Agent skill

Computing Ecqms

by maziyarpanahi in maziyarpanahi/openmed

Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived numerator and exclusion facts from OpenMed to improve measure capture.

Apache-2.0Auto-check passedResearch & Science

Install Computing Ecqms

skills CLI
$ npx skills add maziyarpanahi/openmed --skill computing-ecqms -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install maziyarpanahi/openmed computing-ecqms --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/computing-ecqms .claude/skills/computing-ecqms && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
computing-ecqms
GitHub stars
5.5k
Token cost
~1.6k tokens
SKILL.md length
609 words
Files
1
Skills in repo
74
Repo updated
First seen
Licence
Apache-2.0

At a glance

Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived numerator and exclusion facts from OpenMed to improve measure capture.

  • Works in 7 steps: Read the measure. Get the human-readable… → De-identify. Run openmed.deidentify on… → Extract facts. openmed.analyze_text for… → …
  • The user wants to compute an eCQM
  • SKILL.md covers When to use this skill, eCQM anatomy (what you're…, Quick start and Workflow, plus 3 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Computing Ecqms is an agent skill from maziyarpanahi/openmed. Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived numerator and exclusion facts from OpenMed to improve measure capture. Use when the user wants to compute an eCQM, evaluate a CMS/ECQI quality measure, improve numerator capture from clinical notes, build CQL/QDM measure logic, or close documentation gaps that structured codes miss. Covers eCQM structure (IPP/denominator/numerator/exclusions), CQL v1.5 and QDM v5.6, MADiE authoring, and mapping…

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Clinical and healthcare research and Schema markup. The repository describes itself as: Local-first healthcare AI: clinical NER & HIPAA PII de-identification that runs 100% on-device. 2,200+ medical models, 21 languages, Apple MLX + Python, no cloud, no patient data…. The licence is Apache-2.0.

When your agent uses it

  • The user wants to compute an eCQM
  • Evaluate a CMS/ECQI quality measure
  • Improve numerator capture from clinical notes
  • Build CQL/QDM measure logic

Example prompts

  • “/computing-ecqms”

Requirements

  • Python 3

Workflow steps

7 steps, taken from the first numbered list in SKILL.md.

  1. Read the measure. Get the human-readable spec + CQL + value sets from
  2. De-identify. Run openmed.deidentify on notes before any logging or
  3. Extract facts. openmed.analyze_text for the concepts the measure needs
  4. Code to value sets. Map entities to the codes the measure's value sets
  5. Materialize QDM data elements. Turn coded, dated facts into QDM elements
  6. Compute with CQL. Feed the structured + note-derived QDM into a
  7. Reconcile & audit. Track which population members were added by

What it can do on your machine

Read from SKILL.md and the folder at commit 252806a. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are python).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • ecqi.healthit.gov
    • cql.hl7.org
    • madie.cms.gov
    • github.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Computing Ecqms loads about 1.6k tokens when it runs. Until then it costs about 179 tokens; SKILL.md has 609 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~179
When it runs · the whole SKILL.md, loaded when a task matches
~1.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from maziyarpanahi/openmed at commit 252806a, republished under its Apache-2.0 licence (© maziyarpanahi). 609 words, ~1,593 tokens.

Download SKILL.mdSave it as .claude/skills/computing-ecqms/SKILL.md (or your agent's skills folder).
name
computing-ecqms
description
Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived numerator and exclusion facts from OpenMed to improve measure capture. Use when the user wants to compute an eCQM, evaluate a CMS/ECQI quality measure, improve numerator capture from clinical notes, build CQL/QDM measure logic, or close documentation gaps that structured codes miss. Covers eCQM structure (IPP/denominator/numerator/exclusions), CQL v1.5 and QDM v5.6, MADiE authoring, and mapping OpenMed entities to QDM data elements. Consumes OpenMed analyze_text facts (coded via the linking skills) to supplement structured EHR data; does not replace certified measure engines.
license
Apache-2.0
metadata.project
OpenMed
metadata.category
analytics-reporting
metadata.pairs
after
metadata.version
1.0

Computing eCQMs

Electronic Clinical Quality Measures (eCQMs) are computed over structured data using CQL (Clinical Quality Language) logic against the QDM (Quality Data Model). Much of what a measure needs — a counseling note, a reason a service wasn't done, a symptom — lives only in free text. This skill uses OpenMed to lift those facts out of notes (on-device) and feed them into measure computation so numerators and valid exclusions aren't undercounted.

