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Deep Research

deep_research
Read-onlyIdempotent

ACCOUNT REQUIRED (free — sign in via GitHub at https://pipeworx.io/signup; depth:"thorough" needs a paid plan). If you are not signed in, use ask_pipeworx instead — it works on every tier. Grounded multi-source research across Pipeworx's 1517 STRUCTURED data sources (SEC filings, FRED/BLS economics, FDA, USPTO patents, markets, science, government records, etc.) in ONE call — this is NOT open-web search. Decomposes your question into focused facets, routes each to the right one of 5,798 tools IN PARALLEL, and returns a findings packet: verbatim evidence + confidence + source + fetched_at + a stable pipeworx:// citation per finding, with explicit gaps[] for facets the data couldn't answer (never invented). Best for broad/multi-part questions over structured data ("compare X and Y's regulatory + financial exposure", "research the filings + market picture for ACME"). For a single lookup use ask_pipeworx (one LLM call, not many). For BREAKING or colloquial CURRENT-NEWS / "what's the world saying about X" topics, prefer ask_pipeworx — it routes to live news APIs and the *-news-feeds packs; deep_research returns mostly empty gaps[] when the topic isn't in the structured catalog. Second-hop iteration: depth:"standard" re-angles unanswered gaps (gap recovery); depth:"thorough" additionally chases the best leads from the first pass — so multi-step questions resolve in one call. Every finding carries a hop field and a citation_uri — a resolvable pipeworx:// record URI, present only when the source emits one that resources/read can actually serve, so a citation you get back is always fetchable. "standard" and "thorough" also return contradictions[] flagging findings that disagree. Large records are semantically excerpted to the passages relevant to each facet (not head-truncated), so answers deep in a long filing/series aren't missed. Expect 15-60s (thorough with its follow-up + contradiction pass: up to ~90s).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
depthNoHow many facets to research in parallel: quick=3 (single hop), standard=3 (default; adds a gap-recovery hop that re-angles unanswered facets + a contradictions[] scan across findings), thorough=6 (paid; adds a full iterative hop that chases leads + recovers gaps, plus the contradictions[] scan).
questionYesThe research question, in natural language. Broad/multi-part is fine — decomposition is the point.

Schema Changelog

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

  1. Changed1 schema field changed
    • changedInput schema / properties / depth / description
      Previous value: -"How many facets to research in parallel: quick=3 (single hop), standard=5 (default; adds a gap-recovery hop that re-angles unanswered facets + a contradictions[] scan across findings), thorough=8 (paid; adds a full iterative hop that chases leads + recovers gaps, plus the contradictions[] scan)."New value: +"How many facets to research in parallel: quick=3 (single hop), standard=3 (default; adds a gap-recovery hop that re-angles unanswered facets + a contradictions[] scan across findings), thorough=6 (paid; adds a full iterative hop that chases leads + recovers gaps, plus the contradictions[] scan)."
  2. Changed1 schema field changed
    • changedInput schema / properties / depth / description
      Previous value: -"How many facets to research in parallel: quick=3 (single hop), standard=5 (default; adds a gap-recovery hop that re-angles unanswered facets), thorough=8 (paid; adds a full iterative hop that chases leads + recovers gaps, plus a contradictions[] scan across findings)."New value: +"How many facets to research in parallel: quick=3 (single hop), standard=5 (default; adds a gap-recovery hop that re-angles unanswered facets + a contradictions[] scan across findings), thorough=8 (paid; adds a full iterative hop that chases leads + recovers gaps, plus the contradictions[] scan)."
  3. Changed1 schema field changed
    • changedInput schema / properties / depth / description
      Previous value: -"How many facets to research in parallel: quick=3, standard=5 (default), thorough=8 (paid plans). \"thorough\" also runs a second ITERATIVE hop — a planner inspects the first-pass findings/gaps and chases the most valuable leads or recovers gaps, resolving multi-step questions in one call."New value: +"How many facets to research in parallel: quick=3 (single hop), standard=5 (default; adds a gap-recovery hop that re-angles unanswered facets), thorough=8 (paid; adds a full iterative hop that chases leads + recovers gaps, plus a contradictions[] scan across findings)."
  4. Changed1 schema field changed
    • changedInput schema / properties / depth / description
      Previous value: -"How many facets to research in parallel: quick=3, standard=5 (default), thorough=8 (paid plans)."New value: +"How many facets to research in parallel: quick=3, standard=5 (default), thorough=8 (paid plans). \"thorough\" also runs a second ITERATIVE hop — a planner inspects the first-pass findings/gaps and chases the most valuable leads or recovers gaps, resolving multi-step questions in one call."
  5. Added

TDQS

A4.7/5.0
Behavior5/5

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

Beyond the readOnly/openWorld/idempotent annotations, the description discloses rich behavioral details: it decomposes questions, routes to tools in parallel, returns gaps[] for unanswered facets, never invents answers, provides contradictions[] scans for standard/thorough, returns citation_uri only when fetchable, semantically excerpts large records, and gives expected latency. This greatly exceeds what annotations provide.

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 long but every sentence adds distinct value: auth prerequisites, fallback routing, tool scope, parallel execution, output packet contents, gap handling, latency, and depth-specific behaviors. The most important constraint (account required and fallback) is front-loaded, and the structure is dense 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?

For a complex research tool with no output schema, the description fully covers what an agent needs: input examples, depth semantics, return packet structure, evidence and citation format, failure/gap behavior, latency expectations, and explicit alternatives. The description is complete enough to invoke the tool correctly without external knowledge.

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

Parameters3/5

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 some contextual color around depth (e.g., latency implications, paid plan for thorough, contradiction behavior), but the schema already documents the key parameter semantics for both question and depth, including the quick/standard/thorough distinctions. The description does not materially change the agent's understanding of the parameters.

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 a specific verb and resource: grounded multi-source research over Pipeworx's 1,517 structured data sources in one call. It explicitly distinguishes itself from open-web search and from sibling tools like ask_pipeworx, noting that ask_pipeworx is the alternative for single lookups and for users without an account.

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?

The description gives explicit when-to-use guidance: best for broad/multi-part questions over structured data. It also states when not to use it—for a single lookup, use ask_pipeworx—and gives a concrete fallback if the user is not signed in. These exclusions and alternatives are unambiguous.

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

A3.8/5.0
Disambiguation2/5

Several tools have heavily overlapping purposes, notably ask_pipeworx vs ask_pipeworx_beta vs ask_pipeworx_grounded, and the cluster of polymarket tools covers adjacent prediction-market analysis territory. The PomBase-specific tools are distinct, but the overall set creates real selection ambiguity.

Naming Consistency3/5

Most names follow a readable snake_case style and many use verb-first patterns, but there is notable mixing: ask_pipeworx is a brand-style exception, entity_profile and polymarket_arbitrage are noun-first, and remember/recall/forget form an inconsistent trio. Not chaotic, but not a clean predictable convention.

Tool Count2/5

33 tools is excessive for a server named Pombase, where only get_gene and get_reference actually serve that domain. Even as a broad data-research server, the count is above the 25-tool threshold and includes many auxiliary utilities that feel bolted on rather than part of a focused surface.

Completeness2/5

The PomBase-specific coverage is severely thin: only systematic-ID gene lookup and PubMed-ID reference lookup, with no gene-name search, annotations browsing, phenotype data, or sequence access. The broader Pipeworx surface is extensive, but for the apparent Pombase purpose, agents will frequently hit dead ends.