Server Quality Checklist

Tool Scores

• fetch_entryC
  2.4/5.0
  Behavior2/5

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

  With no annotations, the description is the sole source of behavioral info. It only says 'structured' without explaining behavior like auth, errors, or idempotency. Output schema exists but is not described.

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

  Conciseness3/5

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

  The description is one sentence, concise, but so minimal that it sacrifices informativeness. It could be expanded while staying concise.

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

  Completeness1/5

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

  Given 3 parameters, no annotations, and existing output schema, the description fails to provide sufficient context for correct usage. It omits parameter roles, output format, and use cases.

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

  Parameters1/5

  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 adds no explanation for parameters (accession, fields, version) beyond their names, leaving the agent uninformed.

  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 (return) and resource (structured UniProt entry). However, it does not differentiate from sibling tools like fetch_entry_flatfile, so it could be more specific.

  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 guidance on when to use this tool versus alternatives. Sibling tools exist but are not mentioned, and no usage context is provided.

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

• search_uniprotC
  2.4/5.0
  Behavior2/5

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

  Without annotations, the description should disclose behavioral traits. It only says 'search and return curated hits,' offering no details on pagination, rate limits, or mutation (if any). The tool's behavior remains opaque.

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

  Conciseness3/5

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

  The description is a single sentence, which is concise but lacks structure and fails to provide necessary details in a front-loaded manner. It is not overly verbose but under-informative.

  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 6 parameters, no annotations, and an output schema exists but is not described, the description is incomplete. It does not explain what 'curated hits' entails or how parameters affect behavior.

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

  Parameters1/5

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

  The input schema has 6 parameters with 0% description coverage, and the tool description adds no parameter information. The agent is left to infer meaning from parameter names alone, which is insufficient.

  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 (search) and resource (UniProtKB) and mentions 'curated hits' as output, which differentiates from sibling tools that retrieve specific entries or sequences. However, 'curated hits' is somewhat vague, preventing a perfect score.

  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 guidance is provided on when to use this tool versus siblings like fetch_entry or get_sequence. There is no mention of prerequisites or alternatives, leaving the agent without context for selection.

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

• map_idsC
  2.7/5.0
  Behavior2/5

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

  No annotations are provided, so the description must carry the full burden. It only mentions 'map identifiers' without disclosing behavioral traits such as id limits, mapping directionality, or side effects.

  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?

  Single sentence, no wasted words. However, a slight expansion to clarify parameter roles would improve utility without harming conciseness.

  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?

  Despite having an output schema, the description fails to cover parameter semantics and usage context. For a tool with three undocumented parameters, this is insufficient.

  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?

  Input schema has 0% description coverage. The description implies that 'from_db' and 'to_db' are namespaces and 'ids' are identifiers, but it does not explain valid values or formats, leaving ambiguity.

  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 states it maps identifiers between UniProt-supported namespaces, clearly indicating the verb and resource. It distinguishes from sibling tools that fetch entries or sequences. However, it lacks specificity about the mapping operation itself.

  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 guidance on when to use this tool versus alternatives. The description does not provide context on prerequisites, limitations, or scenarios for exclusion.

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

• fetch_entry_flatfileC
  2.9/5.0
  Behavior2/5

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

  Without annotations, the description must fully disclose behavior. It only states it returns a flatfile, but omits potential rate limits, authentication, size limits, error handling, or whether the response is file content or a URL. This leaves significant uncertainty for the agent.

  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 a single concise sentence that conveys the core purpose. However, it could be considered slightly under-specified; still, it is well-structured and avoids unnecessary words.

  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 has 3 parameters, no annotations, and an output schema (which reduces need to describe return values), the description still lacks crucial context about parameter usage, default behaviors, and edge cases. It is insufficient for an agent to use it confidently without further inference.

  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 should explain parameters. It clarifies 'format' can be 'txt or fasta', but fails to define 'accession' and 'version' beyond being entry identifiers. No constraints or allowed values are given for these parameters.

  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 a UniProt flatfile for a specific entry version, explicitly mentioning the available formats (txt or fasta). This distinguishes it from siblings like fetch_entry (likely returns structured data) and get_sequence (returns sequence only).

  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 guidance is provided on when to use this tool versus alternatives such as fetch_entry, get_sequence, or search_uniprot. The agent is left to infer from the name and description alone.

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

• get_sequenceA
  3.7/5.0
  Behavior2/5

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

  No annotations are provided, so the description carries full burden. It does not disclose behavioral traits such as read-only nature, required permissions, or what 'sequence metadata' includes. The output schema is present but not described.

  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, front-loaded sentence with no unnecessary words. It is highly concise.

  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?

  For a simple tool with an output schema, the description is adequate but minimal. It lacks usage guidance and behavioral context, but the output schema may cover return values.

  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 description mentions 'for an accession', which maps to the single required parameter. However, with 0% schema description coverage, it adds only minimal clarity without examples, format, or constraints.

  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 uses a specific verb 'Return' and resource 'sequence metadata for an accession'. It clearly distinguishes itself from siblings like 'fetch_entry' which likely returns full entry 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 phrase 'only the sequence metadata' implies this tool is for cases where only metadata is needed, contrasting with other tools that return more. However, it does not explicitly name alternatives or 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.