orphanet-link

Server Quality Checklist

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Latest release: v0.4.3
Disambiguation5/5
Each tool targets a distinct operation on Orphanet data, such as searching by gene or phenotype, retrieving specific disease aspects (genes, phenotypes, prevalence), traversing classification hierarchy, or resolving identifiers. The descriptions clearly differentiate overlapping tools (e.g., immediate vs. transitive classification).
Naming Consistency5/5
All tool names follow a clear verb_noun or verb_noun_preposition pattern in snake_case (e.g., get_disease_genes, find_diseases_by_phenotype, resolve_disease_batch). There are no mixed conventions or vague verbs.
Tool Count5/5
With 19 tools, the server provides a well-scoped set for a rare disease database. Each tool covers a specific need without being excessive, and the count is typical for a domain-specific MCP server.
Completeness5/5
The tool set covers all expected read operations for the Orphanet domain: searching, resolving, fetching full records, retrieving specific data facets (genes, phenotypes, prevalence, natural history, disability), navigating the classification hierarchy, mapping cross-ontologies, and batch operations. No obvious gaps are present.
Average 4.3/5 across 19 of 19 tools scored.
See the Tool Scores section below for per-tool breakdowns.
- No community issues in the last 6 months
- 84 commits in the last 12 weeks
- Last stable release on August 10, 2026
- No critical vulnerability alerts
- No high-severity vulnerability alerts
- No code scanning findings
- CI is failing
This repository is licensed under MIT License.
This repository includes a README.md file.
No tool usage detected in the last 30 days. Usage tracking helps demonstrate server value.
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```
{
  "$schema": "https://glama.ai/mcp/schemas/server.json",
  "maintainers": [
    "your-github-username"
  ]
}
```
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How is the quality score calculated?

The overall quality score combines two components: Tool Definition Quality (70%) and Server Coherence (30%).

Tool Definition Quality measures how well each tool describes itself to AI agents. Every tool is scored 1–5 across six dimensions: Purpose Clarity (25%), Usage Guidelines (20%), Behavioral Transparency (20%), Parameter Semantics (15%), Conciseness & Structure (10%), and Contextual Completeness (10%). The server-level definition quality score is calculated as 60% mean TDQS + 40% minimum TDQS, so a single poorly described tool pulls the score down.

Server Coherence evaluates how well the tools work together as a set, scoring four dimensions equally: Disambiguation (can agents tell tools apart?), Naming Consistency, Tool Count Appropriateness, and Completeness (are there gaps in the tool surface?).

Tiers are derived from the overall score: A (≥3.5), B (≥3.0), C (≥2.0), D (≥1.0), F (<1.0). B and above is considered passing.

Tool Scores

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.
Behavior3/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint, so the bar is lower. The description adds minimal behavioral context: it specifies the type of data returned (prevalence class, geographic area, source) but does not disclose any additional traits like rate limits, pagination, or error handling.
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: the first clearly states purpose and outputs, the second provides the signature. No extraneous information, front-loaded with the key action.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness3/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has only two parameters and rich annotations, the description is adequate but not comprehensive. It lacks details about the structure of the prevalence response (e.g., array vs single object, required fields) and does not mention potential edge cases (e.g., unknown term). With no output schema, more detail would improve completeness.
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 schema already documents both parameters with descriptions and examples. The description only repeats the function signature without adding new semantic meaning beyond what the schema provides.
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 the verb 'Return' and specifies the resource 'prevalence data for an Orphanet disorder' along with the specific outputs: prevalence class, geographic area, and source reference. This distinguishes it from sibling tools like get_disease (general info) or get_disease_genes.
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 explains what the tool does but does not provide explicit guidance on when to use it versus alternatives. It lacks when-not-to-use scenarios or mentions of sibling tools. The purpose is clear but usage context is only implied.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, idempotentHint, destructiveHint, covering safety and idempotency. The description adds context on ambiguous label handling and response_mode, but does not detail error cases like no match.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Conciseness4/5
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise with two sentences and a signature. However, the signature line is somewhat redundant given the schema. No unnecessary content, but could be slightly tighter.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness3/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description covers the main resolution behavior and ambiguous case, but lacks explicit handling of no-match scenarios and omits full output structure. Given no output schema, more detail would be beneficial.
