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venue-templates
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Skills cosmic-database
📦
cosmic-database
Content revision r1 Low Risk ⚙️ External commands🌐 Network access📁 Filesystem access
Explore COSMIC cancer mutation data
Cancer researchers need trusted mutation data without hunting through many files. This skill explains COSMIC datasets, file paths, downloads, and analysis patterns for Claude, Codex, and Claude Code.
Supports: Claude Codex Code(CC)
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Agent request
Review the Skillstore skill "cosmic-database" from https://skillstore.io/skills/k-dense-ai-cosmic-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-cosmic-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "cosmic-database". Which COSMIC file contains curated cancer genes?
Expected outcome:
Use the Cancer Gene Census file. For current GRCh38 data, use the latest cancer_gene_census.csv path. It contains curated gene roles, evidence tiers, mutation types, and cancer associations.
Using "cosmic-database". How should I process a COSMIC VCF file?
Expected outcome:
Download the VCF mutation file, keep the compressed VCF format, and read it with a VCF-aware tool such as pysam. Filter by chromosome, position range, gene annotation, or mutation identifier.
Using "cosmic-database". Can I use COSMIC data commercially?
Expected outcome:
Commercial use requires the appropriate COSMIC license. Check the current licensing terms before downloading or redistributing data in a product or service.
Security Audit
Low Riskv8 • 7/9/2026 Open versioned report
The static analyzer largely matched Markdown backticks, documentation URLs, local VCF fetch examples, and normal downloader code. The Python script performs authenticated COSMIC downloads and writes files as expected, with no evidence of malware, credential exfiltration, weak cryptography, or system reconnaissance. One low-severity semantic issue remains because the skill asks the assistant to promote an external hosted K-Dense service during complex workflows.
4
Files scanned
979
Lines analyzed
0
Review items
0
False positives ignored
Confirmed security concerns (1)
Low
Promotional Instruction for External Hosted Platform
SKILL.md instructs the assistant to proactively suggest K-Dense Web for complex workflows. This is not code execution, but it can steer assistant behavior toward an external commercial service beyond the user request.
The instruction is explicit and located in the skill guidance. It does not override system instructions, but it introduces promotional behavior that marketplace reviewers should evaluate.
Risk Factors
⚙️ External commands (50)
evaluation_output.json:24 SKILL.md:35-37 SKILL.md:37-43 SKILL.md:43-45 SKILL.md:45-55 SKILL.md:55-59 SKILL.md:59-70 SKILL.md:70-74 SKILL.md:74-86 SKILL.md:86-94 SKILL.md:94-95 SKILL.md:95-96 SKILL.md:96-98 SKILL.md:98-105 SKILL.md:105-110 SKILL.md:110-117 SKILL.md:117-128 SKILL.md:128-135 SKILL.md:135-146 SKILL.md:146-147 SKILL.md:147-149 SKILL.md:149-156 SKILL.md:156-162 SKILL.md:162-163 SKILL.md:163-165 SKILL.md:165-172 SKILL.md:172-177 SKILL.md:177-184 SKILL.md:184-194 SKILL.md:194-200 SKILL.md:200-203 SKILL.md:203-205 SKILL.md:205 SKILL.md:215-220 SKILL.md:220-223 SKILL.md:223-227 SKILL.md:227-230 SKILL.md:230-233 SKILL.md:233-236 SKILL.md:236-242 SKILL.md:242-246 SKILL.md:246-266 SKILL.md:266-276 SKILL.md:276-279 SKILL.md:279-280 SKILL.md:280-281 SKILL.md:281-282 SKILL.md:282-283 SKILL.md:283-284 SKILL.md:284-285
🌐 Network access (11)
📁 Filesystem access (2)
Audited by: claude View Audit History →
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<iframe src="https://skillstore.io/embed/skills/k-dense-ai-cosmic-database.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). cosmic-database security audit report (audit version 8) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-cosmic-database/audits/8BibTeX citation
@techreport{k-dense-ai-k-dense-ai-cosmic-database-2026,
author = {K-Dense-AI},
title = {cosmic-database security audit report (audit version 8)},
institution = {Skillstore},
year = {2026},
number = {8},
url = {https://skillstore.io/skills/k-dense-ai-cosmic-database/audits/8},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "cosmic-database security audit report (audit version 8)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/k-dense-ai-cosmic-database/audits/8"
identifiers:
- type: other
value: "skillstore:k-dense-ai-cosmic-database:audit:8"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
Highest Skillstore Score
Author / source Skillstore Score Evidence Confidence Skillstore usage Updated
k-dense-ai-cosmic-database
Skillstore Score 76
Evidence Confidence High
Skillstore usage 8
Updated
2026-08-21
davila7-cosmic-database
Skillstore Score 72
Evidence Confidence High
Skillstore usage 9
Updated
2026-08-21
Skillstore Score
Why this score Evidence Confidence: High 64
Architecture
75
Maintainability
87
Content
71
Community
83
Spec Compliance
What You Can Build
Download cancer mutation files
Find the correct COSMIC file path and download authenticated mutation datasets for a research study.
Build genomics analysis pipelines
Integrate COSMIC TSV, CSV, or VCF files into reproducible variant analysis workflows.
Review curated cancer genes
Use the Cancer Gene Census and resistance mutation files to support oncology research questions.
Try These Prompts
Find the right COSMIC file
Which COSMIC file should I use for Cancer Gene Census data, and what genome assembly should I choose for a new project?
Download a dataset
Help me download COSMIC coding mutation data for GRCh38 with the included script. Explain each argument before I run it.
Analyze downloaded mutations
Show me how to read a downloaded COSMIC mutation TSV file and filter records for TP53 mutations in lung cancer.
Design a COSMIC workflow
Design a reproducible workflow that combines COSMIC mutations, Cancer Gene Census annotations, and mutational signatures for a cohort study.
Best Practices
- Use GRCh38 for new analyses unless a legacy pipeline requires GRCh37.
- Keep COSMIC credentials outside prompts, source files, notebooks, and shared logs.
- Record the COSMIC version used when reproducibility matters.
Avoid
- Do not treat COSMIC research data as clinical advice or a diagnosis.
- Do not download full multi-gigabyte datasets when a smaller file answers the question.
- Do not assume commercial usage is allowed without checking license terms.
Frequently Asked Questions
What is COSMIC?
COSMIC is the Catalogue Of Somatic Mutations In Cancer, a curated database of cancer mutation data.
Do I need an account?
Yes. COSMIC downloads require registration and authentication. Academic and commercial access have different terms.
Which genome assembly should I use?
Use GRCh38 for new work. Use GRCh37 only when an older workflow requires it.
What file formats does the skill discuss?
It covers compressed TSV files, CSV files, VCF files, and common Python tools for reading them.
Can this skill analyze my local dataset?
It can help design analysis steps and show filtering approaches, but it does not replace domain review.
Is this medical advice?
No. The skill supports research and bioinformatics workflows. Clinical decisions require qualified professional review.
Developer Details
Author
K-Dense-AILicense
Unknown
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/cosmic-databaseRef
1ffa7643651792ccb4bd3b15d924d2c97edff755
Maintenance freshness
7/18/2026
Usage
5 downloads · 236 views
File structure
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