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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

A4.8/5.0
Behavior5/5

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

Beyond the read-only, open-world, and idempotent hints, the description discloses account/paid-tier requirements, parallel routing across 5,798 tools, the findings packet shape, gaps[] semantics, fetchable citations, contradiction scans, semantic excerpting, and latency expectations. It adds substantial behavioral context without contradicting the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is dense but every sentence earns its place, and the access gate plus sibling alternative are front-loaded. Some sentences are long and parenthetical-heavy, but the overall order is logical: account requirement, core mechanism, output contract, depth behavior, performance.

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 compensates by specifying the return contract: verbatim evidence, confidence, source, fetched_at, pipeworx:// citations, gaps[], contradictions[], and excerpting behavior. It also covers auth, paid tiers, and latency, leaving an agent well-equipped to invoke and interpret results.

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 real value beyond the schema. It clarifies that the question can be broad/multi-part and that depth controls single-hop versus gap-recovery versus lead-chasing iterations, extending the enum descriptions in the schema.

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 concrete operation: grounded multi-source research across Pipeworx's 1517 structured data sources, with decomposition and parallel routing. It explicitly distinguishes itself from open-web search and from ask_pipeworx, so an agent can tell it apart from siblings.

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?

It gives the account gate and says to use ask_pipeworx instead when signed out. It also defines the intended use ('broad/multi-part questions over structured data') and explicitly excludes single lookups, directing those to ask_pipeworx. Depth tiers are documented with their trade-offs.

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.