building-patient-timelines

Build chronological patient timelines from extracted clinical events with normalized dates.

5.0k|615|Updated Oct 4, 2025
One-click install
npx skills add https://github.com/maziyarpanahi/openmed --skill building-patient-timelines
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: building-patient-timelines
Source: https://github.com/maziyarpanahi/openmed/tree/main/skills/building-patient-timelines
Command: npx skills add https://github.com/maziyarpanahi/openmed --skill building-patient-timelines

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill transforms extracted clinical events from one or more notes into a chronological patient history, resolving absolute and relative dates while preserving uncertainty and date granularity.

Core Features & Use Cases

  • Temporal Normalization: Resolve dates such as 2024-03-08, March 2019, yesterday, and two days after admission using reliable document or encounter anchors.
  • Clinical Event Modeling: Build records for diagnoses, medications, procedures, and encounters with labels, source spans, confidence, temporality, and note identifiers.
  • Timeline Quality Controls: Exclude negated, hypothetical, and family-history mentions, preserve undated events for review, separate planned events, and de-duplicate repeated mentions.
  • Interop Preparation: Produce sorted event lists suitable for charting, FHIR export, OMOP transformation, and clinical-summary cards.

Quick Start

Use this Skill to convert OpenMed analyze_text results from a de-identified clinical note into a sorted patient timeline anchored to the document or admission date.

Frequently Asked Questions about building-patient-timelines

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert clinical notes into a chronological patient timeline?

This Skill builds chronological patient timelines from extracted clinical events by normalizing absolute and relative dates against reliable document or encounter anchors. It resolves temporal references like 'yesterday' or 'two days after admission' while preserving date granularity and uncertainty.

How does temporal normalization handle relative dates in clinical events?

Temporal normalization resolves relative dates like 'yesterday' or 'two days after admission' by anchoring them to reliable document or encounter dates. This ensures accurate chronological sorting while preserving date granularity, tracking confidence, and maintaining original source spans.

Does this timeline generation tool support FHIR export and OMOP transformation?

Yes, this tool produces sorted clinical event lists suitable for FHIR export and OMOP transformation. It models encounters, diagnoses, and procedures with labels and note identifiers, preparing the chronological output for direct integration into interoperability workflows.

What is the best way to exclude negated or hypothetical mentions when building longitudinal histories?

The best way to handle ambiguous or undated events is by using timeline quality controls that safely preserve them for review. The Skill excludes negated, hypothetical, and family-history mentions while de-duplicating repeated entries and separating planned events.

Can I use extracted clinical events from de-identified notes for pre-FHIR charting feeds?

Yes, this Skill processes extracted clinical events from de-identified notes into sorted patient histories suitable for pre-FHIR charting feeds. It applies temporality filtering, tracks confidence and source spans, and separates planned events for accurate encounter summaries.