Instrument Data To Allotrope
aws-samples/amazon-bedrock-agents-healthcare-lifesciences
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV.
Map papers from the core set to each outline subsection and write outline/mapping.tsv with coverage tracking.
Install Section Mapper
$ npx skills add WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills section-mapper --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/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.codex/skills/section-mapper .claude/skills/section-mapper && 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 "section-mapper" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/section-mapper into .claude/skills/section-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "section-mapper", 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/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/section-mapperType 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 WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills section-mapper --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.codex/skills/section-mapper .agents/skills/section-mapper && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "section-mapper" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/section-mapper into .agents/skills/section-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "section-mapper", 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 WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills section-mapper --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.codex/skills/section-mapper .cursor/skills/section-mapper && 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 "section-mapper" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/section-mapper into .cursor/skills/section-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "section-mapper", 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/WILLOSCAR/research-units-pipeline-skills.git --path .codex/skills/section-mapper--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 WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills section-mapper --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.codex/skills/section-mapper .gemini/skills/section-mapper && 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 "section-mapper" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/section-mapper into .gemini/skills/section-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "section-mapper", 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 WILLOSCAR/research-units-pipeline-skills section-mapperInstalls 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 WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/.codex/skills/section-mapper .github/skills/section-mapper && 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 "section-mapper" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/section-mapper into .github/skills/section-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "section-mapper", 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 WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills section-mapper --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.codex/skills/section-mapper .opencode/skills/section-mapper && 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 "section-mapper" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/section-mapper into .opencode/skills/section-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "section-mapper", 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.
Facts
- Skill name
section-mapper- GitHub stars
- 513
- Token cost
- ~1.4k tokens
- SKILL.md length
- 638 words
- Files
- 3 (incl. scripts, assets)
- Skills in repo
- 107
- Repo updated
- First seen
- Licence
- None found
At a glance
Map papers from the core set to each outline subsection and write outline/mapping.tsv with coverage tracking.
- Works in 4 steps: Start from the outline subsections (each… → For each subsection, pick enough papers… → Fill why with a short semantic rationale… → …
- Tasks that involve CSV and tabular files
- SKILL.md covers Triggers & routing, When to use, Inputs and Outputs, plus 5 more sections
- Runs Python scripts from its folder; calls uv
What it does
Section Mapper is an agent skill from WILLOSCAR/research-units-pipeline-skills. Map papers from the core set to each outline subsection and write outline/mapping.tsv with coverage tracking.
Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and assets (for example `assets/domain_packs/rag_evaluation.json` and `scripts/run.py`).
It sits in Documents & Office, covering CSV and tabular files. The repository describes itself as: Research pipelines as semantic execution units: each skill declares inputs/outputs, acceptance criteria, and guardrails. Evidence-first methodology prevents hollow writing…
When your agent uses it
- Tasks that involve CSV and tabular files
Example prompts
- “/section-mapper”
Requirements
- Python 3
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Start from the outline subsections (each subsection should be “mappable”).
- For each subsection, pick enough papers to support evidence-first writing (A150++ default: 28; smaller runs: ~12–20; lightweight: ~3–6)…
- Fill why with a short semantic rationale (one line is enough), e.g.
- After initial mapping, scan for
What it can do on your machine
Read from SKILL.md and the folder at commit c92912a. It shows what the files ask for, not the result of running them.
Tool permissions
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.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
uv
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use uv, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Section Mapper loads about 1.4k tokens when it runs. Until then it costs about 32 tokens; SKILL.md has 638 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.
Safety
Auto-check passed
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); the scripts in this folder are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 638 words (~1,419 tokens).
“Create a paper→subsection map that supports evidence building and later synthesis.”
- name
- section-mapper
Files
SKILL.md and 2 other files (scripts, assets) in .codex/skills/section-mapper of WILLOSCAR/research-units-pipeline-skills.
- SKILL.md
- assets/domain_packs/rag_evaluation.json
- scripts/run.py
Open the folder on GitHubat commit c92912a
Compare with similar skills
Section Mapper 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 |
|---|---|---|---|---|---|---|
| Section Mapper this skillWILLOSCAR/research-units-pipeline-skills | 513 | — | ~1.4k | Automated safety check: Pass | None | |
| Instrument Data To Allotropeaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | 2 repos | ~2.7k | Automated safety check: Pass | Apache-2.0 | |
| Sector Analysttradermonty/claude-trading-skills | 3k | 1 repos | ~2.3k | Automated safety check: Pass | MIT | |
| Cliare Artifact Reviewmodiqo/cliare | 469 | — | ~2.4k | Automated safety check: Pass | Apache-2.0 | |
| Convert Fileduckdb/duckdb-skills | 599 | 1 repos | ~720 | Automated safety check: Notes | MIT | |
| Research Integrity Auditxuzhougeng/wisp-science | 1k | — | ~2.6k | Automated safety check: Pass | AGPL-3.0 |
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Related
Categories
Questions about Section Mapper
What does Section Mapper do?
Map papers from the core set to each outline subsection and write outline/mapping.tsv with coverage tracking. Section Mapper is an agent skill from WILLOSCAR/research-units-pipeline-skills.tsv with coverage tracking.
When should I use Section Mapper?
Section Mapper fits situations like: tasks that involve CSV and tabular files.
How do I install Section Mapper in Claude Code?
Run `npx skills add WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a claude-code`. Or copy the skill folder (.codex/skills/section-mapper in WILLOSCAR/research-units-pipeline-skills) into .claude/skills/section-mapper in your project. Claude Code loads it when a task matches its description.
How do I install Section Mapper in Codex?
Run `npx skills add WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a codex`. Or copy the skill folder (.codex/skills/section-mapper in WILLOSCAR/research-units-pipeline-skills) into .agents/skills/section-mapper in your project. Codex loads it when a task matches its description.
Can I use Section Mapper in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add WILLOSCAR/research-units-pipeline-skills --skill section-mapper -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/section-mapper, .gemini/skills/section-mapper, .github/skills/section-mapper and .opencode/skills/section-mapper in your project.
What does Section Mapper need to run?
Going by SKILL.md and its folder, Section Mapper needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
Does Section Mapper access the network?
SKILL.md contains no URLs. Its commands use uv, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Section Mapper safe to install?
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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Section Mapper use?
No licence was found for Section Mapper or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Section Mapper use?
About 1.4k tokens (SKILL.md is roughly 5.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Section Mapper?
Skills that share tags, products or a category with Section Mapper: Instrument Data To Allotrope (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Sector Analyst (tradermonty/claude-trading-skills, 3k stars), Cliare Artifact Review (modiqo/cliare, 469 stars) and Convert File (duckdb/duckdb-skills, 599 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Section Mapper?
WILLOSCAR (a GitHub user) maintains it in WILLOSCAR/research-units-pipeline-skills, which has 513 GitHub stars. The repository holds 107 skills in this directory. The repository was last updated on October 5, 2026.
Source: WILLOSCAR/research-units-pipeline-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.