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 description coverage is 100%, so the schema fully documents both parameters. The description largely repeats the schema, adding no new semantic depth beyond what the schema already provides.
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 the tool resolves a disease label, synonym, or ORPHAcode to a canonical Orphanet term, specifying the output fields and handling ambiguous inputs. This distinguishes it from sibling tools like get_disease or search_diseases.
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 implicitly indicates usage for resolving disease identifiers, but lacks explicit guidance on when to choose this tool over alternatives like resolve_disease_batch or get_disease. No when-not-to-use or prerequisites are mentioned.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, idempotentHint, etc. Description adds return format {orpha_code, name} and pagination behavior, plus the function signature, which provides useful context beyond annotations.
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?
Two concise sentences plus a signature, all front-loaded with key information. No wasted words.
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?
For a read-only, idempotent tool with 100% schema coverage and annotations, the description covers return format and pagination. Lacks specifics on response_mode values, but schema handles that. 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?
Schema description coverage is 100%, so the schema already documents parameters. The description only repeats the signature without adding new meaning, so baseline 3 is appropriate.
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?
Description clearly states what the tool does: 'Find all Orphanet disorders associated with an HGNC gene symbol' with specific verb 'find' and resource 'disorders', and distinguishes from sibling find_diseases_by_phenotype by the input type.
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?
Usage is implied by the name and description (use when you have a gene symbol to find associated disorders), but no explicit guidance on when not to use or comparison to alternatives like find_diseases_by_phenotype.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, idempotentHint, and destructiveHint false. The description adds context about pagination and return format (orpha_code, name), which goes beyond annotations.
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 plus a signature line, front-loaded with the main action, and contains no redundant information.
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?
The description explains return structure (orpha_code, name) and pagination, but does not specify types or behavior for empty results. Given no output schema, some small gaps exist but overall it is sufficiently complete for a simple list tool.
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 description coverage is 100%, so the baseline is 3. The description provides a signature line but adds no further semantic detail beyond what the schema already provides for each parameter.
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 the tool finds Orphanet disorders annotated with an HPO term ID, and specifies the return fields (orpha_code, name). This distinguishes it from siblings like find_diseases_by_gene.
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 when an HPO ID is available but does not explicitly state when to use this tool versus alternatives like search_diseases or get_disease_phenotypes. No when-not-to-use guidance is provided.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare the tool as read-only, idempotent, and non-destructive. The description adds value by specifying the exact data returned (age of onset and inheritance patterns), which is useful behavioral context beyond the annotations.
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: the first states the purpose and output, the second gives the signature. It is front-loaded, efficient, and contains no extraneous information.
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?
Without an output schema, the description provides the key output fields (age of onset and inheritance patterns). It lacks structural details but is sufficiently complete for a simple two-parameter tool with clear annotations.
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% with descriptions for both parameters. The description only restates parameter names in the signature without adding new meaning, so it meets the baseline but does not exceed it.
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 natural history data for an Orphanet disorder, specifically age of onset and inheritance patterns. The verb 'Return' and resource 'natural history data' are precise, and the tool is easily distinguished from siblings like get_disease_genes or get_disease_phenotypes.
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 for obtaining natural history information but does not explicitly state when to use this tool versus alternatives. It lacks guidance on when not to use it or mention of alternative tools for related queries.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare the tool is read-only and idempotent. The description adds useful behavioral context: how the 'term' parameter resolves inputs (ORPHAcode, label/synonym, xref CURIE), that xrefs are grouped by source with leaf counts, and response_mode defaults. No contradictions with annotations.
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 a single, well-organized paragraph. It efficiently lists the output contents, explains the input term behavior, describes primary parameters (fields, include, response_mode), and ends with a clear signature. Every sentence is informative 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 the tool has 4 parameters, no output schema, and many siblings, the description provides sufficient context: it explains what the output contains, how inputs work, and how to configure the response. It could mention pagination or rate limits, but for a single-record read tool, it is adequately complete.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters4/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 100% schema coverage, the baseline is 3. The description adds substantial value by explaining the term resolution logic, the meaning of fields ('sparse projection') and include ('compose a full entity'), and providing the function signature. This goes beyond the schema descriptions.
