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io.github.rcsb/rcsb-mcp

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rcsb_find_go_terms

Read-onlyIdempotent

Resolve free-text protein functions, processes, or locations into Gene Ontology (GO) terms to enable precise PDB structure searches.

Instructions

Resolve a free-text molecular function, biological process, or cellular component / location (e.g. kinase activity, ATP binding, DNA repair, apoptosis, signal transduction, mitochondrial membrane, nucleus) to Gene Ontology (GO) terms, so you can run precise GO-based PDB searches instead of keyword guessing.

Use this when a request involves what a protein DOES or where it acts — "proteins that / are involved in / participate in / are responsible for ...", "localized to / located in ...". Resolve the phrase to a GO id here, then search by it — see the resolver guidance in the server instructions for the attribute path and lineage semantics.

Args: query: Free-text function / process / location, e.g. "kinase activity", "DNA repair". namespace: Optional GO aspect to restrict to. Omit to search all three. limit: Max GO terms to return. with_pdb_counts: If true (default), annotate each term with pdb_entry_count (PDB entries carrying it, via annotation_lineage.id).

Returns: {query, namespace, count, terms:[{id, name, aspect, pdb_entry_count?}]}.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes
namespaceNo
with_pdb_countsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

Annotations already declare readOnly/openWorld/idempotent. The description adds valuable behavior: it's a precursor to precise PDB searches, clarifies GO aspect options, and explains the optional PDB count enrichment. It also notes lineage semantics but defers detailed guidance to server instructions.

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 well-structured and front-loaded with the core purpose. It uses compact sections for usage, args, and returns. Every sentence earns its place, with examples that clarify rather than pad.

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

Completeness5/5

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

For a 4-param tool with no schema descriptions and only a prose return format, the description is complete. It covers when to use, what each param means, and the exact return structure. The pointer to server instructions for lineage semantics is an acceptable delegation for deeper details.

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

Parameters5/5

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

Schema description coverage is 0%, so the description carries full responsibility. It explains all four parameters with intent, defaults, and examples (e.g., namespace restriction, limit as max terms, with_pdb_counts behavior). This goes well beyond the schema titles.

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 resolves free-text biological function/process/location phrases to GO terms. It uses a specific verb (resolve) and resource (GO terms), distinguishes from search tools in the sibling list, and provides concrete examples.

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 description explicitly says 'Use this when a request involves what a protein DOES or where it acts' and gives example phrasing patterns. It contrasts with keyword guessing but does not name or exclude specific sibling tools, so it falls short of full when-not/alternatives guidance.

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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