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Agent skill

Cellosaurus API

by aipoch in aipoch/medical-research-skills

Access Cellosaurus database for cell line information and release data.

MITAuto-check passedResearch & Science

Install Cellosaurus API

skills CLI
$ npx skills add aipoch/medical-research-skills --skill cellosaurus-api -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills cellosaurus-api --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/cellosaurus-api' .claude/skills/cellosaurus-api && rm -rf skills-src

Use ~/.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/

Facts

Skill name
cellosaurus-api
GitHub stars
2k
Token cost
~1.7k tokens
SKILL.md length
756 words
Files
4 (incl. scripts)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Access Cellosaurus database for cell line information and release data.

  • Works in 3 steps: Get Release Information → Get Cell Line Details → Search Cell Lines
  • Asks to search cell lines
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 14 more sections
  • Runs Python scripts from its folder; calls python

What it does

Cellosaurus API is an agent skill from aipoch/medical-research-skills. Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info.

Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `cellosaurus-api_audit_result_v2.json`, `scripts/client.py` and `scripts/validate_skill.py`).

It sits in Research & Science. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • Asks to search cell lines
  • Get cell line details by accession
  • Check database release info

Example prompts

  • “/cellosaurus-api”

Requirements

  • Python 3

Workflow steps

3 steps, taken from the step headings in SKILL.md.

  1. Get Release Information
  2. Get Cell Line Details
  3. Search Cell Lines

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. 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 2 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • api.cellosaurus.org

    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

Cellosaurus API loads about 1.7k tokens when it runs. Until then it costs about 50 tokens; SKILL.md has 756 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~50
When it runs · the whole SKILL.md, loaded when a task matches
~1.7k

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

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 756 words, ~1,683 tokens.

Download SKILL.mdSave it as .claude/skills/cellosaurus-api/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
cellosaurus-api
description
Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

  • Use this skill when the request matches its documented task boundary.
  • Use it when the user can provide the required inputs and expects a structured deliverable.
  • Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

Key Features

  • Scope-focused workflow aligned to: "Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info.".
  • Packaged executable path(s): scripts/client.py plus 1 additional script(s).
  • Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

  • Python: 3.10+. Repository baseline for current packaged skills.
  • Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

See ## Usage above for related details.

bash
cd "20260316/scientific-skills/Evidence Insight/cellosaurus-api"
python -m py_compile scripts/client.py
python scripts/client.py --help

Example run plan:

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/client.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

  • Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
  • Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
  • Primary implementation surface: scripts/client.py with additional helper scripts under scripts/.
  • Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
  • Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Validation Shortcut

Run this minimal command first to verify the supported execution path:

bash
python scripts/validate_skill.py --help

Cellosaurus API Skill

This skill allows querying the Cellosaurus database for cell line information.

Capabilities

  1. Get Release Info: Retrieve current database version and stats.
  2. Get Cell Line: Fetch details for a specific cell line by Accession Number (AC).
  3. Search: Query cell lines using Solr syntax.

Usage

1. Get Release Information
bash
python .trae/skills/cellosaurus-api/scripts/client.py info
2. Get Cell Line Details

Get details for HeLa (CVCL_0030):

bash
python .trae/skills/cellosaurus-api/scripts/client.py get CVCL_0030

With specific fields:

bash
python .trae/skills/cellosaurus-api/scripts/client.py get CVCL_0030 --fields id,ac,sy
3. Search Cell Lines

Search for 'HeLa':

bash
python .trae/skills/cellosaurus-api/scripts/client.py search "id:HeLa"

Search with limit:

bash
python .trae/skills/cellosaurus-api/scripts/client.py search "id:HeLa" --rows 5

References

When Not to Use

  • Do not use this skill when the required source data, identifiers, files, or credentials are missing.
  • Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
  • Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Required Inputs

  • A clearly specified task goal aligned with the documented scope.
  • All required files, identifiers, parameters, or environment variables before execution.
  • Any domain constraints, formatting requirements, and expected output destination if applicable.
Show full SKILL.md (321 more words)Show less
  1. Validate the request against the skill boundary and confirm all required inputs are present.
  2. Select the documented execution path and prefer the simplest supported command or procedure.
  3. Produce the expected output using the documented file format, schema, or narrative structure.
  4. Run a final validation pass for completeness, consistency, and safety before returning the result.