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 the tool returns an Orphanet disease record and lists the specific contents (definition, synonyms, cross-references, etc.). It differentiates from sibling tools by implying it's the comprehensive endpoint, especially with the 'include' parameter to compose a full entity in one call.
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 does not explicitly state when to use this tool versus its many sibling tools (e.g., get_disease_genes, get_disease_phenotypes). It implies usage through the 'include' parameter for composing data, but lacks direct guidance on when not to use it or alternatives.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already indicate read-only, idempotent, non-destructive. Description adds pagination details (truncated, next_commands) and mentions closure computation, providing useful behavioral context.
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?
Two sentences, front-loaded with core purpose, no extraneous information. Efficient and clear.
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?
No output schema, but description explains pagination block structure. For a read-only tool with high schema coverage, this is largely adequate, though return content details are omitted.
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 description adds minimal value beyond schema. The function signature is mentioned but parameter details are already well-documented in schema.
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 'all transitive ancestors (broader diseases)' and distinguishes from sibling tool 'get_disease_classification' which returns immediate parents.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly mentions when to use alternative 'get_disease_classification' for immediate parents, though no additional when-not conditions are given.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already indicate readOnly, idempotent, non-destructive. The description adds transparency about return structure (orpha_code, name, score, pagination), pagination handling (next_offset, truncated), and exclusion of obsolete terms by default. This adds value beyond annotations.
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 concise, front-loaded with the main purpose, and includes essential details without fluff. Every sentence adds value.
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 the complexity (5 parameters, no output schema), the description adequately explains the return data and pagination. It covers key behavioral aspects like obsolete term handling and provides a signature. Missing output schema limits completeness slightly.
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 baseline is 3. The description recaps the signature and notes pagination behavior but does not significantly enhance the meaning of individual parameters beyond the schema's descriptions.
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 the tool performs full-text search over Orphanet disease names, synonyms, and definitions, with relevance ranking. It distinguishes from sibling tools which are specialized (e.g., find_diseases_by_gene, get_disease).
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implicitly indicates when to use this tool (for free-text disease search) by listing what it searches and providing a signature. It does not explicitly state when not to use or mention alternatives, but sibling names provide context.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Beyond annotations (readOnly, openWorld, idempotent, non-destructive), the description explains that empty results are valid and explicitly marked, adding behavioral nuance about data coverage and response structure.
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?
Two sentences plus a signature, each sentence adds value. No redundant or omitted information. Front-loaded with purpose, then coverage nuance, then signature.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness5/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
No output schema exists, but description explains return fields (ability categories, severity grades) and how to interpret coverage and count. Covers edge cases (empty results) and response format. Sufficient for this tool's complexity.
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% with detailed descriptions and examples for both parameters. The description adds only a signature line without new parameter information, so it does not significantly enhance understanding beyond the schema.
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?
Clearly states the verb 'Return' and the resource 'functional consequence (disability) data for an Orphanet disorder', specifying it includes ability categories and severity grades. Differentiates from sibling tools by focusing on a specific data type.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
Provides clear guidance on coverage partiality and how to interpret empty results (coverage:'none' vs 'present'), which helps the agent handle non-standard outcomes. However, it does not explicitly state when to use this tool over siblings or when to avoid it.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already indicate readOnly, openWorld, idempotent, non-destructive. The description adds detailed behavioral context (response includes runtime metrics, cache hit/miss, over-fetch detection) and confirms no parameters.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Conciseness4/5
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is front-loaded with purpose and includes a signature. It is informative but slightly verbose with detailed runtime metrics. Overall efficient.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness5/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given no output schema, the description fully explains the return content (status report with metrics). It covers what the tool does, why to use it, and what to expect, making it complete for agent invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters4/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
No parameters exist and schema coverage is 100%. The description implicitly confirms this by stating 'Signature: get_diagnostics()'. No additional parameter details needed.
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 the tool reports Orphanet index status with specific metrics (freshness, version, counts, runtime). It distinguishes from siblings by focusing on system diagnostics rather than disease data.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly says 'Use this to confirm freshness or diagnose a data_unavailable error'. It provides clear context for when to use, though it doesn't explicitly state when not to use.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, idempotentHint. Description adds pagination block structure (total, returned, limit, offset, truncated, next_offset) and explains next_commands behavior. No contradictions.
