reconciling-problem-lists

Reconciling problem lists

A single note mentions the same condition many ways — "DM2," "type 2 diabetes," "diabetes mellitus" — across PMH, HPI, and A&P, some negated, some historical. A usable problem list collapses those mentions into one concept per problem, drops what the patient does not have, and assigns a clinical status (active / resolved / historical). This skill turns OpenMed's per-mention entity stream plus ConText axes into that reconciled, de-duplicated list, shaped for USCDI "Problem" exchange.

When to use

• After extracting-clinical-entities and resolving-clinical-context, when the user wants a clean problem list, condition reconciliation, or dedup of repeated diagnosis mentions.
• You need active-vs-resolved-vs-historical status per problem, not just raw mentions.
• You are assembling a FHIR Condition list or a USCDI Problem element and need one entry per concept.

Quick start

import openmed
from openmed.clinical import resolve_span_context, NEGATED, HISTORICAL, HYPOTHETICAL

note = ("PMH: type 2 diabetes, prior MI 2019 (resolved). "
        "A&P: poorly controlled DM2; denies chest pain.")

ents = openmed.analyze_text(note, model_name="disease_detection_superclinical",
                            output_format="dict")

def normalize(surface: str) -> str:
    # Cheap synonym folding; replace with SNOMED grounding (out-of-process).
    s = surface.lower().strip()
    return {"dm2": "type 2 diabetes", "diabetes mellitus": "type 2 diabetes"}.get(s, s)

problems = {}  # concept -> reconciled record
for e in ents:
    surface = e["word"]
    ctx = resolve_span_context(surface, note)
    if ctx.negation == NEGATED:
        continue                                   # patient does NOT have it -> exclude
    concept = normalize(surface)
    status = ("resolved" if ctx.temporality == HISTORICAL else
              "active")
    if ctx.temporality == HYPOTHETICAL:
        continue                                   # not asserted as present
    rec = problems.setdefault(concept, {"concept": concept, "status": status,
                                        "mentions": 0})
    rec["mentions"] += 1
    # Active anywhere wins over a historical mention of the same concept.
    if status == "active":
        rec["status"] = "active"

problem_list = list(problems.values())
# -> [{"concept": "type 2 diabetes", "status": "active", "mentions": 2}, ...]
# "chest pain" excluded (negated); "MI" -> historical/resolved.