BiolinkAligner

class BiolinkAligner(force_download: bool | None = None)

Bases: Aligner

Aligner for Biolink.

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 Biolink registry entries.
get_skip()	Get the skipped Biolink identifiers.
getter()	Get Biolink.
prepare_external(external_id, external_entry)	Prepare Biolink data to be added to the Biolink for each BioPortal registry entry.

Attributes Documentation

curation_header: ClassVar[Sequence[str]] = ['uri_format', 'identifiers', 'purl']

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

key: ClassVar[str] = 'biolink'

The key for the external registry

Methods Documentation

get_curation_row(external_id, external_entry) → Sequence[str]

Prepare curation rows for unaligned Biolink registry entries.

get_skip() → Mapping[str, str]

Get the skipped Biolink identifiers.

getter()

Get Biolink.

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

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