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).
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.
$ npx skills add maziyarpanahi/openmed --skill computing-ecqms -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install maziyarpanahi/openmed computing-ecqms --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ 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-srcUse ~/.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/
Install the "computing-ecqms" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/computing-ecqms into .claude/skills/computing-ecqms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "computing-ecqms", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/maziyarpanahi/openmed/tree/master/skills/computing-ecqmsType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add maziyarpanahi/openmed --skill computing-ecqms -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install maziyarpanahi/openmed computing-ecqms --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/computing-ecqms .agents/skills/computing-ecqms && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "computing-ecqms" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/computing-ecqms into .agents/skills/computing-ecqms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "computing-ecqms", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add maziyarpanahi/openmed --skill computing-ecqms -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install maziyarpanahi/openmed computing-ecqms --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/computing-ecqms .cursor/skills/computing-ecqms && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "computing-ecqms" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/computing-ecqms into .cursor/skills/computing-ecqms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "computing-ecqms", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/maziyarpanahi/openmed.git --path skills/computing-ecqms--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add maziyarpanahi/openmed --skill computing-ecqms -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install maziyarpanahi/openmed computing-ecqms --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/computing-ecqms .gemini/skills/computing-ecqms && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "computing-ecqms" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/computing-ecqms into .gemini/skills/computing-ecqms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "computing-ecqms", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install maziyarpanahi/openmed computing-ecqmsInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add maziyarpanahi/openmed --skill computing-ecqms -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/computing-ecqms .github/skills/computing-ecqms && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "computing-ecqms" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/computing-ecqms into .github/skills/computing-ecqms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "computing-ecqms", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add maziyarpanahi/openmed --skill computing-ecqms -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install maziyarpanahi/openmed computing-ecqms --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/computing-ecqms .opencode/skills/computing-ecqms && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "computing-ecqms" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/computing-ecqms into .opencode/skills/computing-ecqms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "computing-ecqms", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
computing-ecqmsCompute 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. 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.
7 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 252806a. It shows what the files ask for, not the result of running them.
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.
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.
Links to these hosts (documentation or services it may open):
ecqi.healthit.govcql.hl7.orgmadie.cms.govgithub.comFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
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.
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.
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.
The full file from maziyarpanahi/openmed at commit 252806a, republished under its Apache-2.0 licence (© maziyarpanahi). 609 words, ~1,593 tokens.
.claude/skills/computing-ecqms/SKILL.md (or your agent's skills folder).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 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.
| Population | Meaning | Where OpenMed helps |
|---|---|---|
| IPP (Initial Population) | everyone the measure could apply to | usually structured (encounters, age) |
| Denominator | IPP meeting base criteria | mostly structured |
| Denominator Exclusion / Exception | valid reasons to remove from denom | notes: "declined", "medical reason", "not indicated" |
| Numerator | met the quality action | notes: counseling delivered, advice given, status documented |
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.
openmed.deidentify on notes before any logging or
storage; keep the measure keyed by internal patient ids.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.Assessment, Performed, Intervention, Performed,
Diagnosis) with the right author/relevant dates
(building-patient-timelines).cqframework engine). OpenMed
does not execute CQL.analyze_text entities + clinical temporality + the
linking skills (to land facts in the measure's value sets) + deidentify
upstream.etl-to-omop-cdm
rows if you compute measures on an OMOP store instead.openmed/processing/ (analyze_text), openmed.clinical
(temporality).© 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
Just SKILL.md in skills/computing-ecqms of maziyarpanahi/openmed.
Open the folder on GitHubat commit 252806a
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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Computing Ecqms this skillmaziyarpanahi/openmed | 5.5k | — | ~1.6k | Automated safety check: Pass | Apache-2.0 | |
| Pxmeterbytedance/PXMeter | 102 | — | ~3.4k | Automated safety check: Pass | Apache-2.0 | |
| Readout Handicaphh-health-AI/healthcare-equity | 101 | — | ~555 | Automated safety check: Pass | MIT | |
| Clinical Trials Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.2k | Automated safety check: Pass | Apache-2.0 | |
| CHARLS Paper Reproduction Guidexjtulyc/MedgeClaw | 617 | 1 repos | ~1.8k | Automated safety check: Pass | None | |
| Model AssessmentAperivue/medsci-skills | 329 | 1 repos | ~4.5k | Automated safety check: Pass | MIT |
bytedance/PXMeter
Used to invoke the PXMeter tool for rigorous quality assessment of biomolecular structure prediction models (e.g., proteins, nucleic acids, small molecules).
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…
google-deepmind/science-skills
Query ClinicalTrials.gov via APIv2. An agent skill from google-deepmind/science-skills.
xjtulyc/MedgeClaw
Guides an agent through reproducing papers built on the CHARLS health and retirement survey, from variable mapping to cognition, depression and isolation scores.
Aperivue/medsci-skills
A skill your agent uses when validating or evaluating a trained medical-imaging model.
xjtulyc/MedgeClaw
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.
maziyarpanahi/openmed
Checks OpenMed de-identified clinical text against the 18 HIPAA Safe Harbor identifier categories and reports gaps and residual re-identification risk.
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.
maziyarpanahi/openmed
Walks a data pipeline against the HIPAA Privacy and Security Rule checklist and produces a gap report before it processes patient data.
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.
maziyarpanahi/openmed
Maps OpenMed-extracted, terminology-coded conditions, drugs and measurements into OMOP CDM v5.4 tables for OHDSI and ATLAS analytics.
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.
Categories
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.
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.
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.
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.
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.
SKILL.md names no scripts, command-line tools or credentials: Computing Ecqms is instructions for the agent only. Our summary lists: Python 3.
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.
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.
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.
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.
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.
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.