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Glama

Rcsb Pdb

by io.github.pipeworx-io

Search Within a Source

search_within
Read-onlyIdempotent

Semantic search INSIDE a fetched record. Pass the text you already pulled (e.g. a SEC 10-K body, an article, a long tool result) plus a natural-language query; get back the top-N passages with character offsets and similarity scores. Use when the record is too big to cram into the prompt — search_within saves context, returns only the passages that matter, and every passage carries an offset so the agent can verify a verbatim quote. Pairs with ask_pipeworx_grounded: fetch with the gateway, ground over the relevant passages instead of the whole document. BGE-base-en embeddings + cosine over 500-char overlapping windows; cap is 200K chars (longer inputs are truncated and flagged).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
textYesThe document text to search inside (max ~200K chars).
limitNoMax passages to return (1-20, default 5).
queryYesNatural-language query — what passages do you want? E.g. "supply-chain risk", "fiscal year 2024 revenue", "drug interactions with warfarin".

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. First observed

TDQS

A4.9/5.0
Behavior5/5

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

Goes beyond the annotations (readOnlyHint, etc.) by disclosing the output format (top-N passages with character offsets and similarity scores), the embedding model (BGE-base-en with cosine over 500-char overlapping windows), and the 200K char cap with truncation behavior. This is rich behavioral context not present in annotations.

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?

Every sentence earns its place: purpose, use case, pairing, technical mechanics, and limitations. The description is front-loaded with the core action and stays focused without redundancy.

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?

Covers what the tool does, when to use it, what it returns, how it works under the hood, and its limits. The absence of an output schema is compensated by the explicit description of return values. No gaps remain for an agent to select and invoke the tool correctly.

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

Parameters4/5

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

Schema coverage is 100%, so the baseline is 3. The description adds value by providing concrete query examples ('supply-chain risk', 'fiscal year 2024 revenue') and framing 'text' as something already fetched (e.g., SEC 10-K body), which enriches the raw schema definitions.

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 opens with 'Semantic search INSIDE a fetched record,' which clearly identifies the tool's specific action and resource. It distinguishes itself from sibling tools like search by emphasizing operating on already-pulled text, and mentions saving context versus cramming the whole record into the prompt.

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

Usage Guidelines5/5

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

Explicitly states when to use: 'Use when the record is too big to cram into the prompt.' It also names a complementary tool (ask_pipeworx_grounded) and suggests a workflow, giving clear context for when this tool is preferable.

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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TDQS

A3.7/5.0
Disambiguation2/5

ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are nearly identical in purpose, and structure/summary both fetch PDB entries. The server name 'Rcsb Pdb' doesn't match most tools, which are Pipeworx data tools, compounding ambiguity.

Naming Consistency3/5

Mostly snake_case verb_noun, but verbs are inconsistent (ask, discover, generate, list, recall) and some names are noun phrases (entity_profile, polymarket_edges). No clear pattern unifies the set.

Tool Count2/5

37 tools is excessive for a server ostensibly about RCSB PDB; only 6 tools relate to PDB while 31 serve unrelated Pipeworx functionality. The count feels like a bundled grab-bag rather than a focused toolset.

Completeness3/5

The PDB-specific tools cover the core operations (search, fetch, assembly, ligand, polymer entity), so the structural biology surface is mostly complete. However, the server's overall purpose is muddled, and the Pipeworx tools are a separate domain that happens to be bundled in, making it unclear what 'completeness' even means for this server.

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