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?
Three efficient sentences: purpose + pagination, sibling guidance, and signature. No fluff, front-loaded with key information.
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, description covers return structure (pagination block) and distinguishes from key sibling. Could mention differences between response_mode options, but overall it's comprehensive.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters4/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, so baseline is 3. Description adds valuable context: term must be a grouping/category (leaf has no descendants) and lists parameter signature. Enhances understanding beyond schema.
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?
Description clearly states the action ('return all transitive descendants') and resource ('Orphanet disorder'), and distinguishes from sibling tool 'get_disease_classification' which returns only immediate children.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly tells when to use the sibling tool instead. Provides pagination details and a signature, but no broader guidance on when not to use this tool.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, idempotentHint. Description adds details on data structure (mappings vs xrefs), count semantics, and function signature, going beyond annotations.
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?
Two focused sentences plus signature line, front-loaded with purpose, no waste.
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?
No output schema, but description explains output grouping and field name, count nuance, and signature. Lacks mapping relation types, but still fairly complete.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters4/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, baseline 3. Description adds value by clarifying prefixes usage, count meaning, and response_mode options, plus examples and signature.
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 the tool lists cross-references to other ontologies grouped by source with mapping relations, and distinguishes from sibling get_disease which returns same data under xrefs.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
Provides clear context on when to use (get cross-references), how to restrict sources (prefixes), and notes alternative get_disease for same data. Lacks explicit when-not-to-use but covers main guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior5/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Beyond the annotations (readOnly, idempotent, openWorld), the description details pagination behavior (truncated, next_commands), distinguishes between malformed (invalid_input) and unmapped (empty page) CURIEs, and discloses the return structure. No contradictions with annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Conciseness4/5
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise (3-4 sentences) and front-loaded with the main purpose. It efficiently conveys key behavioral nuances. Slightly more structured formatting could improve readability, but it is well within acceptable limits.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness5/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Despite lacking an output schema, the description thoroughly explains return fields (matches, pagination block, next_commands) and error cases. No critical information about behavior or usage is missing for a tool with 4 parameters.
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 baseline is 3. The description lists the signature but adds little beyond the schema’s existing descriptions and examples. The extra detail about miss semantics does not directly enhance parameter understanding.
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 the tool resolves external cross-reference CURIEs (OMIM/MONDO/ICD-10/ICD-11/UMLS/GARD/MeSH/MedDRA) to Orphanet disorders. It explicitly distinguishes from the sibling 'resolve_disease' by noting different semantics (list vs. single result), making the purpose unambiguous.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides clear context for use: resolving external identifiers. It contrasts with resolve_disease regarding pagination and miss semantics, and explains error handling (invalid_input vs. empty page). While not explicitly stating when not to use, the differentiation effectively guides selection.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already provide readOnlyHint, openWorldHint, idempotentHint, destructiveHint. Description adds that the tool returns 'immediate parents and children,' which is useful behavioral context not captured by annotations.
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?
Two sentences with no wasted words. First sentence states purpose, second sentence gives alternatives and signature. Front-loaded and efficient.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness5/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's simplicity (2 params, no output schema, full annotation coverage), the description is complete. It tells what the tool returns, its scope, and how to get more information.
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 baseline is 3. Description does not add meaning beyond the schema; it only restates the signature. No new parameter details are provided.
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?
Description clearly states the specific verb 'Return' and resource 'immediate Orphanet classification parents and children' for a disorder. It distinguishes itself from sibling tools like get_disease_ancestors and get_disease_descendants by noting 'immediate' versus transitive closure.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines5/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly provides when-to-use and when-not-to-use: 'Use get_disease_ancestors / get_disease_descendants for the transitive closure.' This directly guides the agent to alternatives for related but different tasks.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior5/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description adds significant behavioral context beyond annotations, including partial success mechanism (each item returns ok=false/error_code/message), max batch size, and default response mode. No contradiction with readOnlyHint=true or other annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Conciseness4/5
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is dense and efficient, conveying key information in two sentences plus a signature line. Minor improvement could be structural clarity, but no superfluous content.
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?
