annotate_function

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

With no annotations present, the description carries the full burden. 'Fetch' implies read-only and it discloses the return shape (MF/BP/CC JSON with evidence codes), which is useful, but it says nothing about rate limits, authentication, network/API dependencies, or behavior when the gene is unknown.

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

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

Front-loaded purpose sentence followed by compact Args/Returns blocks; every line adds information. Slightly bulky for a simple fetch, but no filler.

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

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

An output schema exists, so the Returns section is redundant but harmless. All four parameters are explained despite 0% schema coverage, and the aspect filter values are spelled out. The only real gap is the absence of usage routing against the many sibling finder/lookup tools.

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

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, and it largely does: it explains query accepts a symbol, alias, or UniProt accession with concrete examples, gives the default for taxon_id (9606), enumerates the three valid aspect values, and defines limit as 'maximum annotations per aspect'. This exceeds what the bare schema provides.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Fetch Gene Ontology functional annotations... for a gene or protein') and scopes it to MF/BP/CC, which separates it from siblings like get_go_term (term metadata) and get_pathways. It does not name any sibling explicitly, so an agent must infer the boundary rather than being routed.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is implied by the arguments (aspect filter, taxon_id, limit) rather than stated: there is no 'use this when you want X, use get_go_term when you want Y' guidance. No exclusions, no prerequisites, no mention of what to do for non-model organisms or ambiguous symbols.

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