benchmarking-clinical-ner SKILL.md skillA
benchmarking-clinical-ner from maziyarpanahi/openmed is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add maziyarpanahi/openmed/benchmarking-clinical-ner@v1.0Pins v1.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- maziyarpanahi/openmed
- Path
skills/benchmarking-clinical-ner/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Jul 20, 2026
- Size
- 6,680 bytes
- Repository stars
- 5,784
- License
- Apache-2.0
Score an OpenMed clinical or biomedical NER model against a user-supplied gold corpus with entity-level precision, recall, and F1, then break errors down per label. Use when the user wants a seqeval-style scorecard, strict vs partial (relaxed) span matching, a per-label confusion matrix, false-negative / false-positive examples, or to debug why a model misses entities. Trigger on "evaluate NER", "entity-level F1", "seqeval", "precision recall F1", "confusion matrix", "error analysis…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Benchmarking Clinical NER
This skill produces an honest entity-level scorecard for an OpenMed NER model:
precision / recall / F1 plus a per-label error breakdown. It scores **spans**,
not tokens, because clinical entities are multi-token ("type 2 diabetes
mellitus") and token-level accuracy hides boundary errors. Reported numbers are
**entity-level** in the seqeval tradition (CoNLL-2000 / SemEval-2013 families).
## When to use this skill
- You have a gold-annotated clinical corpus and an OpenMed NER model to score.
- You want strict (exact-boundary) and partial (relaxed-overlap) span F1.
- You need per-label numbers, not one aggregate — DRUG recall ≠ DISEASE recall.
- You need to *explain* the errors: what was missed, what was spurious, what was
mislabeled.
For PHI de-id specifically, gate on leakage with `evaluating-with-leakage-gates`
instead of (or in addition to) F1.
## Match modes
| Mode | Counts a hit when… | Use for |
| --- | --- | --- |
| **Strict / exact** | predicted span boundaries **and** label match gold exactly | release scoring, boundary-sensitive tasks |
…Read the whole file at its exact version.
How to install
mdr add maziyarpanahi/openmed/benchmarking-clinical-ner@sha256:3b009e05549b3151The line at the top of this page pins the label v1.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_imglvik5jdlvm3g2)
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Versions
The registry has recorded 1 version of this file, committed on Jul 20, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (6680 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
maziyarpanahi/openmed · 5,784 stars · license Apache-2.0 · pushed 2026-11-07 · branch master
API
GET https://markdownregistry.com/api/v1/artifacts/art_imglvik5jdlvm3g2 GET https://markdownregistry.com/api/v1/resolve?ref=maziyarpanahi/openmed/benchmarking-clinical-ner GET https://markdownregistry.com/api/v1/blob/3b009e05549b315167fb41a54788bacc969545899fde98a7dd2a22944d6cc252
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.