (``ols``)
4. OBO PURL (``obofoundry``)
5. Name-to-Thing (``n2t``)
6. BioPortal (``bioportal``)
:param prefix_map: A custom prefix map to go with the ``custom`` key in the priority list
:param use_bioregistry_io: Should the bioregistry resolution IRI be used? Defaults to true.
:param provider: The provider code to use for a custom provider
:return: The best possible IRI that can be generated based on the priority list.
A pre-parse CURIE can be given as the first two arguments
>>> get_iri("chebi", "24867")
'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867'
A CURIE can be given directly as a single argument
>>> get_iri("chebi:24867")
'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867'
A priority list can be given
>>> priority = ["obofoundry", "default", "bioregistry"]
>>> get_iri("chebi:24867", priority=priority)
'http://purl.obolibrary.org/obo/CHEBI_24867'
A custom prefix map can be supplied.
>>> prefix_map = {"chebi": "https://example.org/chebi/"}
>>> get_iri("chebi:24867", prefix_map=prefix_map)
'https://example.org/chebi/24867'
>>> get_iri("fbbt:00007294")
'https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:00007294'
A custom prefix map can be supplied in combination with a priority list
>>> prefix_map = {"lipidmaps": "https://example.org/lipidmaps/"}
>>> priority = ["obofoundry", "custom", "default", "bioregistry"]
>>> get_iri("chebi:24867", prefix_map=prefix_map, priority=priority)
'http://purl.obolibrary.org/obo/CHEBI_24867'
>>> get_iri("lipidmaps:1234", prefix_map=prefix_map, priority=priority)
'https://example.org/lipidmaps/1234'
A custom provider is given, which makes the Bioregistry very extensible
>>> get_iri("chebi:24867", provider="chebi-img")
'https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=24867'
"""
return manager.get_iri(
prefix=prefix,
identifier=identifier,
priority=priority,
prefix_map=prefix_map,
use_bioregistry_io=use_bioregistry_io,
provider=provider,
)
[docs]def get_link(
prefix: str,
identifier: str,
priority: Optional[Sequence[str]] = None,
use_bioregistry_io: bool = True,
) -> Optional[str]:
"""Get the best link for the CURIE, if possible."""
warnings.warn("get_link() is deprecated. use bioregistry.get_iri() instead", DeprecationWarning)
return get_iri(prefix=prefix, identifier=identifier, use_bioregistry_io=use_bioregistry_io)
def get_formatted_iri(metaprefix: str, prefix: str, identifier: str) -> Optional[str]:
"""Get an IRI using the format in the metaregistry.
:param metaprefix: The metaprefix of the registry in the metaregistry
:param prefix: A bioregistry prefix (will be mapped to the external one automatically)
:param identifier: The identifier for the entity
:returns: An IRI generated from the ``resolver_url`` format string of the registry, if it
exists.
>>> get_formatted_iri("miriam", "hgnc", "16793")
'https://identifiers.org/hgnc:16793'
>>> get_formatted_iri("n2t", "hgnc", "16793")
'https://n2t.net/hgnc:16793'
>>> get_formatted_iri("obofoundry", "fbbt", "00007294")
'http://purl.obolibrary.org/obo/FBbt_00007294'
"""
return manager.get_formatted_iri(metaprefix=metaprefix, prefix=prefix, identifier=identifier)