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Agent skill

Cosmic Database

by aipoch in aipoch/medical-research-skills

Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.

MITAuto-check passedResearch & Science

Install Cosmic Database

skills CLI
$ npx skills add aipoch/medical-research-skills --skill cosmic-database -a claude-code

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

GitHub CLI
$ gh skill install aipoch/medical-research-skills cosmic-database --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/cosmic-database' .claude/skills/cosmic-database && 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
cosmic-database
GitHub stars
2k
Token cost
~1.4k tokens
SKILL.md length
587 words
Files
4 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.

  • Works in 5 steps: When to Use → Key Features → Dependencies → …
  • Tasks that involve Bioinformatics
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 6 more sections
  • Runs Python scripts from its folder; calls python

What it does

Cosmic Database is an agent skill from aipoch/medical-research-skills. Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.

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 reference files (for example `cosmic-database_audit_result_v1.json`, `references/cosmic_data_reference.md` and `scripts/download_cosmic.py`).

It sits in Research & Science, covering Bioinformatics. 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

  • Tasks that involve Bioinformatics

Example prompts

  • “/cosmic-database”

Requirements

  • Python 3

Workflow steps

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

  1. When to Use
  2. Key Features
  3. Dependencies
  4. Example Usage
  5. Implementation Details

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 1 file 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):

    • cancer.sanger.ac.uk

    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

Cosmic Database loads about 1.4k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 48 tokens; SKILL.md has 587 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~48
When it runs · the whole SKILL.md, loaded when a task matches
~1.4k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.6k

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). 587 words, ~1,441 tokens.

Download SKILL.mdSave it as .claude/skills/cosmic-database/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
cosmic-database
description
Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.
license
MIT
author
AIPOCH

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

COSMIC Database Skill

When to Use

  • Use this skill when you need access cosmic to download mutation datasets, query cancer gene census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources in a reproducible workflow.
  • Use this skill when a evidence insight task needs a packaged method instead of ad-hoc freeform output.
  • Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
  • Use this skill when scripts/download_cosmic.py is the most direct path to complete the request.
  • Use this skill when you need the cosmic-database package behavior rather than a generic answer.

Key Features

  • Scope-focused workflow aligned to: Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.
  • Packaged executable path(s): scripts/download_cosmic.py.
  • Reference material available in references/ for task-specific guidance.
  • 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

bash
cd "20260316/scientific-skills/Evidence Insight/cosmic-database"
python -m py_compile scripts/download_cosmic.py
python scripts/download_cosmic.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/download_cosmic.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/download_cosmic.py.
  • Reference guidance: references/ contains supporting rules, prompts, or checklists.
  • 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.

1. When to Use

Use this skill when you need COSMIC data for tasks such as:

  • Downloading COSMIC mutation exports (TSV/VCF) for cohort or sample-level variant analysis.
  • Retrieving Cancer Gene Census (CGC) gene lists for oncogene/tumor suppressor annotation and prioritization.
  • Working with COSMIC mutational signatures (SBS/DBS/ID) for signature attribution or comparative studies.
  • Accessing additional COSMIC genomics datasets (e.g., copy number, fusions, expression) for multi-omics integration.
  • Building reproducible pipelines that programmatically fetch the latest COSMIC releases.
Show full SKILL.md (202 more words)Show less

2. Key Features

  • Authenticated downloads of COSMIC files (e.g., TSV/VCF; often GZIP-compressed).
  • Cancer Gene Census access for curated cancer gene information.
  • Mutational signature retrieval including SBS, DBS, and ID signatures.
  • Support for multiple COSMIC dataset types, such as mutation, copy number, fusion, and expression resources.
  • Pandas-friendly workflow for loading and filtering downloaded tables.

3. Dependencies

  • Python 3.9+
  • pandas >= 1.5
  • requests >= 2.28

External requirements:

4. Example Usage

The following example downloads a COSMIC file and loads it into a pandas DataFrame.

python
from scripts.download_cosmic import download_cosmic_file
import pandas as pd

# 1) Download a COSMIC dataset (example path; adjust to your target release/build)
download_cosmic_file(
    email="user@email.com",
    password="pwd",
    filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz"
)

# 2) Load the downloaded GZIP-compressed TSV
df = pd.read_csv(
    "CosmicMutantExport.tsv.gz",
    sep="\t",
    compression="gzip"
)

# 3) Example analysis: filter by gene symbol (column name depends on the dataset)

# df_gene = df[df["Gene name"] == "TP53"]

For dataset field definitions and COSMIC file specifics, see: references/cosmic_data_reference.md.

5. Implementation Details

  • Authentication: Downloads require COSMIC account credentials (email/password) and are performed via an authenticated HTTP session.
  • File targeting: The filepath parameter specifies the COSMIC resource path (e.g., genome build such as GRCh38, release channel such as latest, and the target filename).
  • Data format: Many COSMIC exports are distributed as GZIP-compressed TSV (and sometimes VCF). Use pandas.read_csv(..., sep="\t", compression="gzip") for TSV .gz files.
  • Typical workflow:
    1. Download the desired COSMIC export.
    2. Load into a DataFrame (or parse VCF with an appropriate library if needed).
    3. Filter/aggregate by gene, tumor type, sample, or signature depending on the analysis goal.

© 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, references) in scientific-skills/Evidence Insight/cosmic-database of aipoch/medical-research-skills.

  • SKILL.md
  • cosmic-database_audit_result_v1.json
  • references/cosmic_data_reference.md
  • scripts/download_cosmic.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Cosmic Database 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.

Cosmic Database compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Cosmic Database this skillaipoch/medical-research-skills2k—~1.4kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k3 repos~3.4kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw15k—~923Automated safety check: PassMIT

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Categories

Questions about Cosmic Database

What does Cosmic Database do?

Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources. Cosmic Database is an agent skill from aipoch/medical-research-skills. Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.

When should I use Cosmic Database?

Cosmic Database fits situations like: tasks that involve Bioinformatics.

How do I install Cosmic Database in Claude Code?

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

How do I install Cosmic Database in Codex?

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

Can I use Cosmic Database 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 cosmic-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/cosmic-database, .gemini/skills/cosmic-database, .github/skills/cosmic-database and .opencode/skills/cosmic-database in your project.

What does Cosmic Database need to run?

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

Does Cosmic Database access the network?

SKILL.md names 1 domain. As links in the text: cancer.sanger.ac.uk. This is read from the text; nothing was executed.

Is Cosmic Database 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 Cosmic Database use?

Cosmic Database 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 Cosmic Database use?

About 1.4k tokens (SKILL.md is roughly 5.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 144 tokens, read only when the agent opens those files.

What are the alternatives to Cosmic Database?

Skills that share tags, products or a category with Cosmic Database: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Cosmic Database?

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.