Output Contract

  • Return a structured deliverable that is directly usable without reformatting.
  • If a file is produced, prefer a deterministic output name such as cellosaurus_api_result.md unless the skill documentation defines a better convention.
  • Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.

Validation and Safety Rules

  • Validate required inputs before execution and stop early when mandatory fields or files are missing.
  • Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
  • Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
  • Keep the output safe, reproducible, and within the documented scope at all times.

Failure Handling

  • If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
  • If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
  • If partial output is returned, label it clearly and identify which checks could not be completed.

Quick Validation

Run this minimal verification path before full execution when possible:

bash
python scripts/client.py --help

Expected output format:

text
Result file: cellosaurus_api_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any

Deterministic Output Rules

  • Use the same section order for every supported request of this skill.
  • Keep output field names stable and do not rename documented keys across examples.
  • If a value is unavailable, emit an explicit placeholder instead of omitting the field.

Completion Checklist

  • Confirm all required inputs were present and valid.
  • Confirm the supported execution path completed without unresolved errors.
  • Confirm the final deliverable matches the documented format exactly.
  • Confirm assumptions, limitations, and warnings are surfaced explicitly.

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts) in scientific-skills/Evidence Insight/cellosaurus-api of aipoch/medical-research-skills.

  • SKILL.md
  • cellosaurus-api_audit_result_v2.json
  • scripts/client.py
  • scripts/validate_skill.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Cellosaurus API 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.

Cellosaurus API compared with similar skills
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Cellosaurus API this skillaipoch/medical-research-skills2k—~1.7kAutomated safety check: PassMIT
Hypothesis Generationspacering-net/codeg3.8k15 repos~3.6kAutomated safety check: NotesMIT
GitHub Deep Researchbytedance/deer-flow83k5 repos~1.3kAutomated safety check: PassMIT
Nature Paper CardYuan1z0825/nature-skills46k2 repos~2.1kAutomated safety check: PassApache-2.0
Read arXiv Paperkarpathy/nanochat58k2 repos~494Automated safety check: PassMIT
Content Research Writerweapp-tailwindcss/weapp-tailwindcss1.9k25 repos~3.5kAutomated safety check: PassMIT

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Categories

Questions about Cellosaurus API

What does Cellosaurus API do?

Access Cellosaurus database for cell line information and release data. Cellosaurus API is an agent skill from aipoch/medical-research-skills. Access Cellosaurus database for cell line information and release data.

When should I use Cellosaurus API?

Cellosaurus API fits situations like: asks to search cell lines; get cell line details by accession; check database release info.

How do I install Cellosaurus API in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill cellosaurus-api -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/cellosaurus-api in aipoch/medical-research-skills) into .claude/skills/cellosaurus-api in your project. Claude Code loads it when a task matches its description.

How do I install Cellosaurus API in Codex?

Run `npx skills add aipoch/medical-research-skills --skill cellosaurus-api -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/cellosaurus-api in aipoch/medical-research-skills) into .agents/skills/cellosaurus-api in your project. Codex loads it when a task matches its description.

Can I use Cellosaurus API 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 aipoch/medical-research-skills --skill cellosaurus-api -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/cellosaurus-api, .gemini/skills/cellosaurus-api, .github/skills/cellosaurus-api and .opencode/skills/cellosaurus-api in your project.

What does Cellosaurus API need to run?

Going by SKILL.md and its folder, Cellosaurus API needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Cellosaurus API access the network?

SKILL.md names 1 domain. As links in the text: api.cellosaurus.org. This is read from the text; nothing was executed.

Is Cellosaurus API 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 Cellosaurus API use?

Cellosaurus API is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Cellosaurus API use?

About 1.7k tokens (SKILL.md is roughly 6.7k 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 Cellosaurus API?

Skills that share tags, products or a category with Cellosaurus API: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Cellosaurus API?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.