Source code for bioregistry.resolve_identifier

# -*- 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_known_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",
    "miriam_standardize_identifier",
]


[docs]def is_known_identifier(prefix: str, identifier: str) -> Optional[bool]: """Check that an identifier can be normalized and also matches a prefix's local unique identifier pattern. :param prefix: The prefix in the CURIE :param identifier: The identifier in the CURIE :return: Whether this identifier passes validation, after normalization >>> is_known_identifier("chebi", "1234") True >>> is_known_identifier("chebi", "CHEBI:12345") True >>> is_known_identifier("chebi", "CHEBI:ABCD") False """ resource = get_resource(prefix) if resource is None: return None return resource.is_known_identifier(identifier)
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, )
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)