Source code for curies.sources

# -*- coding: utf-8 -*-

"""External sources of contexts."""

from typing import Any

from .api import Converter

__all__ = [


[docs] def get_obo_converter() -> Converter: """Get the latest OBO Foundry context. :returns: A converter object representing the OBO Foundry's JSON-LD context, which contains a simple mapping from OBO Foundry preferred prefixes for ontologies that contain case stylization (e.g., ``GO``, not ``go``; ``VariO``, not ``vario``). It does not include synonyms nor any non-ontology prefixes - e.g., it does not include semantic web prefixes like ``rdfs``, it does not include other useful biomedical prefixes like ``hgnc``. If you want a more comprehensive prefix map, consider using the Bioregistry via :func:`get_bioregistry_converter` or by chaining the OBO converter in front of the Bioregistry depending on your personal/project preferences using :func:`curies.chain`. Provenance: - This JSON-LD context is generated programmatically by - The file is accessed via from, which is configured through the OBO Foundry's PURL server with and ultimately points to """ # See configuration on # to see where this PURL points url = "" return Converter.from_jsonld(url)
[docs] def get_prefixcommons_converter(name: str) -> Converter: """Get a Prefix Commons-maintained context. :param name: The name of the JSON-LD file (e.g., ``monarch_context``). See the full list at :returns: A converter """ url = ( "" f"prefixcommons/registry/{name}.jsonld" ) return Converter.from_jsonld(url)
[docs] def get_monarch_converter() -> Converter: """Get the Prefix Commons-maintained Monarch context.""" return get_prefixcommons_converter("monarch_context")
[docs] def get_go_converter() -> Converter: """Get the Prefix Commons-maintained GO context.""" return get_prefixcommons_converter("go_context")
[docs] def get_bioregistry_converter(web: bool = False, **kwargs: Any) -> Converter: """Get the latest extended prefix map from the Bioregistry [hoyt2022]_. :param web: If false, tries to import :mod:`bioregistry` and use :func:`bioregistry.get_converter` to get the converter. Otherwise, falls back to using the GitHub-hosted EPM export. :param kwargs: Keyword arguments to pass to :meth`:curies.Converter.from_extended_prefix_map` when using web-based loading. :returns: A converter representing the Bioregistry, which includes a comprehensive collection of prefixes, prefix synonyms, and URI prefix synonyms. Short summary of the Bioregistry: 1. It deduplicates and harmonizes dozens of different resources that curate partially overlapping and conflicting prefix maps 2. It contains detailed CURIE prefix synonyms to support standardization 3. It enforces the generation of a self-consistent extended prefix map The Bioregistry's primary prefixes are all standardized to be lowercase, have minimal punctuation, and be the most idiomatic possible. When this conflicts with your personal preferences/community preferences, you can chain another converter in front of the Bioregistry converter using :func:`curies.chain`. However, the Bioregistry itself presents a more sustainable way of documenting these deviations in a community-oriented way using its "context" configurations. See for more information. One excellent example of a community context is for the OBO community (see, which prioritizes OBO capitalized prefixes and makes a few minor changes for backwards compatibility (e.g., renaming Orphanet). .. [hoyt2022] `Unifying the identification of biomedical entities with the Bioregistry <>`_ """ if not web: try: import bioregistry except ImportError: # pragma: no cover pass else: return bioregistry.manager.get_converter() # type:ignore url = f"{BIOREGISTRY_CONTEXTS}/bioregistry.epm.json" return Converter.from_extended_prefix_map(url, **kwargs)