tooluniverse-gene-disease-association

name	tooluniverse-gene-disease-association
description	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). Use for 'which diseases is gene X associated with' or 'which genes cause disease Y' queries with quantitative confidence.

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.

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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.

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Core Principles

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

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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
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Phase 2: DisGeNET Associations (scored, multi-evidence)
  Gene-disease association scores with evidence type filtering
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Phase 3: OpenTargets Associations (integrated evidence)
  Disease phenotypes and genetic associations from OpenTargets
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Phase 4: Monarch Initiative (cross-species evidence)
  Gene-disease associations integrating OMIM, ClinVar, model organisms
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Phase 5: Mendelian Disease Evidence (curated)
  OMIM gene-disease map, GenCC validity classifications, Orphanet rare diseases
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Phase 6: Variant-Disease Associations (optional, if gene query)
  DisGeNET variant-disease links, ClinVar pathogenic variants
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Phase 7: Evidence Synthesis
  Unified table, concordance scoring, confidence levels, final report