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Paleobiodb

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?

Annotations already declare readOnlyHint and idempotentHint, but the description goes further by disclosing technical behavior: BGE-base-en embeddings, cosine similarity, 500-char overlapping windows, 200K character cap, and truncation with a flag. It also explains the return includes offsets and similarity scores, which is important for verifying quotes. No contradictions with 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?

The description is concise yet information-dense: three sentences covering purpose, use case, and technical details. It is front-loaded with the core function and progressively adds operational context without waste.

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?

With no output schema, the description must explain return values, which it does: 'top-N passages with character offsets and similarity scores.' It also covers limits, truncation behavior, and integration with another tool. This makes the tool fully understandable for an agent.

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, but the description adds practical meaning: it clarifies that 'text' should be an already-fetched record (e.g., SEC filing, article), gives example queries for 'query', and reinforces the 200K character limit mentioned in the schema. This adds context beyond the 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 states a specific verb and resource: 'Semantic search INSIDE a fetched record.' It clearly distinguishes from siblings by emphasizing 'inside a fetched record' and by naming the complementary tool ask_pipeworx_grounded. The scope (pass text + query, get passages) is explicit.

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?

Provides explicit when-to-use: 'Use when the record is too big to cram into the prompt.' It also describes the alternative workflow: 'Pairs with ask_pipeworx_grounded: fetch with the gateway, ground over the relevant passages instead of the whole document.' This clarifies usage context and relationship to alternatives.

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

A3.6/5.0
Disambiguation2/5

The tool set mixes general-purpose Pipeworx tools (ask_pipeworx, ai_visibility_check, bet_research) with only three paleontology-specific tools (find_fossils, get_taxon, list_subtaxa). Multiple similar 'ask_pipeworx' variants further blur distinctions, making it difficult for an agent to select the right tool without deep domain knowledge.

Naming Consistency3/5

Tool names are mostly in snake_case and somewhat descriptive, but the naming conventions vary widely: imperative verbs (find_fossils), interrogative (suggest_questions), and nouns (recent_alerts). The presence of multiple 'ask_pipeworx' variants with inconsistent suffixes (beta, grounded) adds confusion.

Tool Count2/5

With 34 tools, the server is oversized for its claimed paleontology focus. The vast majority of tools are unrelated to Paleobiology, making the server feel more like a general-purpose data API than a specialized paleontology tool. A focused server should have a smaller, targeted set.

Completeness2/5

For the Paleobiology Database purpose, the coverage is severely lacking: only three tools are directly relevant (find_fossils, get_taxon, list_subtaxa). Missing essential operations like searching taxa by name, retrieving occurrences by location, or accessing collections data. The tool set is not a coherent interface for the domain.

Resources