D011 患者时间线构建｜个人思维图谱小站

正文

SKILL.md

v0.2.1 发布合同（优先于历史版本说明）

保留relative时间元数据，缺绝对锚点留在未定时间；人工时间决策也不得顺便丢relative metadata。既有UTC/精度/anchor完整性检查保留。

详见 references/repair-v0.2.1.md。完整替换D001–D014并重新生成中间产物，不混用历史伪ID、清单或staging编号。测试通过不表示临床生产批准。

v0.2.0 修复合同（优先于旧版说明）

日期/时区用真实日历与 UTC 时间比较；未给时区不补 UTC。保留结束时间、文档时间及原始结束值。相对时间需要存在、同患者、同包的已解析 anchor，以及 offset_days/elapsed_days 约定。人工改时间不得顺便改变其他医学字段。

具体运行界限见 references/repair-v0.2.md；任何自测通过都不等于临床生产批准。

Mission

D011 converts D010 CanonicalClinicalFact objects into longitudinal patient timelines.

It answers:

When did this clinical event occur?
How precise is that time?
Is the event occurred, planned, or still undated?
Does a relative expression have a valid anchor?
Can state transitions be ordered without contradiction?
Which events share a calendar bucket but have no defensible within-bucket order?

D011 does not change diagnosis, medication, measurement, or problem semantics.

Required input

A finalized D010 clinical_fact_merger_manifest.json with:

overall_status = ready_for_timeline

The manifest must reference:

canonical_clinical_facts.jsonl
clinical_fact_relations.jsonl

D011 never reads pre-D003 raw patient sources.

Time model

Every timeline event keeps:

event_time != document_time

and never upgrades time precision without evidence.

Supported precision:

minute
hour
day
month
year
unknown

Examples:

2019           -> precision=year
2026-03        -> precision=month
2026-03-12     -> precision=day
2026-03-12T09:30:00+08:00 -> precision=minute

D011 may compute hidden lower/upper sort bounds for coarse time, but it must not rewrite:

2019 -> 2019-01-01

as if the source had day precision.

Time source hierarchy

D011 records the source of every resolved time:

structured_event_time
explicit_text_time
relative_time_resolved
upstream_event_candidate
document_time_approved
agent_review
unresolved

The hierarchy is evidence guidance, not a universal overwrite rule.

Relative time rule

Relative expressions such as:

昨日
2天前
入院后第2天
术后第3天

must not be resolved without a defensible anchor.

If the anchor is not already explicit in D010, Codex may write a text-free decision to agent_time_decisions.jsonl:

{
  "canonical_fact_id": "cf_x",
  "decision": "resolve",
  "normalized_start": "2026-03-14",
  "normalized_end": "2026-03-14",
  "precision": "day",
  "time_source": "relative_time_resolved",
  "anchor_fact_id": "cf_admission",
  "reason_codes": ["relative_to_confirmed_admission_date"]
}

Do not copy clinical prose into this file.

Lanes

Every final timeline event is assigned to exactly one lane:

occurred
planned
undated

planned is based on explicit future/planned semantics, not on a date merely being later than today's date.

Historical events with unknown dates belong in undated with historical assertion retained.

Same-day ordering

Two date-only events on the same day are not given a clinical order just because a deterministic file order is required.

D011 records:

within_bucket_order = unordered
order_confidence = low

The output row may still have a stable display index based on IDs.

State-transition ordering

For D010 relations of:

state_transition
superseding

D011 validates direction only when both endpoints have enough time evidence.

If an allegedly later state is earlier than the prior state, the relation goes to review and is not silently reordered.

Workflow

1. Prepare

python "$SKILL_DIR/scripts/prepare_timeline.py" \
  --d010-manifest /path/to/d010/clinical_fact_merger_manifest.json \
  --output-root ./runs/haonan-d011

Outputs:

timeline_event_drafts.jsonl
timeline_relation_drafts.jsonl
time_review_queue.csv
agent_time_decisions.jsonl
agent_time_completion.json
patient_timeline_manifest.json

2. Review unresolved time only by ID

Codex may edit:

agent_time_decisions.jsonl
agent_time_completion.json

The decision file contains IDs, normalized dates/times, enum values and reason codes only.

3. Finalize

python "$SKILL_DIR/scripts/finalize_timeline.py" \
  --run-dir /path/to/d011/<package-id>