Pathology result profile¶

openmed.clinical.pathology_profile provides a small, deterministic contract for explicitly reported pathology fields. It extracts specimen, diagnosis, grade, and reported biomarker name/result pairs from labelled fields or supported report sections.

The profile is intentionally conservative. It does not infer a diagnosis, derive a grade, interpret a positive or negative biomarker, calculate stage, normalize terminology, or make a treatment recommendation. It is not a diagnostic decision engine and requires pathologist or clinician review.

Python API¶

from openmed.clinical import extract_pathology_result

result = extract_pathology_result(
    """SPECIMEN: Synthetic core biopsy
FINAL DIAGNOSIS: Explicitly reported lesion
HISTOLOGIC GRADE: 2 of 3
BIOMARKERS:
ER: positive
HER2 (IHC): 0 (negative)
"""
)

The result contains four lists and a fixed advisory string:

result["specimen"]      # [{"value": ..., "span": {"start": ..., "end": ...}}]
result["diagnosis"]     # same span-linked field shape
result["grade"]         # explicitly reported grades only
result["biomarkers"]    # name/result plus name_span, result_span, and span

Values are kept in source order. A field is empty when it is absent or not explicitly reported; an empty list never means that a negative result was inferred. Every span is half-open and indexes the exact input string, so a caller can display evidence from a protected source buffer without storing the whole document in the result.

Supported section headings include SPECIMEN, FINAL DIAGNOSIS, HISTOLOGIC GRADE, GLEASON SCORE, BIOMARKERS, IMMUNOHISTOCHEMISTRY, and MOLECULAR RESULTS. Labelled forms such as Diagnosis: ... and Grade: ... are also accepted. Biomarker results are copied as reported; strings such as positive, negative, CPS 10, and not detected are not clinically interpreted.

Privacy and offline behavior¶

The parser imports no model, terminology package, or network client and makes no mandatory network call. It returns only the selected structured values, offsets, and advisory text. It does not return the source document, patient metadata, accession identifiers, or logging payloads. Use synthetic fixtures for tests and keep the caller-owned source buffer under the caller's privacy controls.

This profile is assistive extraction only. It does not provide a compliance certification, diagnostic guarantee, or clinical decision support.