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berntpopp
by berntpopp

Get Disease Genes

get_disease_genes
Read-onlyIdempotent

Retrieve gene-disease associations for a rare disease using ORPHAcode, label, or cross-reference. Returns gene symbol, HGNC ID, association type, and links to OMIM, Ensembl.

Instructions

Return gene-disease associations for an Orphanet disorder: gene symbol, HGNC id, association type, and cross-references (OMIM, Ensembl, etc.). count is the number of leaf gene rows, not grouped associations. Signature: get_disease_genes(term, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
termYesAn ORPHAcode (ORPHA:166024 or 166024), a disease label/synonym, or an external xref CURIE that resolves to a single Orphanet term.
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
hintNo
nameNo
_metaNo
countNo
fieldNo
genesNo
messageNo
successNo
retryableNo
candidatesNo
error_codeNo
orpha_codeNo
allowed_valuesNo
recovery_actionNo
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, etc. The description adds meaningful behavioral context: it explains the return fields, clarifies count meaning, and specifies the signature. This goes beyond annotations without contradicting them.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two sentences long, front-loads the main purpose, and includes a concise signature. Every sentence is informative with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present and only 2 parameters, the description is sufficiently complete. It explains what the tool returns and clarifies the count. Minor gaps: no mention of limitations (e.g., only Orphanet terms) but overall adequate.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema already has 100% parameter descriptions, so the description adds little new about the parameters themselves. It does provide a helpful clarification about count meaning in the output, but for parameter semantics it meets the baseline.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it returns gene-disease associations for an Orphanet disorder, listing specific fields (gene symbol, HGNC id, etc.) and clarifying count semantics. This distinguishes it from siblings like find_diseases_by_gene which does the reverse.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage by giving a signature and parameters, but it does not explicitly state when to use this tool versus alternatives (e.g., find_diseases_by_gene, get_disease). No when/when-not guidance is provided for the 17 sibling tools.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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