batch-processing-clinical-text SKILL.md skillA
batch-processing-clinical-text 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/batch-processing-clinical-text@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/batch-processing-clinical-text/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Jul 20, 2026
- Size
- 8,925 bytes
- Repository stars
- 5,784
- License
- Apache-2.0
Run large-scale batch NER, PII extraction, or de-identification over many clinical notes on-device with OpenMed, with sharding, checkpointing, resumability, and append-only JSONL output. Use when the user needs to process a corpus or folder of notes, de-identify a dataset, run NER over thousands of documents, build a resumable batch pipeline, or stream results to JSONL without holding everything in memory. Covers process_batch / BatchProcessor / BatchItem / BatchResult, the operation= selector…
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
# Batch processing clinical text
`openmed.processing` runs OpenMed over many documents efficiently, with progress
tracking, per-item error isolation, and streaming. It runs **fully on-device**:
the corpus, the model, and the output never leave the host. This skill shows a
**resumable** runner — sharded, checkpointed, append-only JSONL — that you can
restart without reprocessing.
## When to use this skill
For corpora, folders, or datasets — anything beyond a handful of notes. For a
single note, just call `openmed.analyze_text` / `deidentify` directly
(`extracting-clinical-entities`, `deidentifying-clinical-text`). For an
always-on HTTP service, see `serving-openmed-rest-api`.
## Quick start
```python
from openmed import process_batch
texts = ["Patient has type 2 diabetes.", "No acute distress. BP 120/80."]
result = process_batch(texts, model_name="disease_detection_superclinical")
print(result.summary()) # PHI-safe counts + timing
print(result.successful_items, "/", result.total_items)
for item in result.get_successful_results():
print(item.id, item.result.to_dict()["entities"]) # spans only; avoid raw text in logs
```
…Read the whole file at its exact version.
How to install
mdr add maziyarpanahi/openmed/batch-processing-clinical-text@sha256:39bbd95d26feba30The 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_f6fmodcptrbqz47t)
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Versions
The registry has recorded 1 version of this file, committed on Jul 20, 2026.
Audit of the latest version
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- pass: Frontmatter declares a description
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- 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
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- 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_f6fmodcptrbqz47t GET https://markdownregistry.com/api/v1/resolve?ref=maziyarpanahi/openmed/batch-processing-clinical-text GET https://markdownregistry.com/api/v1/blob/39bbd95d26feba307a8af5dd11f997f2fb28acc368cd164daa74af3532f2700c
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.