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Gene-Disease Association Analysis · mims-harvard | DecimalAI

scienceby mims-harvard

Gene-Disease Association Analysis

mims-harvard/tooluniverse-gene-disease-association

Source mims-harvard/ToolUniverse ↗License Apache-2.0

Gene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet. Cross-references multiple sources for evidence-graded association reports with concordance scoring (5/5 sources agree → strong, 1/5 → weak).

NewMaintained

Automatic

Clinical / Healthcare pack

Last verified 8/6/2026

What it changes

Passed 10 of 16 test cases with the skill, and 11 of 16 without it.

Without skill68%

With skill64%

Checks it passed that the model alone missed

The response recommends simplifying the disease query phrase to accommodate GenCC's word-tokenized matching.
The response specifies using MyGene_query_genes as the initial step for resolving Ensembl and HGNC gene identifiers.
The response details a unified table schema containing columns for Disease name, DisGeNET Score, OpenTargets Score, Monarch, OMIM, GenCC, Orphanet, and total supporting sources count.

3 fixed13 passed either way5 still failing4 broke

Pass-rate lift: -4 pp
Tokens: +162%
Agent turns: 0%
Response time: +27%

Model gemini-3.6-flashMeasured 8/6/2026v116 of 25 cases passed with skill · 16 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mims-harvard-tooluniverse-gene-disease-association/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-gene-disease-association/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mims-harvard-tooluniverse-gene-disease-association, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mims-harvard-tooluniverse-gene-disease-association/ and pins it in .decimal/skills.lock

decimalai skills add mims-harvard-tooluniverse-gene-disease-association

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mims-harvard-tooluniverse-gene-disease-association/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-gene-disease-association/SKILL.md

Raw file: /s/mims-harvard-tooluniverse-gene-disease-association/SKILL.md ↗ · machine-readable summary at /s/mims-harvard-tooluniverse-gene-disease-association.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 3

Prompt

I have a gene symbol 'APOE'. Which primary identifier resolution tool should be queried first in Phase 1 to retrieve Ensembl ID, HGNC ID, and Entrez Gene ID simultaneously?

What was checked, without and with the skill
Checked	Without skill	With skill
The response specifies using MyGene_query_genes as the initial step for resolving Ensembl and HGNC gene identifiers.	Missed	Passed

case-23 · gemini-3.6-flash · 8/6/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md210 linessingle file

Gene-Disease Association Analysis

Systematically query and compare gene-disease associations across 6+ databases to produce a unified, evidence-graded report. Cross-references DisGeNET scores, OpenTargets evidence, Monarch Initiative cross-species data, OMIM Mendelian mappings, GenCC curated validity, and Orphanet rare disease links.

IMPORTANT: Always use English gene names and disease terms in tool calls. Respond in the user's language.

LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first (PubMed, UniProt, ChEMBL, ClinVar, etc.) rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

Core Principles

Report-first approach - Create report file FIRST, then populate progressively
Multi-database triangulation - Query 4+ sources minimum, cross-validate
Quantitative scoring - Report numeric scores from each database
Concordance analysis - Count how many databases support each association and reason about independence
Evidence reasoning - Assess each association using evidence hierarchy, concordance, and mechanism plausibility
Mendelian vs complex - Distinguish monogenic (OMIM/Orphanet) from complex (GWAS/DisGeNET) associations
Negative results documented - "No association found in [database]" is informative

Workflow Overview

Phase 1: Gene/Disease Identification & ID Resolution
  Resolve gene symbol to Ensembl ID, HGNC CURIE, MIM number
  OR resolve disease name to UMLS CUI, EFO ID, MONDO ID, ORPHA code
      |
Phase 2: DisGeNET Associations (scored, multi-evidence)
  Gene-disease association scores with evidence type filtering
      |
Phase 3: OpenTargets Associations (integrated evidence)
  Disease phenotypes and genetic associations from OpenTargets
      |
Phase 4: Monarch Initiative (cross-species evidence)
  Gene-disease associations integrating OMIM, ClinVar, model organisms

Track record

Benchmark

10 / 16

test cases passed, vs 11 / 16 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/2/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mims-harvard / ToolUniverse

plugins/tooluniverse/skills/tooluniverse-gene-disease-association/SKILL.md

View on GitHub ↗

License Apache-2.0Imported 8/2/2026Version v1

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

tooluniverse-gene-disease-associationGene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet. Cross-references multiple sources for evidence-graded association reports with concordance scoring (5/5 sources agree → strong, 1/5 → weak). Use for 'which diseases is gene X associated with' or 'which genes cause disease Y' queries with quantitative confidence.Near-identical description+4 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

Gene-Disease Association Analysis

LOOK UP, DON'T GUESS

Core Principles

Workflow Overview

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills