BioContextAligner

class BioContextAligner(force_download: bool | None = None)

Bases: Aligner

Aligner for BioContext.

Instantiate the aligner.

Attributes Summary

curation_header	Header to put on the curation table, corresponding to get_curation_row()
key	The key for the external registry

Methods Summary

get_curation_row(external_id, external_entry)	Prepare curation rows for unaligned BioContext registry entries.
get_skip()	Get entries for BioContext that should be skipped.
getter()	Get the BioContext context map.
prepare_external(external_id, external_entry)	Prepare BioContext data to be added to the BioContext for each BioPortal registry entry.

Attributes Documentation

curation_header: ClassVar[Sequence[str]] = ['uri_format']

Header to put on the curation table, corresponding to get_curation_row()

key: ClassVar[str] = 'biocontext'

The key for the external registry

Methods Documentation

get_curation_row(external_id, external_entry) → Sequence[str]

Prepare curation rows for unaligned BioContext registry entries.

get_skip() → Mapping[str, str]

Get entries for BioContext that should be skipped.

getter() → Mapping[str, Mapping[str, Any]]

Get the BioContext context map.

Parameters:

force_download – If true, forces download. If false and the file is already cached, reuses it.

Returns:

The biocontext data dictionary

See also

https://github.com/prefixcommons/biocontext

prepare_external(external_id, external_entry) → Dict[str, Any]

Prepare BioContext data to be added to the BioContext for each BioPortal registry entry.