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berntpopp
by berntpopp

Get Disease Genes

get_disease_genes
Read-onlyIdempotent

Retrieve gene-disease associations for a rare disorder from Orphanet, including gene symbols, HGNC IDs, and cross-references.

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:33069 or 33069), 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
Behavior4/5

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

The description adds valuable details beyond annotations, such as the interpretation of 'count' as leaf gene rows, and the output fields. Annotations already indicate read-only, idempotent, and non-destructive behavior.

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?

Extremely concise: two sentences and a signature, front-loaded with purpose. Every sentence adds value without 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?

Given no output schema, the description adequately explains the return content (gene symbol, HGNC ID, etc.) and the meaning of 'count'. It could note the effect of response_mode on verbosity, but the signature implies it.

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?

Schema coverage is 100%, so the baseline is 3. The description mentions parameters in the signature but adds no additional semantic detail beyond what is in the schema.

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

Purpose4/5

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 and lists specific fields. However, it does not explicitly differentiate from sibling tools like find_diseases_by_gene, which performs the reverse mapping.

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

Usage Guidelines2/5

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

No explicit guidance on when to use this tool versus alternatives. The description does not mention scenarios where it is appropriate or when to choose other tools like find_diseases_by_gene or get_disease.

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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