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Ensembl Database

Listed
jimmc414·vlatest·database

Access and query Ensembl genome data (gene annotations, variants, expression) for biological research insights.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add jimmc414/kosmos --skill ensembl-database -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

jimmc414

Taken from the source listing. We haven't verified who controls this account.

Install target

Live repository

Not pinned. Installing fetches whatever the repository holds at the time you run the command.

No human has reviewed this code. The checks below are a static scan of the files at one commit — nobody has run this skill or judged whether it works. A skill runs with whatever access you give your agent, so read the source before you install it.

Automated safety checks

scanned

This skill failed 1 of 6 checks. A failure is not proof of bad intent; it means something in the code needs a human to look at it before you run it.

  • No undeclared network calls: failed

    Contacts 2 hosts that are neither well-known infrastructure nor declared in the skill's frontmatter: grch37.rest.ensembl.org, rest.ensembl.org.

    Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.

    Hosts contacted

    rest.ensembl.orgundeclaredgrch37.rest.ensembl.orgundeclared

    What it found

    • kosmos-claude-scientific-skills/scientific-skills/ensembl-database/scripts/ensembl_query.py:22contacts rest.ensembl.org
      def __init__(self, server: str = "https://rest.ensembl.org", rate_limit: int = 15):
    • kosmos-claude-scientific-skills/scientific-skills/ensembl-database/scripts/ensembl_query.py:356contacts rest.ensembl.org
      server = "https://rest.ensembl.org"
    • kosmos-claude-scientific-skills/scientific-skills/ensembl-database/scripts/ensembl_query.py:358contacts grch37.rest.ensembl.org
      server = "https://grch37.rest.ensembl.org"

  • Declares what it does: passed

    SKILL.md parses and declares a name and a description.

    SKILL.md exists, its frontmatter parses, and it declares a name and a description.

  • No obfuscated payloads: passed

    No encoded or obfuscated payloads.

    No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.

  • No credential access: passed

    Reads no keys, tokens, keychains or credential files.

    Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.

  • No pipe-to-shell installers: passed

    No pipe-to-shell or download-and-run installers.

    No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.

  • Pinned to a commit: passed

    Scanned jimmc414/kosmos at 6cfe7f690d.

    The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.

Commit
6cfe7f690d
Manifest
kosmos-claude-scientific-skills/scientific-skills/ensembl-database/SKILL.md
Scanned
3 files, 1,059 lines
This is a static scan, not a review. It reads the skill's files; it does not run them, and it cannot tell you whether the skill is any good or whether the code does what its description says. A skill runs with whatever access you give your agent.
What each check looks for →

About this skill

What it does

This skill provides access to the Ensembl database, a comprehensive resource for genomic data. It allows querying of gene annotations, sequence information, and variant data. The skill can retrieve specific genes or regions based on identifiers like gene names, chromosome coordinates, or Ensembl IDs.

When to use it

  • Researching Gene Function: Investigate the function and characteristics of a particular gene by retrieving its annotation details from Ensembl.
  • Variant Analysis: Retrieve information about genetic variants within specific genomic regions.
  • Genome Browser Integration: Obtain coordinates and annotations for genes or regions to be visualized in a genome browser.
  • Identifying Orthologs: Find corresponding genes (orthologs) in other species using Ensembl's cross-species mapping data.

Key capabilities

  • Gene annotation retrieval
  • Sequence information access
  • Variant data querying
  • Cross-species gene mapping

Example prompts

  • "Get the Ensembl ID for the BRCA1 gene."
  • "What is the genomic location of the TP53 gene?"
  • "Find all variants in the EGFR gene with a frequency greater than 1% in the population."

Tips & gotchas

  • Familiarity with Ensembl database identifiers (e.g., Ensembl IDs, chromosome coordinates) will improve query accuracy.