tooluniverse-rare-disease-diagnosis
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain significance. Use when clinician asks about rare disease diagnosis, unexplained phenotypes, or genetic testing interpretation.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-rare-disease-diagnosis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain significance. Use when clinician asks about rare disease diagnosis, unexplained phenotypes, or genetic testing interpretation.
How it works
- Follows a report-first workflow: create a report file named
[PATIENT_ID]_rare_disease_report.mdwith headers and placeholder text[Researching...], then progressively update. - Converts symptoms to HPO terms, identifying core vs variable features and noting onset and family history.
- Performs disease matching using Orphanet and OMIM data, cross-referencing OpenTargets and DisGeNET for gene-disease associations.
- Assigns phenotype overlap scores (Excellent/Good/Possible/Unlikely) to rank differential diagnoses.
- Generates a differential diagnosis table with ORPHA, OMIM, inheritance, and key genes, and includes DisGeNET evidence.
- Produces a gene panel from top diseases, with optional ClinGen gene-disease validity checks and dosage sensitivity data to prioritize genes.
- Outputs additional data files for genes and variants when provided.
When to use it
Apply when user asks:
- "Patient has [symptoms], what rare disease could this be?"
- "Unexplained developmental delay with [features]"
- "WES found VUS in [gene], is this pathogenic?"
- "What genes should we test for [phenotype]?"
- "Differential diagnosis for [rare symptom combination]"
What it can touch
- Uses tools like Orphanet, OMIM, OpenTargets, DisGeNET, ClinGen, HPO search; calls to
Orphanet_search_diseases,Orphanet_get_genes,OMIM_search,OMIM_get_entry,OMIM_get_clinical_synopsis,DisGeNET_search_gene,DisGeNET_search_disease,ClinGen_search_gene_validity,ClinGen_search_dosage_sensitivity,ClinGen_search_actionability. - Outputs generate:
[PATIENT_ID]_rare_disease_report.md,[PATIENT_ID]_gene_panel.csv,[PATIENT_ID]_variant_interpretation.csv.
Caveats
- Enforces a mandatory report-first approach and mandatory citation of sources for each finding.
- Requires verification of tool parameters (phase 0 workflow) and ClinGen data before including genes in the panel.
- Final results depend on availability and quality of external databases (Orphanet, OMIM, DisGeNET, ClinGen).
# Rare Disease Diagnosis Advisor Systematic diagnosis support for rare diseases using phenotype matching, gene panel prioritization, and variant interpretation across Orphanet, OMIM, HPO, ClinVar, and structure-based analysis. **KEY PRINCIPLES**: 1. **Report-first approach** - Create report file FIRST, update progressively 2. **Phenotype-driven** - Convert symptoms to HPO terms before searching 3. **Multi-database triangulation** - Cross-reference Orphanet, OMIM, OpenTargets 4. **Evidence grading** - Grade diagnoses by supporting evidence strength 5. **Actionable output** - Prioritized differential diagnosis with next steps 6. **Genetic counseling aware** - Consider inheritance patterns and family history 7. **English-first queries** - Always use English terms in tool calls (phenotype descriptions, gene names, disease names), even if the user writes in another language. Only try original-language terms as a fallback. Respond in the user's language --- ## When to Use Apply when user asks: - "Patient has [symptoms], what rare disease could this be?" - "Unexplained developmental delay with [features]" - "WES found VUS in [gene], is this pathogenic?" - "What genes should we test for [p
- When to Use
- Critical Workflow Requirements
- 1. Report-First Approach (MANDATORY)
- 2. Citation Requirements (MANDATORY)
- Phase 0: Tool Verification
- Known Parameter Corrections
- Workflow Overview
- Phase 1: Phenotype Standardization
- 1.1 Convert Symptoms to HPO Terms
- 1.2 Phenotype Categories
- 1.3 Output for Report
- Phase 2: Disease Matching
- 2.1 Orphanet Disease Search (NEW TOOLS)
- 2.2 OMIM Cross-Reference (NEW TOOLS)
What does the tooluniverse-rare-disease-diagnosis skill do?
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain significance. Use when clinician asks about rare disease diagnosis, unexplained phenotypes, or genetic testing interpretation.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-rare-disease-diagnosis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.