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Tooluniverse Gwas Trait To Gene

Listed
mims-harvard·vlatest·other·Apache-2.0

This skill translates GWAS traits into potential genes, accelerating genetic discovery and understanding disease mechanisms.

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 mims-harvard/tooluniverse --skill tooluniverse-gwas-trait-to-gene -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

mims-harvard

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 1 host that is neither well-known infrastructure nor declared in the skill's frontmatter: www.ebi.ac.uk.

    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

    www.ebi.ac.ukundeclared

    What it found

    • plugin/skills/tooluniverse-gwas-trait-to-gene/SKILL.md:232contacts www.ebi.ac.uk
      assocs = requests.get(f"https://www.ebi.ac.uk/gwas/rest/api/studies/{study_id}/associations").json()
    • plugins/tooluniverse/skills/tooluniverse-gwas-trait-to-gene/SKILL.md:232contacts www.ebi.ac.uk
      assocs = requests.get(f"https://www.ebi.ac.uk/gwas/rest/api/studies/{study_id}/associations").json()
    • skills/tooluniverse-gwas-trait-to-gene/SKILL.md:232contacts www.ebi.ac.uk
      assocs = requests.get(f"https://www.ebi.ac.uk/gwas/rest/api/studies/{study_id}/associations").json()

  • 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 mims-harvard/tooluniverse at f5c37eebeb.

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

Commit
f5c37eebeb
Manifest
skills/tooluniverse-gwas-trait-to-gene/SKILL.md
Scanned
8 files, 2,280 lines
Copies in repo
3 — all of them scanned
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 helps discover genes associated with diseases and traits by analyzing data from genome-wide association studies (GWAS). It leverages two primary resources: the GWAS Catalog and Open Targets Genetics, which provides locus-to-gene (L2G) predictions integrating eQTL, chromatin interaction, and distance data. The tool prioritizes gene candidates for validation rather than presenting them as confirmed causal genes.

When to use it

  • Clinical Research: Identifying genes associated with conditions like type 2 diabetes, coronary artery disease, or Alzheimer's disease susceptibility.
  • Drug Target Discovery: Prioritizing potential drug targets based on genetic evidence and L2G scores.
  • Functional Genomics: Mapping disease-associated variants to candidate genes and analyzing the genetic architecture of complex traits.

Key capabilities

  • GWAS Catalog Search: Searches the GWAS Catalog for associations related to a given trait or disease.
  • SNP Aggregation: Collects genome-wide significant SNPs (p < 5e-8).
  • Gene Mapping: Extracts mapped genes from GWAS associations.
  • Locus-to-Gene (L2G) Scoring: Uses L2G scores from Open Targets Genetics to rank potential gene candidates. A score above 0.5 is considered a strong prediction.
  • Evidence Ranking: Ranks candidate genes based on p-value, replication across studies, and fine-mapping data.

Example prompts

  • "What genes are associated with type 2 diabetes?"
  • "Find genetic risk factors for coronary artery disease."
  • "Which genes contribute to Alzheimer's disease susceptibility?"

Tips & gotchas

  • Always retrieve current data: Use gwas_search_associations and OpenTargets_get_study_credible_sets to obtain the latest information, as associations are updated with new GWAS publications. Do not assume trait-to-gene mappings or L2G scores.
  • Replication is key: A single GWAS study with p < 5e-8 is suggestive; replication across independent cohorts is required for high confidence.
  • Ancestry matters: Effect sizes and implicated genes can vary across ancestries due to differing LD patterns.