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Agent skill

Cosmic Database

by jaechang-hits in jaechang-hits/SciAgent-Skills

Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.

CC-BY-NC-SA-4.0Auto-check passedResearch & Science

Install Cosmic Database

skills CLI
$ npx skills add jaechang-hits/SciAgent-Skills --skill cosmic-database -a claude-code

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

GitHub CLI
$ gh skill install jaechang-hits/SciAgent-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/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/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
371
Used in
1 other repo
Token cost
~4.6k tokens
SKILL.md length
811 words
Files
1
Skills in repo
169
Repo updated
First seen
Licence
CC-BY-NC-SA-4.0

At a glance

Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.

  • Works in 5 steps: Authenticate via Base64: COSMIC uses… → Paginate large gene queries: Popular… → Use COSM IDs for cross-study comparison:… → …
  • Tasks that involve Bioinformatics
  • SKILL.md covers Overview, When to Use, Prerequisites and Quick Start, plus 9 more sections
  • Calls pip; reaches cancer.sanger.ac.uk

What it does

Cosmic Database is an agent skill from jaechang-hits/SciAgent-Skills. Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.

Its SKILL.md is about 4.6k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics and REST APIs. The repository describes itself as: 197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.

When your agent uses it

  • Tasks that involve Bioinformatics
  • Tasks that involve REST APIs

Example prompts

  • “/cosmic-database”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Authenticate via Base64: COSMIC uses HTTP Basic Auth with base64-encoded email:password. Store credentials in environment variables, not…
  2. Paginate large gene queries: Popular cancer genes (TP53, KRAS) have 100,000+ mutation records; use skip/limit pagination and cache results…
  3. Use COSM IDs for cross-study comparison: Amino acid change strings may have formatting variations (p.G12D vs G12D); use COSMIC mutation…
  4. Check data license for commercial use: COSMIC data is free for academic use but requires a commercial license for industry applications…
  5. Complement with clinical data: COSMIC captures somatic mutations from cancer sequencing; complement with clinvar-database for germline…

What it can do on your machine

Read from SKILL.md and the folder at commit 82c862c. 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

    Shell commands in SKILL.md call:

    • pip

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

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • cancer.sanger.ac.uk

    Also links to:

    • doi.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

Cosmic Database loads about 4.6k tokens when it runs. Until then it costs about 76 tokens; SKILL.md has 811 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~76
When it runs · the whole SKILL.md, loaded when a task matches
~4.6k

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); files beside SKILL.md are not scanned.

SKILL.md

Its licence (CC-BY-NC-SA-4.0) doesn't allow us to republish the file, so here is its outline and opening line. It has 811 words (~4,555 tokens).

“COSMIC (Catalogue Of Somatic Mutations In Cancer) is the world's largest expert-curated database of somatic mutations in cancer, covering 6.7M+ coding mutations, 40,000+ cancer samples, 19,000+ genes across all cancer types. It includes the Cancer Gene Census (critical cancer genes)…”

— opening of SKILL.md by jaechang-hits, CC-BY-NC-SA-4.0
name
cosmic-database
license
CC-BY-NC-SA-4.0

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/genomics-bioinformatics/databases/cosmic-database of jaechang-hits/SciAgent-Skills.

Open the folder on GitHubat commit 82c862c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in jaechang-hits/SciAgent-Skills, which our catalogue first saw on October 7, 2026.

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 skilljaechang-hits/SciAgent-Skills3711 repos~4.6kAutomated safety check: PassCC-BY-NC-SA-4.0
Bio Ensembl RESTGPTomics/bioSkills1.2k2 repos~3.6kAutomated safety check: PassMIT
Pride FetchClawBio/ClawBio1.2k—~4.2kAutomated safety check: PassMIT
Ensembl Databaseaipoch/medical-research-skills2k—~1.5kAutomated safety check: PassMIT
UniProt Database Accessdavila7/claude-code-templates32k14 repos~1.7kAutomated safety check: PassMIT
Singlecell Portalaipoch/medical-research-skills2k—~1.2kAutomated safety check: PassMIT

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Categories

Questions about Cosmic Database

What does Cosmic Database do?

Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. Cosmic Database is an agent skill from jaechang-hits/SciAgent-Skills. Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.

When should I use Cosmic Database?

Cosmic Database fits situations like: tasks that involve Bioinformatics; tasks that involve REST APIs.

How do I install Cosmic Database in Claude Code?

Run `npx skills add jaechang-hits/SciAgent-Skills --skill cosmic-database -a claude-code`. Or copy the skill folder (skills/genomics-bioinformatics/databases/cosmic-database in jaechang-hits/SciAgent-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 jaechang-hits/SciAgent-Skills --skill cosmic-database -a codex`. Or copy the skill folder (skills/genomics-bioinformatics/databases/cosmic-database in jaechang-hits/SciAgent-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 jaechang-hits/SciAgent-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 the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does Cosmic Database access the network?

SKILL.md names 2 domains. In commands or code: cancer.sanger.ac.uk; the agent is likely to contact it when it follows the instructions. As links in the text: doi.org. 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. Review the folder before installing.

What licence does Cosmic Database use?

Cosmic Database is published under the CC-BY-NC-SA-4.0 licence (declared in SKILL.md).

How many tokens does Cosmic Database use?

About 4.6k tokens (SKILL.md is roughly 18k 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 Cosmic Database?

Skills that share tags, products or a category with Cosmic Database: Bio Ensembl REST (GPTomics/bioSkills, 1.2k stars), Pride Fetch (ClawBio/ClawBio, 1.2k stars), Ensembl Database (aipoch/medical-research-skills, 2k stars) and UniProt Database Access (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Cosmic Database?

jaechang-hits (a GitHub user) maintains it in jaechang-hits/SciAgent-Skills, which has 371 GitHub stars. The repository holds 169 skills in this directory. The repository was last updated on September 29, 2026.

Source: jaechang-hits/SciAgent-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.