Server Quality Checklist

Tool Scores

• over_representation_analysisC
  2.7/5.0
  Behavior2/5

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

  With no annotations provided, the description carries full burden for behavioral disclosure. While it indicates this is an analysis tool (likely non-destructive), it doesn't describe what the tool actually does behaviorally - whether it makes API calls, computes locally, has rate limits, requires authentication, returns specific data formats, or has any side effects. The description is too minimal for a 9-parameter tool with complex functionality.

  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 extremely concise - a single sentence that gets straight to the point. While arguably too brief for such a complex tool, it's efficiently structured with zero wasted words. The front-loading is good, immediately stating the core functionality.

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

  Completeness2/5

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

  For a complex bioinformatics analysis tool with 9 parameters, no annotations, no output schema, and 0% schema description coverage, this description is severely incomplete. It doesn't explain what ORA analysis entails, what results to expect, how to interpret parameters, or provide any context about the miEAA system. The agent would struggle to use this tool effectively.

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

  Parameters2/5

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

  With 0% schema description coverage and 9 parameters (6 optional), the description provides no information about parameter meanings or usage. It mentions 'miRNA or precursor' which relates to the 'entity' parameter, but doesn't explain what 'species', 'ids', 'category_selection', 'reference_set', 'p_adjust', 'p_scope', 'alpha', or 'min_hits' represent or how they should be used.

  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 the action ('Run miEAA over-representation analysis (ORA)') and the target resources ('for miRNA or precursor'), providing a specific verb+resource combination. However, it doesn't explicitly differentiate this tool from its siblings (list_enrichment_categories, mirbase_version_converter, mirna_precursor_converter), which appear to be related but distinct bioinformatics tools.

  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?

  The description provides no guidance on when to use this tool versus its siblings or alternatives. It mentions the analysis type (ORA) and target entities (miRNA/precursor), but doesn't specify use cases, prerequisites, or exclusions. This leaves the agent without context for tool selection.

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

• list_enrichment_categoriesC
  2.8/5.0
  Behavior2/5

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

  With no annotations provided, the description carries the full burden of behavioral disclosure. It states the tool lists categories but does not describe any behavioral traits such as rate limits, authentication needs, or what the output looks like (e.g., format, pagination). This leaves significant gaps in understanding how the tool behaves.

  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, efficient sentence that directly states the tool's purpose without unnecessary words. It is appropriately sized and front-loaded, making it easy to parse quickly.

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

  Completeness2/5

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

  Given the complexity (2 required parameters, no annotations, no output schema), the description is incomplete. It lacks details on parameter usage, behavioral context, and output expectations, making it insufficient for an AI agent to fully understand how to invoke and interpret results from this tool.

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

  Parameters2/5

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

  The schema description coverage is 0%, so the description must compensate for undocumented parameters. It mentions 'species' and implies 'entity' through 'miEAA enrichment categories', but does not explain what these parameters mean, their expected values, or how they affect the listing. This adds minimal semantic value beyond the bare 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 the action ('List available') and the resource ('miEAA enrichment categories for a species'), making the purpose understandable. However, it does not explicitly differentiate this tool from its siblings (e.g., converters and analysis tools), which slightly limits its clarity in context.

  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?

  The description provides no guidance on when to use this tool versus its siblings (mirbase_version_converter, mirna_precursor_converter, over_representation_analysis). It lacks context on prerequisites, alternatives, or exclusions, leaving usage decisions ambiguous.

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

• mirna_precursor_converterC
  2.8/5.0
  Behavior2/5

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

  With no annotations provided, the description carries the full burden of behavioral disclosure. It states the conversion action but lacks details on permissions, rate limits, error handling, or output format. For a tool with two parameters and no output schema, this is a significant gap in transparency.

  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, efficient sentence that directly states the tool's function without unnecessary words. It's appropriately sized and front-loaded, making it easy to parse quickly.

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

  Completeness2/5

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

  Given the tool's complexity (two parameters, no output schema, no annotations), the description is incomplete. It doesn't cover parameter meanings, usage scenarios, or behavioral traits, leaving gaps that could hinder correct tool invocation by an AI agent.

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

  Parameters2/5

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

  Schema description coverage is 0%, so the description must compensate. It mentions 'convert between miRNA names and precursor names', which implies the 'input' and 'direction' parameters, but doesn't explain their semantics, formats, or constraints. This adds minimal value beyond the schema's structure.

  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 the tool's purpose: converting between miRNA names and precursor names. It specifies the verb 'convert' and the resources involved, making the function unambiguous. However, it doesn't differentiate from sibling tools like 'mirbase_version_converter', which might handle similar data but different operations.

  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?

  The description provides no guidance on when to use this tool versus alternatives. It doesn't mention sibling tools like 'mirbase_version_converter' or 'over_representation_analysis', nor does it specify prerequisites or contexts for usage, leaving the agent to infer applicability.

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

• mirbase_version_converterB
  3.1/5.0
  Behavior2/5

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

  With no annotations provided, the description carries the full burden of behavioral disclosure. It states the conversion action but does not cover critical aspects like whether this is a read-only or mutative operation, error handling, rate limits, or output format. This leaves significant gaps in understanding the tool's 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?

  The description is a single, efficient sentence that directly states the tool's purpose without any extraneous information. It is front-loaded and wastes no words, making it highly concise and well-structured.

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

  Completeness2/5

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

  Given the complexity of a conversion tool with 3 undocumented parameters, no annotations, and no output schema, the description is inadequate. It fails to address behavioral traits, parameter details, or output expectations, leaving the agent poorly equipped to use the tool effectively.

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

  Parameters2/5

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

  The input schema has 0% description coverage, so the description must compensate. It implies parameters for miRNA identifiers and versions but does not explain their semantics, such as format requirements, valid version strings, or array constraints. This adds minimal value beyond the bare 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 the specific action ('Convert') and resource ('miRNA identifiers between miRBase versions'), distinguishing it from sibling tools like 'mirna_precursor_converter' which handles different conversions. It precisely communicates the tool's function without redundancy.

  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?

  The description provides no guidance on when to use this tool versus alternatives, such as 'mirna_precursor_converter' or other sibling tools. It lacks context about prerequisites, typical use cases, or exclusions, leaving the agent with minimal direction.

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