parse_bioc_json()

Build documents from BioC JSON: a collection, a list of collections, or a PubTator3 export.

Usage

Source

parse_bioc_json(
    content,
    *,
    verify="raise",
    offset_unit="utf8",
    label_key="type",
    concept_keys=("identifier",)
)

Parameters

content: str

The JSON text.

verify: Verify = "raise"

Check every annotation’s stored text against its offsets: "raise" an IntegrityError on mismatch, "warn", or "off".

offset_unit: OffsetUnit = "utf8"

The unit offsets count in. The BioC specification says UTF-8 bytes.

label_key: str = "type"

The annotation infon holding the label.

concept_keys: Sequence[str] = ("identifier",)

Annotation infons holding concept identifiers (kept verbatim).