extracting-lab-tables SKILL.md skillA
extracting-lab-tables 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/extracting-lab-tables@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/extracting-lab-tables/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Jul 20, 2026
- Size
- 8,431 bytes
- Repository stars
- 5,784
- License
- Apache-2.0
Detects and extracts tabular laboratory panels from PDFs, scans, and images into structured rows ready for OpenMed and FHIR. Use when the user has a CBC, CMP, lipid panel, or other lab report as a scanned image / PDF / spreadsheet and needs the test name, value, unit, reference range, and abnormal flag as clean rows. Trigger keywords: lab table extraction, lab panel, OCR labs, table detection, layout analysis, header detection, reference range column, abnormal flag column, LOINC, UCUM, CBC…
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
# Extracting lab tables from documents and scans Lab results arrive as **tables**: a column of test names, a value column, units, a reference range, and an abnormal flag (H/L/Crit). To use them downstream you must recover that grid from a PDF, scan, or spreadsheet into clean rows — then code each test to **LOINC**, normalize units with **UCUM**, and flag abnormals. This skill is the **intake** step: it OCRs/parses the table on-device with `openmed.multimodal`, de-identifies any embedded PHI, and emits structured rows. It pairs **before** OpenMed's clinical helpers — the LOINC/UCUM coding and the high/low/critical flag are downstream (see `parsing-lab-values`). ## When to use - You have a lab report as a **scanned image / photo / PDF page** and need the panel as rows, not pixels. - The source is a **CSV/TSV** export and you need columns classified (which is the value, the unit, the range, the flag) and PHI columns redacted. - You need machine-readable rows to feed LOINC mapping and a FHIR `Observation`/`DiagnosticReport`. ## What OpenMed gives you here `openmed.multimodal` ships the intake primitives (no heavy deps at import; the OCR backend loads lazily): …
Read the whole file at its exact version.
How to install
mdr add maziyarpanahi/openmed/extracting-lab-tables@sha256:231ad52cc6a59f83The 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_5amtxi7nv6b4p2xx)
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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 (8431 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_5amtxi7nv6b4p2xx GET https://markdownregistry.com/api/v1/resolve?ref=maziyarpanahi/openmed/extracting-lab-tables GET https://markdownregistry.com/api/v1/blob/231ad52cc6a59f83b9abe63423048e8867e95b0dbc10ec12a74623180c57ac19
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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.