The description covers all essential aspects for a batch retrieval tool: partial failure, input constraints, and verbosity options. Without an output schema, it adequately explains the response structure. Could mention error handling for invalid terms.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters5/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 100% schema coverage, the description still adds value by clarifying acceptable input formats for terms (ORPHAcode, label, or xref CURIE), sparse projection via fields, default compact mode, and the signature pattern.
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 'Fetch many disease records in one call' with specifics about partial success and per-item structure. It distinguishes itself from sibling tools like get_disease (single record) and resolve_disease_batch by emphasizing batch retrieval with partial failures.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides clear context for when to use this tool (batch fetching) and includes important constraints (max 50 items, input types). It does not explicitly exclude alternatives but implies its role among siblings.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior5/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, idempotentHint, destructiveHint=false. Description adds valuable behavioral details: exact matching requirement for frequency labels (including the consequence of unrecognized label rejection with invalid_input), and the return structure (HPO id, term name, frequency category). This goes beyond annotation coverage.
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?
Two concise sentences: first states purpose and return fields, second explains filtering and list frequency values. No redundant information, front-loaded, and every sentence adds value.
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, description adequately covers return fields (HPO id, term name, frequency category) and error handling for frequency. For a query tool with 3 parameters and no output schema, this provides sufficient context. No missing critical information.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters4/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100% with detailed parameter descriptions. Description adds the function signature, enumeration of frequency values with percentage ranges, and explicit matching rules (exact label required). This enhances understanding beyond schema alone.
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?
Description clearly states the verb 'Return' and resource 'HPO phenotype annotations for an Orphanet disorder', specifying returned fields (HPO id, term name, frequency category) and optional filtering. This distinguishes it from siblings like find_diseases_by_phenotype (reverse lookup) and get_disease (general info).
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
Description provides clear context for when to use this tool (need HPO annotations for a specific disorder). It does not explicitly state when not to use or name alternatives, but the sibling list provides implicit guidance. The context is sufficient for an agent to infer appropriate usage.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior5/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false. The description adds significant behavioral context beyond annotations, detailing exactly what the tool returns (call signatures, response modes, workflows, ranking, taxonomy, limits) and how detail='full' extends that. No contradiction.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Conciseness4/5
Is the description appropriately sized, front-loaded, and free of redundancy?
Description is informative but slightly verbose; it front-loads the main purpose well. Could be trimmed by removing the signature line since it's implied by the tool name, but overall it's structurally sound.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness5/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given only one optional parameter, no output schema, and rich annotations, the description provides complete context for the tool: what it returns, when to use it, and how to control detail level. No gaps remain.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters4/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100% with clear enum and default. Description adds value by explaining what 'summary' and 'full' mean in terms of content (light vs adds policy notes), though the schema's description already covers the enum values well.
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 the tool returns the 'orphanet-link discovery surface' including multiple specific components like tool list, call signatures, response modes, etc. This is a specific verb+resource that distinguishes it from sibling tools which focus on disease or gene queries.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines5/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly states 'Call this first in a cold session' and provides alternative URI schemes (orphanet://tools / orphanet://capabilities). Also explains the two detail levels (summary vs full) with clear guidance on when to use each.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Behavior5/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already provide readOnlyHint=true, openWorldHint=true, idempotentHint=true, destructiveHint=false. The description adds critical behavioral details: partial success with per-item errors, never wholesale failure, and compact per-item signature. No contradictions with annotations.
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?
Two sentences covering purpose, behavior, parameters, limits. High information density with no filler. Front-loaded with the core action.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Completeness5/5
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Despite lacking an output schema, the description explains the return format (orpha_code, name, match_type, ok=false/error details). Combined with rich annotations and schema, the agent has sufficient context to use the tool correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Parameters5/5
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%. The description adds value by explaining queries must be a list of strings (not comma-joined), provides examples, and clarifies response_mode enum with default. This surpasses what the schema alone offers.
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 the tool resolves multiple labels/ORPHAcodes/xrefs in one call, with per-item resolution details. It distinguishes from the single-item resolve_disease and resolve_xref siblings by emphasizing batch capability and partial success behavior.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Usage Guidelines4/5
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description specifies a max of 50 items, partial success behavior, and the response structure. It does not explicitly mention when not to use, but the batch context is clear. Sibling tools like get_disease_batch and resolve_disease provide alternatives for different use cases.
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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