lab-column-mapper

lab-column-mapper is a skill for Claude Code, Codex from microsoft/cat-agent-skills. It costs 133 tokens per session (1,610 once invoked), scanned A, original, MIT.

A helper for matching an unknown column in a laboratory results file to the correct field in a standard clinical data schema. It uses sample values and laboratory context to make a suggested match.

In plain words
What is it for?
Use it to investigate failed lab-file imports, map source headers to canonical fields, explain the proposed mapping, and send it to a review queue.
Why use it?
It helps recover when an Azure Data Factory data pipeline cannot recognize a source column. The suggestion is recorded for review, while patient identifiers must be removed or hashed first.

Skill for Claude CodeCodex

About the project

microsoft/cat-agent-skills is a static website that catalogs reusable instruction sets and related packages for AI agents. People use it to search, filter, rate, and download skills for Cowork, Copilot Studio, and Scout, along with Copilot plugins and Scout automations. The catalogue entries are the skills, instructions, plugins, and settings displayed by the site.

microsoft/cat-agent-skills · 63 stars · on GitHub

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/microsoft/cat-agent-skills/lab-column-mapper
Any agent
npx skills add microsoft/cat-agent-skills --skill lab-column-mapper
Clone the repo
git clone --depth 1 https://github.com/microsoft/cat-agent-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for lab-column-mapper

README.md
[![agentmods](https://agentmods.dev/badge/skills/microsoft/cat-agent-skills/lab-column-mapper.svg)](https://agentmods.dev/skills/microsoft/cat-agent-skills/lab-column-mapper)
Your own site
<a href="https://agentmods.dev/skills/microsoft/cat-agent-skills/lab-column-mapper"><img src="https://agentmods.dev/badge/skills/microsoft/cat-agent-skills/lab-column-mapper.svg" alt="Measured on agentmods" height="20"></a>
Per session 133 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,610 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00133 $0.01610
Opus 5 $0.00067 $0.00805
Sonnet 5 $0.00027 $0.00322
Haiku 4.5 $0.00013 $0.00161

Measured 5d ago against content hash 6335573951b9, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

lab-column-mapper scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/rank_column_matches.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

submissions/lab-column-mapper/SKILL.md · 119 lines

How it starts

The opening of the file, as written. The whole thing — 119 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Lab Column Mapper

What this skill does

Given an unknown column from an incoming lab results file, retrieve the most likely canonical destination column from a health system's clinical warehouse, explain why, and write the suggestion to the review queue.

Input payload

The skill is invoked with a JSON payload delivered by Power Automate. Every field is required unless marked optional.

Field Type Description
source_column_name string The unrecognized column header from the incoming file (e.g., PT_MRN, spec_collected_dt).
source_column_sample_values array of strings Up to 5 sample values, de-identified. Never include raw PHI — the caller must hash or redact patient identifiers before invoking.
source_lab_id string Stable identifier for the sending lab (e.g., LAB-QUEST-001).
source_lab_name string Human-readable lab name (e.g., Quest Diagnostics).
source_file_name string Name of the file that failed ingestion.
source_domain string One of lab-observations, orders, specimens, results. Used to scope the search.
pipeline_run_id string ADF pipeline run ID for traceability.
source_column_description string, optional If the sending lab publishes a data dictionary, the human description of the column. Boosts match confidence significantly when present.

Retrieval steps

Perform these steps in order. Do not skip to a broader search until the previous scope has been tried.

Step 1 — Same-lab scoped search

Query the Azure AI Search index lab-canonical-schema with:

  • Search text: source_column_name + source_column_description (if present) + a synthesized query from the sample values (e.g., if samples look like dates, add "date time timestamp"; if samples look like numeric with units, add "quantity measurement value").
  • Filter: source_lab_id eq '{source_lab_id}' or previously_mapped_from_labs/any(l: l eq '{source_lab_id}')
  • Top: 5
  • Semantic ranking: on. Use the column-descriptions semantic configuration.

Read the full file on GitHub · 119 lines

Files

What ships with it

3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 5d ago First seen · 119 lines · 133 tokens per session scan A 6335573951b9

Subscribe to this mod's changes

lab-column-mapper is a skill published in the GitHub repository microsoft/cat-agent-skills (63 stars, last pushed 3d ago), licensed MIT. It adds 133 tokens to every session and 1,610 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Related

Other skills, from other repositories

instrument-data-to-allotrope

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…

anthropics/knowledge-work-plugins · 123 tokens

exploratory-data-analysis

Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…

K-Dense-AI/scientific-agent-skills · 83 tokens

mapping-to-snomed

Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…

maziyarpanahi/openmed · 205 tokens

auditing-subgroup-fairness

Audit an OpenMed NER or de-identification model for performance disparities across demographic subgroups (sex, age band, race/ethnicity when available) using openmed.eval.fairnessreport. Use when the user wants per-subgroup recall and leakage, wants to check whether de-identification under-protects a group, wants to…

maziyarpanahi/openmed · 148 tokens

mixed-precision

Use FP16/BF16 mixed precision to accelerate training and reduce memory. Use when optimizing GPU performance.

aiming-lab/AutoResearchClaw · 25 tokens

tooluniverse-drug-research

Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory…

mims-harvard/ToolUniverse · 71 tokens