When to use this skill

When structured codes under-capture a measure population and the evidence is in notes: documented exclusions ("patient declined screening"), numerator-relevant findings, or symptoms gating a measure. Use it alongside a certified measure engine — OpenMed supplements capture; it does not compute or certify the measure.

eCQM anatomy (what you're populating)

PopulationMeaningWhere OpenMed helps
IPP (Initial Population)everyone the measure could apply tousually structured (encounters, age)
DenominatorIPP meeting base criteriamostly structured
Denominator Exclusion / Exceptionvalid reasons to remove from denomnotes: "declined", "medical reason", "not indicated"
Numeratormet the quality actionnotes: counseling delivered, advice given, status documented

Quick start

python
import openmed

note = (
    "Tobacco use screened today; patient is a current every-day smoker. "
    "Cessation counseling provided and cessation medication offered."
)

result = openmed.analyze_text(note, output_format="dict")
# entities -> {text, label, confidence, start, end}

# Lift two measure-relevant facts (illustrative, for a tobacco-screening eCQM):
facts = {
    "tobacco_status_documented": any(e["label"] in {"smoking_status", "tobacco_use"}
                                     for e in result["entities"]),
    "cessation_intervention_documented": "counseling" in note.lower(),
}
# These become QDM data elements your CQL references (see workflow).

Pick the model whose labels match the measure concept (choosing-openmed-models) and code spans to value-set vocabularies via the linking skills before they enter QDM.

Workflow

  1. Read the measure. Get the human-readable spec + CQL + value sets from ECQI / MADiE. Identify which populations depend on documentation that structured data misses.
  2. De-identify. Run openmed.deidentify on notes before any logging or storage; keep the measure keyed by internal patient ids.
  3. Extract facts. openmed.analyze_text for the concepts the measure needs (status, intervention, reason-not-done). Use resolving-clinical-context to drop negated/hypothetical/family-history mentions — a negated exclusion is not an exclusion.
  4. Code to value sets. Map entities to the codes the measure's value sets expect (SNOMED/LOINC/RxNorm via the linking skills). QDM data elements are defined by code membership, not raw strings.
  5. Materialize QDM data elements. Turn coded, dated facts into QDM elements (e.g. Assessment, Performed, Intervention, Performed, Diagnosis) with the right author/relevant dates (building-patient-timelines).
  6. Compute with CQL. Feed the structured + note-derived QDM into a certified CQL engine (e.g. the open-source cqframework engine). OpenMed does not execute CQL.
  7. Reconcile & audit. Track which population members were added by note-derived facts and at what confidence, so QA can review.
Show full SKILL.md (238 more words)Show less

Hand-off to / from OpenMed

  • From OpenMed: analyze_text entities + clinical temporality + the linking skills (to land facts in the measure's value sets) + deidentify upstream.
  • To measure tooling: materialized QDM data elements feed a CQL engine and MADiE test decks. Note-derived QDM can also originate from etl-to-omop-cdm rows if you compute measures on an OMOP store instead.

Edge cases & gotchas

  • OpenMed supplements, it does not certify. Measure scoring must run in a validated CQL engine. Treat note-derived facts as additional evidence subject to review, not as authoritative measure results.
  • Negation flips meaning. "Screening declined" is an exclusion; "screening not declined" / "no contraindication" is the opposite. Always run the temporality/negation pass before counting.
  • Dates drive measurement periods. A fact only counts if its relevant date falls in the measurement period. Resolve dates first; undated facts can't be placed.
  • Value-set membership, not keywords. A QDM data element is defined by codes in the measure's value set. Map entities to those codes — don't match on the surface word.
  • No restricted terminology bundling. SNOMED/LOINC/RxNorm content stays out-of-process under your own license; OpenMed provides spans/labels only.
  • No raw PHI in logs or audit. Record measure provenance by offset, label, confidence, and internal id.

Standards & references

© maziyarpanahi, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/computing-ecqms of maziyarpanahi/openmed.

Open the folder on GitHubat commit 252806a

Compare with similar skills

Computing Ecqms next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Computing Ecqms compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Computing Ecqms this skillmaziyarpanahi/openmed5.5k—~1.6kAutomated safety check: PassApache-2.0
Pxmeterbytedance/PXMeter102—~3.4kAutomated safety check: PassApache-2.0
Readout Handicaphh-health-AI/healthcare-equity101—~555Automated safety check: PassMIT
Clinical Trials Databasegoogle-deepmind/science-skills3.2k2 repos~3.2kAutomated safety check: PassApache-2.0
CHARLS Paper Reproduction Guidexjtulyc/MedgeClaw6171 repos~1.8kAutomated safety check: PassNone
Model AssessmentAperivue/medsci-skills3291 repos~4.5kAutomated safety check: PassMIT

Similar skills

  • Pxmeter

    bytedance/PXMeter

    Used to invoke the PXMeter tool for rigorous quality assessment of biomolecular structure prediction models (e.g., proteins, nucleic acids, small molecules).

    102 GitHub stars~3.4k tokensUpdated 2 mo ago
    Research & ScienceAuto-check passed
  • Readout Handicap

    hh-health-AI/healthcare-equity

    This skill should be used when the user says "handicap this readout", "pre-mortem the Phase 3", "what are the odds this trial works", "assess the trial design for [TICKER]", or before any binary…

    101 GitHub stars~555 tokensUpdated 2 days ago
    Research & ScienceAuto-check passed
  • Clinical Trials Database

    google-deepmind/science-skills

    Query ClinicalTrials.gov via APIv2. An agent skill from google-deepmind/science-skills.

