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Glama

Pdbe

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

A4.7/5.0
Behavior5/5

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

Goes beyond annotations by specifying embedding model (BGE-base-en), window size (500-char overlapping), similarity metric (cosine), and truncation behavior (200K char cap with flag). Annotations already declare safety properties; description adds technical detail.

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?

Four sentences, each adding unique value. Front-loaded with purpose, no redundancy. Efficiently covers usage, behavior, and technical details.

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?

No output schema, but description explains return format (passages with offsets and scores). Covers input constraints, truncation, and pairing with a sibling tool. Complete for a search tool.

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 baseline is 3. The description adds value by providing query examples and clarifying the 'limit' default and range, plus embedding details that inform parameter usage.

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 'semantic search INSIDE a fetched record' with specific verb and resource. It distinguishes from siblings by highlighting context-saving, character offsets, and pairing with ask_pipeworx_grounded.

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?

Explicitly says 'Use when the record is too big to cram into the prompt' and mentions pairing with ask_pipeworx_grounded. Provides clear context for when to use, though does not explicitly list when not to use.

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

B3.3/5.0
Disambiguation2/5

Many tools overlap in purpose: ask_pipeworx, ask_pipeworx_grounded, ask_pipeworx_beta, and deep_research all perform similar data lookups with slight variations. Prediction market tools (bet_research, polymarket_arbitrage, polymarket_edges) also overlap. Only the three PDBe-specific tools are clearly distinct, but overall the set is confusing.

Naming Consistency1/5

Tool names follow no consistent pattern: some are verb_noun (ask_pipeworx, get_molecules), others are noun_verb (ai_visibility_check), or have mixed conventions (generate_llms_txt, uniprot_mappings). The variety of verbs (ask, bet, compare, discover, generate, get, list, recall, remember) makes it hard to predict tool names.

Tool Count2/5

With 34 tools, the server is overstuffed for a single domain. It mixes PDBe-specific tools (3) with a large set of general-purpose data tools, prediction market tools, subscriptions, and memory tools. This bloat suggests the server should be split into focused services.

Completeness1/5

For the stated PDBe domain, only three tools exist (get_molecules, get_summary, uniprot_mappings), missing essential operations like search, download, or advanced queries. The server's overall purpose is unclear, and it feels like a random collection of tools rather than a coherent API.

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