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search_literature_signals

Search biomedical literature for associations between genes, chemicals, and diseases using PubTator3 signals. Query by entity pairs and relation types to retrieve evidence.

Instructions

Search biomedical literature signals via PubTator3.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryNo
entity1No
entity2No
entity2_typeNochemical
relation_typeNointeract

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

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 of behavioral disclosure. It only says 'Search' and 'via PubTator3', which implies a read-only external lookup but does not explain result behavior, rate limits, authentication, or the meaning of 'signals'. This is insufficient for a tool with no annotation support.

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 sentence that is front-loaded with the action and includes a meaningful qualifier ('via PubTator3'). It contains no fluff or redundancy, but the brevity comes at the cost of critical detail, which is a completeness concern rather than a conciseness flaw.

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 absence of annotations, six optional parameters, and the existence of a closely related sibling 'search_literature', this one-sentence description is inadequate. It does not explain what a 'signal' is, when to prefer this tool, or how parameters combine. The presence of an output schema helps but cannot compensate for the lack of contextual guidance.

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?

With 0% schema description coverage, the description was expected to explain the roles of the 6 parameters, especially 'entity1', 'entity2', 'entity2_type', and 'relation_type'. It adds no parameter information beyond the raw property names, leaving the interaction between parameters and the 'signal' concept completely unexplained.

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 uses the verb 'Search' and identifies the resource as 'biomedical literature signals via PubTator3', which distinguishes it from the generic sibling tool 'search_literature'. However, 'signals' is not defined, so the purpose is clear but not fully precise about what constitutes a signal.

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 'search_literature' or 'find_related_articles'. There are no exclusions, prerequisites, or context cues about appropriate 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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