    3.2k GitHub starsUsed in 2 repos~3.2k tokens
    Research & ScienceAuto-check passed
  • Guides an agent through reproducing papers built on the CHARLS health and retirement survey, from variable mapping to cognition, depression and isolation scores.

    617 GitHub starsUsed in 1 repo~1.8k tokens
    Research & ScienceAuto-check passed
  • Model Assessment

    Aperivue/medsci-skills

    A skill your agent uses when validating or evaluating a trained medical-imaging model.

    329 GitHub starsUsed in 1 repo~4.5k tokens
    Research & ScienceAuto-check passed
  • Routes bioinformatics, drug discovery, clinical and multi-omics tasks from a chat interface to Claude Code sessions running K-Dense scientific skills, with a live dashboard per task.

    617 GitHub starsUsed in 1 repo~2k tokens
    Research & ScienceAuto-check passed

More from maziyarpanahi/openmed

All 74 skills in this repo
  • Checks OpenMed de-identified clinical text against the 18 HIPAA Safe Harbor identifier categories and reports gaps and residual re-identification risk.

    5.5k GitHub stars~1.7k tokensUpdated yesterday
    Auto-check passed
  • OpenMed Model Card Writer

    maziyarpanahi/openmed

    Fills in a model card for an OpenMed clinical NER or de-identification model from its evaluation reports: intended use, metrics, subgroups and limitations.

    5.5k GitHub stars~1.8k tokensUpdated yesterday
    Auto-check passed
  • Walks a data pipeline against the HIPAA Privacy and Security Rule checklist and produces a gap report before it processes patient data.

    5.5k GitHub stars~2k tokensUpdated yesterday
    Auto-check passed
  • ICD-10 Coding Assistant

    maziyarpanahi/openmed

    Suggests candidate ICD-10-CM diagnosis and ICD-10-PCS procedure codes for clinical text extracted by OpenMed, with rationale for a certified coder to review.

    5.5k GitHub stars~2k tokensUpdated yesterday
    Auto-check passed
  • OpenMed ETL to OMOP CDM

    maziyarpanahi/openmed

    Maps OpenMed-extracted, terminology-coded conditions, drugs and measurements into OMOP CDM v5.4 tables for OHDSI and ATLAS analytics.

    5.5k GitHub stars~1.9k tokensUpdated yesterday
    Auto-check passed
  • Extracting SDOH and Z-Codes

    maziyarpanahi/openmed

    Finds social risks such as housing instability or food insecurity in clinical notes and proposes matching ICD-10-CM Z-codes for a coder to confirm.

    5.5k GitHub stars~1.9k tokensUpdated yesterday
    Auto-check passed

Questions about Computing Ecqms

What does Computing Ecqms do?

Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived numerator and exclusion facts from OpenMed to improve measure capture. Computing Ecqms is an agent skill from maziyarpanahi/openmed. Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived numerator and exclusion facts from OpenMed to improve measure capture.

When should I use Computing Ecqms?

Computing Ecqms fits situations like: the user wants to compute an eCQM; evaluate a CMS/ECQI quality measure; improve numerator capture from clinical notes; build CQL/QDM measure logic.

How do I install Computing Ecqms in Claude Code?

Run `npx skills add maziyarpanahi/openmed --skill computing-ecqms -a claude-code`. Or copy the skill folder (skills/computing-ecqms in maziyarpanahi/openmed) into .claude/skills/computing-ecqms in your project. Claude Code loads it when a task matches its description.

How do I install Computing Ecqms in Codex?

Run `npx skills add maziyarpanahi/openmed --skill computing-ecqms -a codex`. Or copy the skill folder (skills/computing-ecqms in maziyarpanahi/openmed) into .agents/skills/computing-ecqms in your project. Codex loads it when a task matches its description.

Can I use Computing Ecqms in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add maziyarpanahi/openmed --skill computing-ecqms -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/computing-ecqms, .gemini/skills/computing-ecqms, .github/skills/computing-ecqms and .opencode/skills/computing-ecqms in your project.

What does Computing Ecqms need to run?

SKILL.md names no scripts, command-line tools or credentials: Computing Ecqms is instructions for the agent only. Our summary lists: Python 3.

Does Computing Ecqms access the network?

SKILL.md names 4 domains. As links in the text: ecqi.healthit.gov, cql.hl7.org, madie.cms.gov and github.com. This is read from the text; nothing was executed.

Is Computing Ecqms safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Computing Ecqms use?

Computing Ecqms is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Computing Ecqms use?

About 1.6k tokens (SKILL.md is roughly 6.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Computing Ecqms?

Skills that share tags, products or a category with Computing Ecqms: Pxmeter (bytedance/PXMeter, 102 stars), Readout Handicap (hh-health-AI/healthcare-equity, 101 stars), Clinical Trials Database (google-deepmind/science-skills, 3.2k stars) and CHARLS Paper Reproduction Guide (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Computing Ecqms?

maziyarpanahi (a GitHub user) maintains it in maziyarpanahi/openmed, which has 5,452 GitHub stars. The repository holds 74 skills in this directory. The repository was last updated on October 6, 2026.

Source: maziyarpanahi/openmed on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.