Server Quality Checklist

Tool Scores

• fetch_entryC
  2.9/5.0
  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 but only states it returns structured data without detailing aspects like rate limits, authentication needs, error handling, or what 'structured' entails. It misses critical behavioral traits for a read operation.

  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 with zero waste, front-loading the core purpose. It's appropriately sized for a simple tool, though its brevity contributes to gaps in other dimensions.

  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 3 parameters with 0% schema coverage and no annotations, the description is incomplete as it lacks parameter semantics and behavioral details. However, the presence of an output schema reduces the need to explain return values, making it minimally adequate but with clear gaps.

  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 but adds no parameter information. It doesn't explain what 'accession', 'fields', or 'version' mean, their formats, or how they affect the output, leaving all three parameters semantically undocumented.

  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 the resource ('a structured UniProt entry'), providing specific verb+resource pairing. However, it doesn't differentiate from sibling tools like 'fetch_entry_flatfile' or 'get_sequence', which likely retrieve similar data in different formats or scopes.

  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 like 'fetch_entry_flatfile' or 'get_sequence'. The description lacks context about use cases, prerequisites, or exclusions, leaving the agent to infer usage from tool names alone.

  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?

  No annotations are provided, so the description carries the full burden of behavioral disclosure. It states the tool returns a flatfile but doesn't describe aspects like rate limits, authentication needs, error handling, or whether it's a read-only operation (implied by 'Return' but not explicit). This leaves significant gaps for a tool with no 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?

  The description is a single, efficient sentence that front-loads the key action and resource. There is no wasted wording, making it highly concise and well-structured for quick understanding.

  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 an output schema (which should cover return values), no annotations, and low schema coverage, the description is minimally adequate. It states the purpose but lacks details on parameters, behavioral traits, and usage context, making it incomplete for full agent guidance without relying heavily on the output schema.

  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 for undocumented parameters. It mentions 'specific entry version' and 'format' but doesn't explain what 'accession' or 'version' represent (e.g., UniProt identifiers), nor does it detail valid formats beyond 'txt or fasta'. This adds minimal value beyond 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 the action ('Return') and the specific resource ('UniProt flatfile for a specific entry version'), distinguishing it from siblings like 'fetch_entry' or 'get_sequence' by specifying the flatfile format. However, it doesn't explicitly differentiate from all siblings (e.g., 'search_uniprot' might also return flatfiles), so it's not a perfect 5.

  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 like 'fetch_entry' or 'get_sequence', nor does it mention any prerequisites or exclusions. It implies usage for retrieving flatfiles but lacks explicit 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.

• get_sequenceC
  2.9/5.0
  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 returns metadata, implying a read-only operation, but doesn't specify details like rate limits, error handling, or what 'sequence metadata' includes (e.g., format, size). 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, clear sentence with zero wasted words, making it highly concise and front-loaded. It efficiently communicates the core purpose without unnecessary elaboration.

  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's low complexity (one parameter) and the presence of an output schema, the description is minimally adequate. However, with no annotations and poor parameter documentation, it lacks completeness for safe and effective use, such as clarifying the 'accession' parameter or behavioral traits.

  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, with one undocumented parameter 'accession'. The description adds minimal semantics by implying 'accession' is used to retrieve sequence metadata, but it doesn't explain what an accession is (e.g., a database identifier), its format, or examples, failing to compensate for the schema's lack of documentation.

  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 verb ('return') and resource ('sequence metadata for an accession'), making the purpose specific and understandable. However, it doesn't explicitly differentiate from sibling tools like 'fetch_entry' or 'fetch_entry_flatfile', which might also retrieve sequence-related data, so it doesn't reach the highest 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?

  The description provides no guidance on when to use this tool versus alternatives like 'fetch_entry' or 'search_uniprot'. It lacks context about prerequisites, such as what an 'accession' refers to or any constraints, leaving the agent without usage direction.

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

• map_idsC
  2.9/5.0
  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 action but lacks details on permissions, rate limits, error handling, or what the mapping entails (e.g., one-to-one, many-to-many). This is a significant gap for a tool with parameters and an output schema.

  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 with zero waste. It's appropriately sized and front-loaded, clearly stating the core function without unnecessary elaboration.

  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 3 parameters with 0% schema coverage and an output schema, the description is incomplete. It covers the basic purpose but lacks parameter details and behavioral context. The output schema mitigates some gaps, but overall it's minimally adequate with clear room for improvement.

  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 implies parameters for source/target databases and IDs but doesn't explain what 'UniProt-supported namespaces' are, valid values for from_db/to_db, or ID formats. This leaves key semantics undocumented.

  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: mapping identifiers between UniProt-supported namespaces. It specifies the verb 'map' and the resource 'identifiers', but doesn't differentiate from sibling tools like fetch_entry or search_uniprot, which have different functions (fetching entries vs. searching).

  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 prerequisites, context, or exclusions, leaving the agent to infer usage based on the purpose alone.

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

• search_uniprotB
  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 mentions 'curated hits' but doesn't explain what that entails, such as result format, pagination, rate limits, or authentication needs. This is inadequate for a search tool with 6 parameters.

  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 with no wasted words. It's front-loaded with the core action and outcome, making it easy to parse quickly.

  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 complexity (6 parameters, no annotations) and the presence of an output schema, the description is minimally adequate but lacks depth. It doesn't explain what 'curated hits' means or how results are structured, though the output schema may cover return values. For a search tool, more context on behavior and usage 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 0%, so the description must compensate, but it adds no parameter-specific information beyond the generic 'search' context. The baseline is 3 because the schema provides parameter details (e.g., defaults, types), but the description doesn't enhance understanding of what parameters like 'fields' or 'sort' mean in practice.

  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 UniProtKB') and the outcome ('return curated hits'), making the purpose understandable. It doesn't explicitly differentiate from sibling tools like 'fetch_entry' or 'map_ids', which is why it's not a 5.

  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 like 'fetch_entry' or 'map_ids'. It lacks context about use cases, prerequisites, or exclusions, leaving the agent to infer usage from the tool name alone.

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