Clinic Protocol Cds

Clinic Protocol Decision-Support Skill

This skill turns a clinical case-task prompt into one JSON object that conforms exactly to the answer_template.json contract supplied with the task. It does not invent clinical facts: every populated value is grounded in data read from the clinic runtime, and every field shape matches the template.

When to use

A task matches this skill when it has all of:

• A case id named in the prompt (e.g. CASE-…-…).
• A runtime environment reachable over HTTP, described by an environment_access.md file (base URL + allowed endpoints + any auth header).
• An answer_template.json that defines the required top-level keys, field types, enums, null rules, numeric precision, and list ordering rules.
• An instruction to return only a single JSON object (no markdown, no prose).

If any of these are missing, stop and report what is missing before proceeding.

Inputs you must read first

1. The task prompt.txt — gives the case id and lists which clinical dimensions the answer must cover.
2. input/payloads/answer_template.json — the contract. This is the source of truth for every field. Read it end to end before fetching anything.
3. environment_access.md — base URL, allowed endpoints, and the auth header required for protected endpoints. Treat the base URL as a placeholder (<TASK_ENV_BASE_URL>); substitute the real base URL from this file.

Do not read or rely on any train_answers/ material. Those are grading references for a different purpose and are out of scope for producing a new answer. Do not copy case-specific values (patient ids, medication names, doses, lab values, observation ids) from anywhere other than the live runtime.

Procedure

1. Parse the contract

From answer_template.json, extract and keep a working checklist of:

• Required top-level keys (in order). The output must contain exactly these keys unless the template explicitly says extra keys are ignored.
• Constant fields — some templates pin task_id and case_id to fixed values (e.g. expected_constant / required_value). Use the constant verbatim; do not recompute it.
• Enums — list the allowed values for every enum field. Output values must match an allowed value character-for-character. Watch for underscores vs spaces, and singular vs plural.
• Null rules — for each field note whether null is permitted (string_or_null, integer_or_null, [type, null], nullable: true). Use null only where explicitly allowed; otherwise populate with a real value.
• Numeric precision — e.g. "one decimal place", "two decimal places", "whole hours". Round/format the final number to that precision.
• List ordering — three kinds appear:
  • "No semantic ordering" → order does not matter (evaluator normalizes as a set). Still emit each value at most once unless duplicates are allowed.
  • Explicit ordering rule (e.g. "case identifier first", "sort by effective_time ascending then observation_id ascending") → apply it exactly.
  • "use an empty list when none" → emit [], never omit the key.
• Conditional presence — e.g. required_when: "lab_found is true" → include the sub-object only when the condition holds; otherwise use null if the field is nullable, or omit per the template.

See references/conformance_checklist.md for the full validation pass.

2. Resolve the case

Using the base URL and allowed endpoints from environment_access.md:

1. GET /api/cases/{case_id} (or locate it via GET /api/cases then filter) to fetch the case bundle. The bundle is the primary evidence source and typically nests: case, findings, allergies, medications, problems, observations, imaging, care_registry, sdoh.
2. Read case.patient_id from the bundle — this is the patient_id to put in the answer (never guess one).
3. Note the case_type; it maps to the protocol you need next.

The runtime also contains many distractor records (synthetic, marked as a "generated distractor feed" or with ids like CASE-D…, PAT-D…, OBS-D…). Scope every query to the target case id / patient id so distractors do not leak into your evidence.

3. Fetch supporting resources

Pull only the resources that the template's fields require, scoped to the target case/patient. Available GET endpoints (confirm against environment_access.md, since the allowed list is run-specific):

• /api/patients/{patient_id} — demographics, identifiers.
• /api/observations — lab and vital Observation resources (filter by patient_id/case_id, code, status, effective_time).
• /api/medications, /api/allergies, /api/problems — current meds, allergy list (note status: active vs inactive), problem list.
• /api/imaging — imaging studies and reads.
• /api/care-registry, /api/sdoh — care-management registry and social determinants.
• /api/protocols and /api/protocols/{protocol_id} — the decision rules.

Resource shapes are documented in references/runtime_api.md.

4. Use the query endpoint for filtered retrieval

POST /api/query runs a SQL-style read query and is the right tool when you need to filter across many resources (e.g. "all final potassium observations for this patient in this time window"). It requires the header from environment_access.md (e.g. X-Clinic-Token: …) and a JSON body of the form:

{ "sql": "select ... from <table> where <col> = ?", "params": ["..."] }

Response: { "columns": [...], "rows": [...], "count": N, "truncated": bool }. Never write/mutate (update/insert/delete) — these tasks are read-only. If truncated is true, narrow the filter rather than paging blindly.

5. Load the matching protocol

GET /api/protocols lists protocols by id/title; pick the one whose scope covers the case_type, then GET /api/protocols/{protocol_id} for the full body. The protocol body is structured, not prose — it holds the decision thresholds, escalation rules, controlled code mappings, follow-up timing, and red-flag definitions that drive the answer. Apply its rules literally:

• Compare numeric findings to the protocol's thresholds (e.g. oxygen saturation < a value, respiratory rate >= a value) to derive risk tier, disposition, and escalation.
• Use the protocol's controlled_codes / code mappings to translate clinical concepts into the exact enum/code strings the template expects.
• Copy follow-up timing, return-precaution codes, and gate definitions from the protocol rather than from general knowledge.

6. Populate each field

For every required top-level key, fill the value from runtime evidence + protocol rules. Keep these disciplines:

• Evidence ids: list real resource ids you actually read (case id, observation ids, imaging ids, protocol id, visit/encounter source ids). Apply the template's ordering rule. Never fabricate ids.
• Safety-check booleans: these assert you did not make an unsupported claim (e.g. no_penicillin_or_sulfa is true only when the medication plan avoids those classes; no_normal_cxr_claim is true only when you did not assert a normal chest x-ray). Set each from the actual content of your answer, not by default.
• Allergy-aware medication plans: cross-check the chosen medication class against the patient's active allergies (inactive allergies do not bind) and populate avoid_allergens accordingly.
• Window/lab-gate tasks: when the task is about an observation time window, enumerate the candidate observations for the patient, partition them into matched (correct code + final status + inside window) vs excluded (wrong code, wrong status, or outside window), sort each list per the template rule, and derive the protocol gate from the latest matched final value.

7. Conformance-check before returning

Run the validation pass in references/conformance_checklist.md against your draft. Fix any violation. Then return exactly one JSON object — no markdown fences, no commentary, no trailing text. If the task says "Return only a JSON object", the entire response body is that object.

What never to do

• Do not copy case-specific values (patient ids, medication names/doses, lab numbers, observation ids) from training/answer material or from memory — only from the live runtime for the current case.
• Do not add top-level keys the template did not list (unless it explicitly says extra keys are ignored).
• Do not use an enum value that is not in the template's allowed_values.
• Do not use null where the template forbids it, or omit a required key.
• Do not mutate the runtime or place orders.
• Do not include narrative prose, markdown, or explanations in the final output.

Files in this skill

• SKILL.md — this entry procedure.
• references/runtime_api.md — the clinic runtime API contract: endpoints, auth, query DSL, and resource shapes.
• references/conformance_checklist.md — the output validation pass to run against answer_template.json before returning.